Starting phenix.real_space_refine on Sun Mar 17 17:59:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7t_10112/03_2024/6s7t_10112_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7t_10112/03_2024/6s7t_10112.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7t_10112/03_2024/6s7t_10112_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7t_10112/03_2024/6s7t_10112_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7t_10112/03_2024/6s7t_10112_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7t_10112/03_2024/6s7t_10112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7t_10112/03_2024/6s7t_10112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7t_10112/03_2024/6s7t_10112_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s7t_10112/03_2024/6s7t_10112_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 52 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 2 5.21 5 S 68 5.16 5 C 12182 2.51 5 N 2843 2.21 5 O 3339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 88": "NH1" <-> "NH2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A ARG 778": "NH1" <-> "NH2" Residue "A ARG 786": "NH1" <-> "NH2" Residue "A ARG 804": "NH1" <-> "NH2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D ARG 74": "NH1" <-> "NH2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "E ARG 294": "NH1" <-> "NH2" Residue "E ARG 317": "NH1" <-> "NH2" Residue "E PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 391": "NH1" <-> "NH2" Residue "E TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 437": "NH1" <-> "NH2" Residue "F ARG 536": "NH1" <-> "NH2" Residue "F ARG 628": "NH1" <-> "NH2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 139": "NH1" <-> "NH2" Residue "G ARG 250": "NH1" <-> "NH2" Residue "G ARG 307": "NH1" <-> "NH2" Residue "G ARG 365": "NH1" <-> "NH2" Residue "G ARG 420": "NH1" <-> "NH2" Residue "H ARG 240": "NH1" <-> "NH2" Residue "H ARG 299": "NH1" <-> "NH2" Residue "H ARG 322": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18445 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5739 Classifications: {'peptide': 706} Link IDs: {'PTRANS': 24, 'TRANS': 681} Chain breaks: 1 Chain: "B" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 258 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "C" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 634 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 817 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "E" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3461 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 23, 'TRANS': 404} Chain breaks: 1 Chain: "F" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1979 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3233 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 21, 'TRANS': 388} Chain: "H" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 872 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain breaks: 1 Chain: "I" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 280 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 5, 'TRANS': 31} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 40 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 331 Unusual residues: {' MG': 1, '0K3': 1, 'EGY': 6, 'KZB': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'EGY': 1, 'KZB': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 139 Unusual residues: {'EGY': 1, 'KZB': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 15 Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 108 Unusual residues: {' MG': 1, 'EGY': 1, 'KZB': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 139 Unusual residues: {'EGY': 1, 'KZB': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 15 Chain: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'KZB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 9.79, per 1000 atoms: 0.53 Number of scatterers: 18445 At special positions: 0 Unit cell: (106.68, 155.4, 161.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 11 15.00 Mg 2 11.99 O 3339 8.00 N 2843 7.00 C 12182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 ALPHA1-2 " MAN L 4 " - " MAN L 5 " " MAN L 5 " - " MAN L 6 " " MAN N 4 " - " MAN N 5 " ALPHA1-3 " BMA L 3 " - " MAN L 4 " " BMA N 3 " - " MAN N 4 " " MAN N 6 " - " MAN N 7 " ALPHA1-6 " BMA L 3 " - " MAN L 7 " " MAN L 7 " - " MAN L 8 " " BMA N 3 " - " MAN N 6 " " MAN N 6 " - " MAN N 8 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG J 1 " - " ASN A 616 " " NAG L 1 " - " ASN A 627 " " NAG M 1 " - " ASN A 641 " " NAG N 1 " - " ASN E 299 " Time building additional restraints: 7.20 Conformation dependent library (CDL) restraints added in 3.1 seconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4070 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 19 sheets defined 38.6% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 65 through 86 Processing helix chain 'A' and resid 103 through 117 removed outlier: 3.564A pdb=" N ASN A 107 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 110 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS A 117 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 122 No H-bonds generated for 'chain 'A' and resid 119 through 122' Processing helix chain 'A' and resid 146 through 159 Processing helix chain 'A' and resid 166 through 192 removed outlier: 5.243A pdb=" N ALA A 174 " --> pdb=" O CYS A 170 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 3.549A pdb=" N LEU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 4.254A pdb=" N ALA A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 removed outlier: 5.347A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 243 removed outlier: 3.952A pdb=" N PHE A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 262 Processing helix chain 'A' and resid 266 through 282 Proline residue: A 274 - end of helix Processing helix chain 'A' and resid 288 through 307 removed outlier: 3.978A pdb=" N THR A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 317 No H-bonds generated for 'chain 'A' and resid 314 through 317' Processing helix chain 'A' and resid 322 through 343 Processing helix chain 'A' and resid 350 through 374 Processing helix chain 'A' and resid 382 through 389 removed outlier: 4.678A pdb=" N LEU A 387 " --> pdb=" O ARG A 383 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP A 388 " --> pdb=" O PHE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 421 through 434 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 438 through 456 removed outlier: 3.932A pdb=" N PHE A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 456 " --> pdb=" O TYR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 482 removed outlier: 3.991A pdb=" N LEU A 462 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 534 through 560 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 605 through 614 removed outlier: 4.637A pdb=" N TYR A 609 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 611 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 613 " --> pdb=" O GLN A 610 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A 614 " --> pdb=" O ILE A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 639 Processing helix chain 'A' and resid 642 through 651 Processing helix chain 'A' and resid 675 through 685 removed outlier: 3.761A pdb=" N GLU A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 695 Processing helix chain 'A' and resid 716 through 721 Processing helix chain 'B' and resid 4 through 31 Processing helix chain 'C' and resid 15 through 41 Proline residue: C 19 - end of helix removed outlier: 4.008A pdb=" N VAL C 23 " --> pdb=" O HIS C 20 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL C 24 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA C 27 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILE C 28 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 29 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE C 37 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL C 38 " --> pdb=" O TRP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 74 Processing helix chain 'D' and resid 11 through 19 Processing helix chain 'D' and resid 22 through 48 Processing helix chain 'D' and resid 53 through 77 Processing helix chain 'D' and resid 79 through 81 No H-bonds generated for 'chain 'D' and resid 79 through 81' Processing helix chain 'D' and resid 90 through 111 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 433 through 456 Proline residue: E 439 - end of helix removed outlier: 4.103A pdb=" N VAL E 442 " --> pdb=" O PRO E 439 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR E 452 " --> pdb=" O LEU E 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 563 Proline residue: F 552 - end of helix Processing helix chain 'F' and resid 574 through 595 Processing helix chain 'F' and resid 599 through 629 removed outlier: 3.659A pdb=" N LYS F 627 " --> pdb=" O GLN F 623 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG F 628 " --> pdb=" O GLN F 624 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 70 removed outlier: 5.687A pdb=" N LEU G 62 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE G 63 " --> pdb=" O THR G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 122 Processing helix chain 'G' and resid 136 through 145 Processing helix chain 'G' and resid 184 through 187 No H-bonds generated for 'chain 'G' and resid 184 through 187' Processing helix chain 'G' and resid 261 through 264 Processing helix chain 'G' and resid 288 through 299 Processing helix chain 'G' and resid 423 through 446 Proline residue: G 427 - end of helix Processing helix chain 'H' and resid 216 through 230 Processing helix chain 'H' and resid 236 through 239 No H-bonds generated for 'chain 'H' and resid 236 through 239' Processing helix chain 'H' and resid 266 through 288 removed outlier: 3.500A pdb=" N HIS H 270 " --> pdb=" O VAL H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 324 removed outlier: 3.861A pdb=" N CYS H 303 " --> pdb=" O ARG H 299 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL H 311 " --> pdb=" O ILE H 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 287 Proline residue: I 274 - end of helix Proline residue: I 284 - end of helix removed outlier: 3.646A pdb=" N PHE I 287 " --> pdb=" O ILE I 283 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 569 through 572 Processing sheet with id= B, first strand: chain 'A' and resid 656 through 660 removed outlier: 5.697A pdb=" N LYS A 771 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU A 758 " --> pdb=" O LYS A 771 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 31 through 33 removed outlier: 3.541A pdb=" N VAL E 134 " --> pdb=" O HIS E 83 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS E 83 " --> pdb=" O VAL E 134 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 48 through 53 removed outlier: 6.367A pdb=" N THR E 170 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ARG E 38 " --> pdb=" O THR E 170 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR E 172 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL E 40 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG E 174 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 68 through 72 removed outlier: 3.539A pdb=" N LYS E 116 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU E 95 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 153 through 159 removed outlier: 3.950A pdb=" N SER E 184 " --> pdb=" O HIS E 217 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLU E 219 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL E 182 " --> pdb=" O GLU E 219 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 390 through 392 removed outlier: 4.584A pdb=" N VAL E 410 " --> pdb=" O ALA E 392 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP E 249 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET E 230 " --> pdb=" O ASN E 247 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN E 247 " --> pdb=" O MET E 230 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG E 232 " --> pdb=" O GLU E 245 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU E 245 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE E 234 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA E 243 " --> pdb=" O ILE E 234 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 280 through 284 Processing sheet with id= I, first strand: chain 'E' and resid 342 through 345 Processing sheet with id= J, first strand: chain 'E' and resid 395 through 397 removed outlier: 3.632A pdb=" N GLU E 395 " --> pdb=" O VAL E 408 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 392 through 395 removed outlier: 3.687A pdb=" N LYS F 392 " --> pdb=" O THR F 382 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN F 419 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL F 378 " --> pdb=" O PHE F 417 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE F 417 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU F 380 " --> pdb=" O ALA F 415 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA F 415 " --> pdb=" O LEU F 380 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR F 382 " --> pdb=" O ASN F 413 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASN F 413 " --> pdb=" O THR F 382 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL F 458 " --> pdb=" O ASP F 454 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU F 452 " --> pdb=" O LYS F 460 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 405 through 408 removed outlier: 8.382A pdb=" N PHE F 406 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP F 500 " --> pdb=" O PHE F 406 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA F 408 " --> pdb=" O ASP F 500 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL F 502 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP F 496 " --> pdb=" O LEU F 483 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU F 481 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASP F 500 " --> pdb=" O TYR F 479 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR F 479 " --> pdb=" O ASP F 500 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL F 502 " --> pdb=" O GLY F 477 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLY F 477 " --> pdb=" O VAL F 502 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 73 through 78 removed outlier: 6.835A pdb=" N ASN G 96 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LEU G 50 " --> pdb=" O ASN G 96 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE G 98 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N SER G 125 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE G 99 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU G 127 " --> pdb=" O ILE G 99 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 154 through 157 removed outlier: 3.979A pdb=" N ALA G 155 " --> pdb=" O PHE G 224 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE G 224 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= P, first strand: chain 'G' and resid 245 through 248 Processing sheet with id= Q, first strand: chain 'G' and resid 306 through 308 Processing sheet with id= R, first strand: chain 'G' and resid 312 through 315 removed outlier: 3.685A pdb=" N LYS G 369 " --> pdb=" O SER G 376 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 402 through 410 removed outlier: 4.390A pdb=" N ASP G 393 " --> pdb=" O GLN G 354 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLN G 354 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL G 364 " --> pdb=" O PHE G 357 " (cutoff:3.500A) 751 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: 5.64 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2721 1.31 - 1.43: 5334 1.43 - 1.56: 10700 1.56 - 1.68: 97 1.68 - 1.81: 117 Bond restraints: 18969 Sorted by residual: bond pdb=" C03 KZB G 501 " pdb=" C04 KZB G 501 " ideal model delta sigma weight residual 2.203 1.521 0.682 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C03 KZB D 203 " pdb=" C04 KZB D 203 " ideal model delta sigma weight residual 2.203 1.521 0.682 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C03 KZB D 204 " pdb=" C04 KZB D 204 " ideal model delta sigma weight residual 2.203 1.522 0.681 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C03 KZB F 702 " pdb=" C04 KZB F 702 " ideal model delta sigma weight residual 2.203 1.523 0.680 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C03 KZB G 502 " pdb=" C04 KZB G 502 " ideal model delta sigma weight residual 2.203 1.523 0.680 2.00e-02 2.50e+03 1.16e+03 ... (remaining 18964 not shown) Histogram of bond angle deviations from ideal: 97.15 - 104.54: 399 104.54 - 111.93: 9856 111.93 - 119.32: 5893 119.32 - 126.70: 9444 126.70 - 134.09: 283 Bond angle restraints: 25875 Sorted by residual: angle pdb=" C8 0K3 A 921 " pdb=" C7 0K3 A 921 " pdb=" C9 0K3 A 921 " ideal model delta sigma weight residual 68.21 120.71 -52.50 3.00e+00 1.11e-01 3.06e+02 angle pdb=" C18 0K3 A 921 " pdb=" C17 0K3 A 921 " pdb=" C39 0K3 A 921 " ideal model delta sigma weight residual 68.18 120.17 -51.99 3.00e+00 1.11e-01 3.00e+02 angle pdb=" C27 0K3 A 921 " pdb=" C26 0K3 A 921 " pdb=" C28 0K3 A 921 " ideal model delta sigma weight residual 68.18 119.84 -51.66 3.00e+00 1.11e-01 2.97e+02 angle pdb=" C16 0K3 A 921 " pdb=" C17 0K3 A 921 " pdb=" C39 0K3 A 921 " ideal model delta sigma weight residual 85.83 120.51 -34.68 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C6 0K3 A 921 " pdb=" C7 0K3 A 921 " pdb=" C9 0K3 A 921 " ideal model delta sigma weight residual 85.84 119.83 -33.99 3.00e+00 1.11e-01 1.28e+02 ... (remaining 25870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.95: 11118 32.95 - 65.91: 272 65.91 - 98.86: 64 98.86 - 131.82: 14 131.82 - 164.77: 7 Dihedral angle restraints: 11475 sinusoidal: 5148 harmonic: 6327 Sorted by residual: dihedral pdb=" CA TRP A 131 " pdb=" C TRP A 131 " pdb=" N TYR A 132 " pdb=" CA TYR A 132 " ideal model delta harmonic sigma weight residual -180.00 -155.24 -24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ILE A 205 " pdb=" C ILE A 205 " pdb=" N ALA A 206 " pdb=" CA ALA A 206 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" C38 EGY F 701 " pdb=" C39 EGY F 701 " pdb=" C3A EGY F 701 " pdb=" C3B EGY F 701 " ideal model delta sinusoidal sigma weight residual 180.22 15.45 164.77 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 11472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 2863 0.160 - 0.320: 73 0.320 - 0.480: 51 0.480 - 0.641: 17 0.641 - 0.801: 14 Chirality restraints: 3018 Sorted by residual: chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-02 2.50e+03 1.38e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-02 2.50e+03 4.06e+02 chirality pdb=" C1 MAN N 7 " pdb=" O3 MAN N 6 " pdb=" C2 MAN N 7 " pdb=" O5 MAN N 7 " both_signs ideal model delta sigma weight residual False 2.40 2.05 0.35 2.00e-02 2.50e+03 3.04e+02 ... (remaining 3015 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C 0K3 A 921 " 0.288 2.00e-02 2.50e+03 3.14e-01 1.24e+03 pdb=" C1 0K3 A 921 " -0.566 2.00e-02 2.50e+03 pdb=" C2 0K3 A 921 " 0.289 2.00e-02 2.50e+03 pdb=" C3 0K3 A 921 " -0.065 2.00e-02 2.50e+03 pdb=" C4 0K3 A 921 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 273 " -0.062 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO A 274 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 94 " 0.213 9.50e-02 1.11e+02 9.56e-02 5.61e+00 pdb=" NE ARG A 94 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 94 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 94 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 94 " 0.008 2.00e-02 2.50e+03 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 882 2.72 - 3.27: 17912 3.27 - 3.81: 28227 3.81 - 4.36: 33742 4.36 - 4.90: 59869 Nonbonded interactions: 140632 Sorted by model distance: nonbonded pdb=" NH1 ARG G 297 " pdb=" OE1 GLU G 303 " model vdw 2.177 2.520 nonbonded pdb=" OH TYR A 722 " pdb=" OD2 ASP A 739 " model vdw 2.181 2.440 nonbonded pdb=" NH1 ARG F 437 " pdb=" OE1 GLU F 446 " model vdw 2.191 2.520 nonbonded pdb=" O ILE A 137 " pdb=" OG1 THR A 141 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR A 483 " pdb=" O LEU H 286 " model vdw 2.209 2.440 ... (remaining 140627 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 'J' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 12.630 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 48.340 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.038 0.682 18969 Z= 2.064 Angle : 1.400 52.498 25875 Z= 0.565 Chirality : 0.103 0.801 3018 Planarity : 0.008 0.314 3068 Dihedral : 16.069 164.774 7405 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.24 % Rotamer: Outliers : 2.55 % Allowed : 6.16 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.16), residues: 2136 helix: -0.60 (0.16), residues: 859 sheet: -0.12 (0.25), residues: 404 loop : -2.70 (0.17), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 605 HIS 0.005 0.001 HIS G 235 PHE 0.031 0.002 PHE A 425 TYR 0.018 0.002 TYR E 428 ARG 0.004 0.000 ARG F 628 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 299 time to evaluate : 2.025 Fit side-chains REVERT: A 74 PHE cc_start: 0.8293 (t80) cc_final: 0.8068 (t80) REVERT: A 543 MET cc_start: 0.7950 (mmp) cc_final: 0.7726 (mmp) REVERT: A 579 ASN cc_start: 0.7422 (m-40) cc_final: 0.6901 (p0) REVERT: A 655 ASP cc_start: 0.7971 (m-30) cc_final: 0.7727 (m-30) REVERT: A 679 VAL cc_start: 0.8881 (t) cc_final: 0.8646 (p) REVERT: A 688 LYS cc_start: 0.8289 (mtmt) cc_final: 0.7788 (mmtm) REVERT: A 789 ASN cc_start: 0.7677 (t0) cc_final: 0.7432 (t0) REVERT: A 804 ARG cc_start: 0.7784 (ttt-90) cc_final: 0.7560 (ttt90) REVERT: E 96 ASN cc_start: 0.8101 (p0) cc_final: 0.7879 (p0) REVERT: E 376 GLU cc_start: 0.5734 (OUTLIER) cc_final: 0.5472 (pm20) REVERT: E 455 ILE cc_start: 0.8697 (tp) cc_final: 0.8451 (tp) REVERT: F 570 PHE cc_start: 0.8040 (t80) cc_final: 0.7764 (t80) REVERT: G 152 GLU cc_start: 0.6941 (pt0) cc_final: 0.6573 (tt0) REVERT: G 202 MET cc_start: 0.8846 (ptp) cc_final: 0.8434 (ptp) REVERT: H 225 CYS cc_start: 0.7874 (t) cc_final: 0.7188 (m) REVERT: H 274 LEU cc_start: 0.7480 (tt) cc_final: 0.6673 (mp) REVERT: H 319 SER cc_start: 0.8334 (t) cc_final: 0.8053 (m) REVERT: H 334 MET cc_start: 0.5020 (tmt) cc_final: 0.4806 (tmm) REVERT: I 272 MET cc_start: 0.5023 (mmt) cc_final: 0.4668 (mmt) outliers start: 48 outliers final: 15 residues processed: 336 average time/residue: 0.3010 time to fit residues: 151.7374 Evaluate side-chains 214 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 198 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 247 ASN Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 251 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 166 optimal weight: 7.9990 chunk 64 optimal weight: 0.0270 chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 195 GLN A 231 GLN A 307 GLN A 406 HIS A 419 HIS A 435 ASN ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 HIS D 41 GLN E 97 ASN E 190 ASN ** E 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 HIS E 358 HIS E 380 ASN E 420 HIS F 377 ASN F 441 GLN F 601 GLN F 623 GLN G 159 HIS G 314 HIS G 415 HIS H 237 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18969 Z= 0.180 Angle : 0.716 24.088 25875 Z= 0.322 Chirality : 0.043 0.198 3018 Planarity : 0.005 0.078 3068 Dihedral : 16.407 159.521 3497 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.97 % Allowed : 10.51 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.18), residues: 2136 helix: 0.49 (0.18), residues: 851 sheet: 0.05 (0.26), residues: 405 loop : -2.22 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 496 HIS 0.005 0.001 HIS A 686 PHE 0.022 0.001 PHE A 732 TYR 0.020 0.001 TYR A 796 ARG 0.007 0.000 ARG E 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 211 time to evaluate : 1.525 Fit side-chains REVERT: A 318 THR cc_start: 0.8912 (p) cc_final: 0.8707 (t) REVERT: A 579 ASN cc_start: 0.7441 (m-40) cc_final: 0.7116 (p0) REVERT: A 650 ARG cc_start: 0.8153 (mmm160) cc_final: 0.7943 (mtp85) REVERT: A 688 LYS cc_start: 0.8304 (mtmt) cc_final: 0.7820 (mmtm) REVERT: A 691 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.6841 (mtm110) REVERT: C 21 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8891 (tp) REVERT: E 96 ASN cc_start: 0.8213 (p0) cc_final: 0.7946 (p0) REVERT: E 434 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8498 (mp) REVERT: E 436 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8783 (pt) REVERT: E 455 ILE cc_start: 0.8638 (tp) cc_final: 0.8419 (tp) REVERT: F 420 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8179 (mt) REVERT: F 485 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8187 (pt) REVERT: F 599 MET cc_start: 0.8910 (tpt) cc_final: 0.8613 (tpp) REVERT: G 152 GLU cc_start: 0.7096 (pt0) cc_final: 0.6699 (tt0) REVERT: G 169 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7505 (mm-40) REVERT: H 274 LEU cc_start: 0.7455 (tt) cc_final: 0.6660 (mp) REVERT: H 319 SER cc_start: 0.8398 (t) cc_final: 0.8046 (m) REVERT: H 334 MET cc_start: 0.5037 (tmt) cc_final: 0.4703 (tmm) REVERT: I 272 MET cc_start: 0.5041 (mmt) cc_final: 0.4697 (mmt) outliers start: 56 outliers final: 26 residues processed: 253 average time/residue: 0.2740 time to fit residues: 108.3931 Evaluate side-chains 218 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain H residue 316 TRP Chi-restraints excluded: chain H residue 323 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 171 optimal weight: 0.2980 chunk 191 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 154 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 HIS H 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18969 Z= 0.179 Angle : 0.658 24.247 25875 Z= 0.297 Chirality : 0.042 0.210 3018 Planarity : 0.004 0.061 3068 Dihedral : 14.841 162.738 3479 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.97 % Allowed : 11.84 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.18), residues: 2136 helix: 0.90 (0.18), residues: 866 sheet: -0.03 (0.26), residues: 406 loop : -2.04 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 496 HIS 0.027 0.001 HIS A 406 PHE 0.018 0.001 PHE A 425 TYR 0.015 0.001 TYR A 796 ARG 0.008 0.000 ARG E 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 192 time to evaluate : 2.136 Fit side-chains REVERT: A 568 VAL cc_start: 0.8996 (t) cc_final: 0.8787 (m) REVERT: A 579 ASN cc_start: 0.7500 (m-40) cc_final: 0.7265 (p0) REVERT: A 688 LYS cc_start: 0.8268 (mtmt) cc_final: 0.7790 (mmtm) REVERT: A 691 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.6848 (mtm110) REVERT: E 96 ASN cc_start: 0.8312 (p0) cc_final: 0.8010 (p0) REVERT: E 198 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8415 (pp) REVERT: E 250 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8642 (pp) REVERT: E 335 ASN cc_start: 0.8344 (p0) cc_final: 0.7935 (p0) REVERT: E 434 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8513 (mp) REVERT: E 436 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8640 (pt) REVERT: E 455 ILE cc_start: 0.8629 (tp) cc_final: 0.8426 (tp) REVERT: F 420 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8220 (mt) REVERT: F 485 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8197 (pt) REVERT: F 599 MET cc_start: 0.8873 (tpt) cc_final: 0.8470 (tpp) REVERT: F 619 ARG cc_start: 0.8397 (tpp80) cc_final: 0.7438 (mmm160) REVERT: G 152 GLU cc_start: 0.7147 (pt0) cc_final: 0.6756 (tt0) REVERT: G 169 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7539 (mm-40) REVERT: H 274 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.6703 (mp) REVERT: H 300 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.5997 (mmtt) REVERT: H 319 SER cc_start: 0.8428 (t) cc_final: 0.8078 (m) REVERT: H 334 MET cc_start: 0.4731 (tmt) cc_final: 0.4425 (tmm) REVERT: I 272 MET cc_start: 0.5076 (mmt) cc_final: 0.4746 (mmt) outliers start: 56 outliers final: 28 residues processed: 234 average time/residue: 0.2873 time to fit residues: 105.2328 Evaluate side-chains 217 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 300 LYS Chi-restraints excluded: chain H residue 316 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 100 optimal weight: 0.0050 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 193 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN ** E 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18969 Z= 0.180 Angle : 0.641 22.041 25875 Z= 0.289 Chirality : 0.042 0.238 3018 Planarity : 0.004 0.050 3068 Dihedral : 13.925 162.942 3476 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.66 % Allowed : 13.00 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2136 helix: 1.21 (0.18), residues: 860 sheet: 0.05 (0.25), residues: 426 loop : -1.81 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 81 HIS 0.006 0.001 HIS A 406 PHE 0.017 0.001 PHE A 425 TYR 0.013 0.001 TYR H 330 ARG 0.008 0.000 ARG E 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 197 time to evaluate : 1.775 Fit side-chains REVERT: A 193 TRP cc_start: 0.8497 (OUTLIER) cc_final: 0.6675 (m-90) REVERT: A 481 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6809 (mm-30) REVERT: A 579 ASN cc_start: 0.7593 (m-40) cc_final: 0.7301 (p0) REVERT: A 679 VAL cc_start: 0.8822 (t) cc_final: 0.8611 (p) REVERT: A 688 LYS cc_start: 0.8280 (mtmt) cc_final: 0.7804 (mmtm) REVERT: A 691 ARG cc_start: 0.7473 (ttm-80) cc_final: 0.6881 (mtm110) REVERT: A 789 ASN cc_start: 0.7317 (t0) cc_final: 0.7057 (t0) REVERT: A 796 TYR cc_start: 0.8050 (t80) cc_final: 0.7300 (t80) REVERT: E 96 ASN cc_start: 0.8362 (p0) cc_final: 0.8098 (p0) REVERT: E 198 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8394 (pp) REVERT: E 250 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8672 (pp) REVERT: E 335 ASN cc_start: 0.8307 (p0) cc_final: 0.7854 (p0) REVERT: E 434 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8590 (mp) REVERT: E 436 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8516 (pt) REVERT: E 455 ILE cc_start: 0.8629 (tp) cc_final: 0.8413 (tp) REVERT: F 420 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8292 (mt) REVERT: F 485 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8277 (pt) REVERT: F 619 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7425 (mmm160) REVERT: G 152 GLU cc_start: 0.7250 (pt0) cc_final: 0.6816 (tt0) REVERT: G 169 GLN cc_start: 0.8357 (mm-40) cc_final: 0.7550 (mm-40) REVERT: H 274 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7166 (tt) REVERT: H 300 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.5934 (mmtt) REVERT: H 319 SER cc_start: 0.8401 (t) cc_final: 0.8063 (m) REVERT: H 334 MET cc_start: 0.4714 (tmt) cc_final: 0.4356 (tmm) REVERT: I 272 MET cc_start: 0.5216 (mmt) cc_final: 0.4906 (mmt) outliers start: 69 outliers final: 39 residues processed: 251 average time/residue: 0.2769 time to fit residues: 109.9428 Evaluate side-chains 228 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 180 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 245 GLU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 300 LYS Chi-restraints excluded: chain H residue 316 TRP Chi-restraints excluded: chain H residue 323 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 152 optimal weight: 0.5980 chunk 84 optimal weight: 0.4980 chunk 174 optimal weight: 0.4980 chunk 141 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 183 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18969 Z= 0.154 Angle : 0.616 22.006 25875 Z= 0.277 Chirality : 0.041 0.230 3018 Planarity : 0.004 0.055 3068 Dihedral : 13.285 163.403 3476 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.66 % Allowed : 14.23 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2136 helix: 1.42 (0.18), residues: 858 sheet: 0.20 (0.26), residues: 417 loop : -1.59 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 604 HIS 0.003 0.001 HIS E 238 PHE 0.016 0.001 PHE H 313 TYR 0.023 0.001 TYR E 166 ARG 0.007 0.000 ARG E 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 190 time to evaluate : 1.735 Fit side-chains REVERT: A 193 TRP cc_start: 0.8376 (OUTLIER) cc_final: 0.6760 (m-90) REVERT: A 579 ASN cc_start: 0.7492 (m-40) cc_final: 0.7283 (p0) REVERT: A 679 VAL cc_start: 0.8847 (t) cc_final: 0.8574 (p) REVERT: A 688 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7788 (mmtm) REVERT: A 691 ARG cc_start: 0.7472 (ttm-80) cc_final: 0.6914 (mtm110) REVERT: A 796 TYR cc_start: 0.8121 (t80) cc_final: 0.7530 (t80) REVERT: E 96 ASN cc_start: 0.8387 (p0) cc_final: 0.8098 (p0) REVERT: E 434 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8609 (mp) REVERT: E 436 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8473 (pt) REVERT: F 420 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8320 (mt) REVERT: F 485 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8284 (pt) REVERT: F 619 ARG cc_start: 0.8346 (tpp80) cc_final: 0.7379 (mmm160) REVERT: G 144 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7244 (mm-30) REVERT: G 152 GLU cc_start: 0.7285 (pt0) cc_final: 0.6841 (tt0) REVERT: G 169 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7566 (mm-40) REVERT: H 274 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7270 (tt) REVERT: H 300 LYS cc_start: 0.6626 (ttmp) cc_final: 0.6012 (mmtt) REVERT: H 319 SER cc_start: 0.8376 (t) cc_final: 0.8142 (m) REVERT: I 272 MET cc_start: 0.5214 (mmt) cc_final: 0.4391 (mmt) outliers start: 69 outliers final: 41 residues processed: 244 average time/residue: 0.2754 time to fit residues: 106.2344 Evaluate side-chains 229 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 182 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 245 GLU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain F residue 554 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 316 TRP Chi-restraints excluded: chain I residue 254 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.1980 chunk 184 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 67 optimal weight: 0.0970 chunk 107 optimal weight: 3.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 ASN ** E 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18969 Z= 0.150 Angle : 0.610 21.985 25875 Z= 0.273 Chirality : 0.040 0.240 3018 Planarity : 0.004 0.053 3068 Dihedral : 12.806 163.302 3476 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.66 % Allowed : 14.54 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.19), residues: 2136 helix: 1.63 (0.18), residues: 850 sheet: 0.25 (0.26), residues: 418 loop : -1.50 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 81 HIS 0.003 0.001 HIS E 252 PHE 0.015 0.001 PHE A 425 TYR 0.012 0.001 TYR E 339 ARG 0.005 0.000 ARG E 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 187 time to evaluate : 1.802 Fit side-chains REVERT: A 193 TRP cc_start: 0.8488 (OUTLIER) cc_final: 0.6539 (m-90) REVERT: A 579 ASN cc_start: 0.7496 (m-40) cc_final: 0.7287 (p0) REVERT: A 688 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7785 (mmtm) REVERT: A 691 ARG cc_start: 0.7456 (ttm-80) cc_final: 0.6881 (mtm110) REVERT: A 796 TYR cc_start: 0.8131 (t80) cc_final: 0.7601 (t80) REVERT: E 96 ASN cc_start: 0.8367 (p0) cc_final: 0.8111 (p0) REVERT: E 434 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8607 (mp) REVERT: E 436 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8429 (pt) REVERT: F 420 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8314 (mt) REVERT: F 485 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8273 (pt) REVERT: F 619 ARG cc_start: 0.8310 (tpp80) cc_final: 0.7329 (mmm160) REVERT: G 80 ASP cc_start: 0.8180 (p0) cc_final: 0.7825 (p0) REVERT: G 144 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7246 (mm-30) REVERT: G 152 GLU cc_start: 0.7323 (pt0) cc_final: 0.6873 (tt0) REVERT: G 169 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7560 (mm-40) REVERT: H 274 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7357 (tt) REVERT: H 300 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6120 (mmtt) REVERT: H 319 SER cc_start: 0.8444 (t) cc_final: 0.8142 (m) REVERT: I 272 MET cc_start: 0.5248 (mmt) cc_final: 0.4415 (mmt) outliers start: 69 outliers final: 46 residues processed: 238 average time/residue: 0.2681 time to fit residues: 102.3896 Evaluate side-chains 236 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 183 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 245 GLU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 300 LYS Chi-restraints excluded: chain H residue 316 TRP Chi-restraints excluded: chain I residue 254 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 116 optimal weight: 0.0070 chunk 149 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 204 optimal weight: 7.9990 chunk 127 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN E 45 HIS ** E 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18969 Z= 0.160 Angle : 0.611 22.027 25875 Z= 0.273 Chirality : 0.041 0.246 3018 Planarity : 0.004 0.054 3068 Dihedral : 12.562 163.257 3476 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.66 % Allowed : 15.23 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.19), residues: 2136 helix: 1.66 (0.18), residues: 850 sheet: 0.24 (0.26), residues: 417 loop : -1.46 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 81 HIS 0.003 0.001 HIS E 252 PHE 0.015 0.001 PHE A 425 TYR 0.011 0.001 TYR F 482 ARG 0.007 0.000 ARG E 268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 187 time to evaluate : 2.057 Fit side-chains REVERT: A 193 TRP cc_start: 0.8432 (OUTLIER) cc_final: 0.6741 (m-90) REVERT: A 579 ASN cc_start: 0.7497 (m-40) cc_final: 0.7280 (p0) REVERT: A 688 LYS cc_start: 0.8281 (mtmt) cc_final: 0.7792 (mmtm) REVERT: A 691 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.6944 (mtm110) REVERT: A 796 TYR cc_start: 0.8184 (t80) cc_final: 0.7646 (t80) REVERT: E 96 ASN cc_start: 0.8386 (p0) cc_final: 0.8086 (p0) REVERT: E 434 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8652 (mp) REVERT: E 436 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8396 (pt) REVERT: F 420 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8339 (mt) REVERT: F 485 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8283 (pt) REVERT: F 619 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7326 (mmm160) REVERT: G 80 ASP cc_start: 0.8165 (p0) cc_final: 0.7832 (p0) REVERT: G 144 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7250 (mm-30) REVERT: G 152 GLU cc_start: 0.7377 (pt0) cc_final: 0.6928 (tt0) REVERT: G 169 GLN cc_start: 0.8389 (mm-40) cc_final: 0.7597 (mm-40) REVERT: H 274 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7314 (tt) REVERT: H 300 LYS cc_start: 0.6680 (OUTLIER) cc_final: 0.6161 (mmtt) REVERT: H 319 SER cc_start: 0.8420 (t) cc_final: 0.8140 (m) REVERT: I 272 MET cc_start: 0.5317 (mmt) cc_final: 0.4500 (mmt) outliers start: 69 outliers final: 55 residues processed: 238 average time/residue: 0.2567 time to fit residues: 97.3602 Evaluate side-chains 241 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 179 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 245 GLU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 251 ASN Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 300 LYS Chi-restraints excluded: chain H residue 316 TRP Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain I residue 254 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.0370 chunk 122 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 185 optimal weight: 0.2980 overall best weight: 0.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN ** E 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18969 Z= 0.149 Angle : 0.607 22.027 25875 Z= 0.272 Chirality : 0.040 0.245 3018 Planarity : 0.004 0.055 3068 Dihedral : 12.279 169.869 3476 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.61 % Allowed : 15.45 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 2136 helix: 1.69 (0.18), residues: 852 sheet: 0.25 (0.26), residues: 417 loop : -1.42 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 411 HIS 0.003 0.001 HIS H 258 PHE 0.014 0.001 PHE A 425 TYR 0.011 0.001 TYR E 339 ARG 0.006 0.000 ARG E 268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 186 time to evaluate : 2.012 Fit side-chains REVERT: A 193 TRP cc_start: 0.8496 (OUTLIER) cc_final: 0.6593 (m-90) REVERT: A 579 ASN cc_start: 0.7502 (m-40) cc_final: 0.7292 (p0) REVERT: A 679 VAL cc_start: 0.8933 (t) cc_final: 0.8605 (p) REVERT: A 688 LYS cc_start: 0.8287 (mtmt) cc_final: 0.7798 (mmtm) REVERT: A 691 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.6993 (mtm110) REVERT: A 796 TYR cc_start: 0.8205 (t80) cc_final: 0.7665 (t80) REVERT: E 96 ASN cc_start: 0.8378 (p0) cc_final: 0.8081 (p0) REVERT: E 434 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8634 (mp) REVERT: E 436 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8337 (pt) REVERT: F 420 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8341 (mt) REVERT: F 485 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8262 (pt) REVERT: F 619 ARG cc_start: 0.8286 (tpp80) cc_final: 0.7303 (mmm160) REVERT: G 80 ASP cc_start: 0.8144 (p0) cc_final: 0.7828 (p0) REVERT: G 144 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7192 (mm-30) REVERT: G 152 GLU cc_start: 0.7400 (pt0) cc_final: 0.6936 (tt0) REVERT: G 169 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7589 (mm-40) REVERT: H 225 CYS cc_start: 0.7750 (t) cc_final: 0.7216 (m) REVERT: H 274 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7393 (tt) REVERT: H 300 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6244 (mmtt) REVERT: H 317 MET cc_start: 0.8316 (tpt) cc_final: 0.8008 (tpt) REVERT: H 319 SER cc_start: 0.8437 (t) cc_final: 0.8158 (m) REVERT: I 272 MET cc_start: 0.5330 (mmt) cc_final: 0.4513 (mmt) outliers start: 68 outliers final: 53 residues processed: 235 average time/residue: 0.2727 time to fit residues: 102.3599 Evaluate side-chains 238 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 178 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 245 GLU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 300 LYS Chi-restraints excluded: chain H residue 316 TRP Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain I residue 254 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 ASN A 794 GLN ** E 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 583 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18969 Z= 0.183 Angle : 0.618 22.035 25875 Z= 0.278 Chirality : 0.041 0.254 3018 Planarity : 0.004 0.056 3068 Dihedral : 11.980 162.934 3474 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.66 % Allowed : 15.39 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 2136 helix: 1.71 (0.18), residues: 850 sheet: 0.29 (0.26), residues: 407 loop : -1.40 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 411 HIS 0.005 0.001 HIS E 57 PHE 0.016 0.001 PHE A 425 TYR 0.012 0.001 TYR H 330 ARG 0.007 0.000 ARG E 268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 180 time to evaluate : 2.057 Fit side-chains REVERT: A 193 TRP cc_start: 0.8541 (OUTLIER) cc_final: 0.6641 (m-90) REVERT: A 579 ASN cc_start: 0.7514 (m-40) cc_final: 0.7304 (p0) REVERT: A 679 VAL cc_start: 0.8955 (t) cc_final: 0.8672 (p) REVERT: A 688 LYS cc_start: 0.8292 (mtmt) cc_final: 0.7795 (mmtm) REVERT: A 691 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.7060 (mtp-110) REVERT: A 796 TYR cc_start: 0.8273 (t80) cc_final: 0.7782 (t80) REVERT: A 811 ASN cc_start: 0.7389 (t0) cc_final: 0.7042 (t0) REVERT: E 96 ASN cc_start: 0.8367 (p0) cc_final: 0.8074 (p0) REVERT: E 434 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8687 (mp) REVERT: E 436 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8304 (pt) REVERT: F 420 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8391 (mt) REVERT: F 485 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8310 (pt) REVERT: F 619 ARG cc_start: 0.8290 (tpp80) cc_final: 0.7302 (mmm160) REVERT: G 144 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7205 (mm-30) REVERT: G 152 GLU cc_start: 0.7384 (pt0) cc_final: 0.6931 (tt0) REVERT: G 169 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7625 (mm-40) REVERT: H 225 CYS cc_start: 0.7784 (t) cc_final: 0.7234 (m) REVERT: H 274 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7383 (tt) REVERT: H 300 LYS cc_start: 0.6700 (OUTLIER) cc_final: 0.6264 (mmtt) REVERT: H 319 SER cc_start: 0.8354 (t) cc_final: 0.8097 (m) REVERT: I 272 MET cc_start: 0.5354 (mmt) cc_final: 0.4535 (mmt) outliers start: 69 outliers final: 51 residues processed: 231 average time/residue: 0.2604 time to fit residues: 95.9774 Evaluate side-chains 234 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 176 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 245 GLU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 300 LYS Chi-restraints excluded: chain H residue 316 TRP Chi-restraints excluded: chain I residue 254 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 168 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN ** E 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18969 Z= 0.198 Angle : 0.632 22.048 25875 Z= 0.284 Chirality : 0.042 0.385 3018 Planarity : 0.004 0.057 3068 Dihedral : 11.687 163.024 3474 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.18 % Allowed : 15.92 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 2136 helix: 1.68 (0.18), residues: 849 sheet: 0.26 (0.27), residues: 399 loop : -1.37 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 411 HIS 0.004 0.001 HIS E 252 PHE 0.017 0.001 PHE A 425 TYR 0.012 0.001 TYR E 428 ARG 0.007 0.000 ARG E 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 180 time to evaluate : 2.126 Fit side-chains REVERT: A 193 TRP cc_start: 0.8552 (OUTLIER) cc_final: 0.6696 (m-90) REVERT: A 679 VAL cc_start: 0.8934 (t) cc_final: 0.8636 (p) REVERT: A 688 LYS cc_start: 0.8292 (mtmt) cc_final: 0.7799 (mmtm) REVERT: A 691 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.7037 (mtp-110) REVERT: A 796 TYR cc_start: 0.8313 (t80) cc_final: 0.7885 (t80) REVERT: A 811 ASN cc_start: 0.7393 (t0) cc_final: 0.7055 (t0) REVERT: E 96 ASN cc_start: 0.8349 (p0) cc_final: 0.8068 (p0) REVERT: E 434 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8694 (mp) REVERT: E 436 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8297 (pt) REVERT: F 420 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8451 (mt) REVERT: F 485 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8334 (pt) REVERT: F 619 ARG cc_start: 0.8284 (tpp80) cc_final: 0.7291 (mmm160) REVERT: G 80 ASP cc_start: 0.8166 (p0) cc_final: 0.7901 (p0) REVERT: G 144 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7273 (mm-30) REVERT: G 152 GLU cc_start: 0.7399 (pt0) cc_final: 0.6923 (tt0) REVERT: G 169 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7621 (mm-40) REVERT: H 225 CYS cc_start: 0.7764 (t) cc_final: 0.7243 (m) REVERT: H 274 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7429 (tt) REVERT: H 300 LYS cc_start: 0.6667 (OUTLIER) cc_final: 0.6255 (mmtt) REVERT: H 317 MET cc_start: 0.8398 (tpt) cc_final: 0.7849 (tpt) REVERT: H 319 SER cc_start: 0.8395 (t) cc_final: 0.8126 (m) REVERT: I 272 MET cc_start: 0.5323 (mmt) cc_final: 0.4522 (mmt) outliers start: 60 outliers final: 49 residues processed: 226 average time/residue: 0.2781 time to fit residues: 98.8772 Evaluate side-chains 233 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 177 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 245 GLU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 361 ASP Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 300 LYS Chi-restraints excluded: chain H residue 316 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 168 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN ** E 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113790 restraints weight = 25405.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117005 restraints weight = 15725.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119136 restraints weight = 11539.747| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18969 Z= 0.233 Angle : 0.651 22.037 25875 Z= 0.295 Chirality : 0.042 0.310 3018 Planarity : 0.004 0.057 3068 Dihedral : 11.614 162.617 3474 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.18 % Allowed : 15.92 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 2136 helix: 1.62 (0.18), residues: 849 sheet: 0.12 (0.26), residues: 405 loop : -1.42 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 411 HIS 0.004 0.001 HIS E 217 PHE 0.020 0.001 PHE A 425 TYR 0.014 0.001 TYR E 428 ARG 0.007 0.000 ARG E 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3514.32 seconds wall clock time: 64 minutes 49.26 seconds (3889.26 seconds total)