Starting phenix.real_space_refine on Fri Feb 16 10:29:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lue_23521/02_2024/7lue_23521.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lue_23521/02_2024/7lue_23521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lue_23521/02_2024/7lue_23521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lue_23521/02_2024/7lue_23521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lue_23521/02_2024/7lue_23521.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lue_23521/02_2024/7lue_23521.pdb" } resolution = 2.9 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 9474 2.51 5 N 2511 2.21 5 O 2946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "J ARG 82": "NH1" <-> "NH2" Residue "L ARG 46": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 77": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N ARG 77": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15018 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3300 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 413} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3300 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 413} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3300 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 413} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain breaks: 1 Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain breaks: 1 Chain: "J" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain breaks: 1 Chain: "L" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "N" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Time building chain proxies: 8.44, per 1000 atoms: 0.56 Number of scatterers: 15018 At special positions: 0 Unit cell: (131.15, 127.925, 123.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2946 8.00 N 2511 7.00 C 9474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.63 Conformation dependent library (CDL) restraints added in 2.8 seconds 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3654 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 33 sheets defined 24.7% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 73 through 95 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 171 removed outlier: 3.566A pdb=" N ILE A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 217 through 241 removed outlier: 4.087A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 376 through 379 Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.141A pdb=" N VAL A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 492 through 506 Processing helix chain 'B' and resid 73 through 95 Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 removed outlier: 3.565A pdb=" N ILE B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 217 through 241 removed outlier: 4.087A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.141A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 492 through 506 Processing helix chain 'C' and resid 73 through 95 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 removed outlier: 3.566A pdb=" N ILE C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 217 through 241 removed outlier: 4.087A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 385 removed outlier: 4.141A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 492 through 506 Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.536A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 31 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.535A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 31 Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.536A pdb=" N THR J 87 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.814A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.814A pdb=" N VAL M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.814A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 358 through 360 removed outlier: 8.155A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 315 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A 43 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N CYS A 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU A 45 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR A 311 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 360 removed outlier: 8.155A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE A 28 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU A 467 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU A 30 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 469 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE A 32 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 11.175A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA A 298 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 406 Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 435 removed outlier: 6.688A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR A 434 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 358 through 360 removed outlier: 8.156A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 315 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY B 43 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N CYS B 313 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU B 45 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR B 311 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 358 through 360 removed outlier: 8.156A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE B 28 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N LEU B 467 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU B 30 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 469 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE B 32 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 180 removed outlier: 11.176A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 298 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB2, first strand: chain 'B' and resid 404 through 406 Processing sheet with id=AB3, first strand: chain 'B' and resid 430 through 435 removed outlier: 6.687A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 358 through 360 removed outlier: 8.155A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 315 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY C 43 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS C 313 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU C 45 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR C 311 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 358 through 360 removed outlier: 8.155A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE C 28 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N LEU C 467 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU C 30 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL C 469 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE C 32 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 180 removed outlier: 11.175A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA C 298 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'C' and resid 404 through 406 Processing sheet with id=AB9, first strand: chain 'C' and resid 430 through 435 removed outlier: 6.688A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.475A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.476A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.475A pdb=" N GLU J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.783A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.783A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.783A pdb=" N GLY M 84 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN M 53 " --> pdb=" O TYR M 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.783A pdb=" N GLY M 84 " --> pdb=" O VAL M 104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.783A pdb=" N GLY N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.783A pdb=" N GLY N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 1917 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: 5.93 Time building geometry restraints manager: 6.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4824 1.34 - 1.46: 3361 1.46 - 1.58: 6971 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 15276 Sorted by residual: bond pdb=" CA THR N 29 " pdb=" C THR N 29 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.43e-02 4.89e+03 9.58e-01 bond pdb=" N GLY H 100 " pdb=" CA GLY H 100 " ideal model delta sigma weight residual 1.449 1.435 0.014 1.45e-02 4.76e+03 9.39e-01 bond pdb=" CG PRO A 246 " pdb=" CD PRO A 246 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.31e-01 bond pdb=" CA THR M 29 " pdb=" C THR M 29 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.43e-02 4.89e+03 9.25e-01 bond pdb=" CG PRO B 246 " pdb=" CD PRO B 246 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.03e-01 ... (remaining 15271 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.70: 356 106.70 - 113.52: 8731 113.52 - 120.34: 5060 120.34 - 127.16: 6453 127.16 - 133.97: 133 Bond angle restraints: 20733 Sorted by residual: angle pdb=" N GLY C 411 " pdb=" CA GLY C 411 " pdb=" C GLY C 411 " ideal model delta sigma weight residual 110.45 114.21 -3.76 1.30e+00 5.92e-01 8.38e+00 angle pdb=" N GLY A 411 " pdb=" CA GLY A 411 " pdb=" C GLY A 411 " ideal model delta sigma weight residual 110.45 114.18 -3.73 1.30e+00 5.92e-01 8.25e+00 angle pdb=" N GLY B 411 " pdb=" CA GLY B 411 " pdb=" C GLY B 411 " ideal model delta sigma weight residual 110.45 114.15 -3.70 1.30e+00 5.92e-01 8.11e+00 angle pdb=" N LYS M 50 " pdb=" CA LYS M 50 " pdb=" C LYS M 50 " ideal model delta sigma weight residual 109.41 105.54 3.87 1.52e+00 4.33e-01 6.47e+00 angle pdb=" N LYS N 50 " pdb=" CA LYS N 50 " pdb=" C LYS N 50 " ideal model delta sigma weight residual 109.41 105.56 3.85 1.52e+00 4.33e-01 6.42e+00 ... (remaining 20728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8902 17.84 - 35.69: 299 35.69 - 53.53: 63 53.53 - 71.37: 18 71.37 - 89.22: 12 Dihedral angle restraints: 9294 sinusoidal: 3627 harmonic: 5667 Sorted by residual: dihedral pdb=" CA LYS M 50 " pdb=" C LYS M 50 " pdb=" N VAL M 51 " pdb=" CA VAL M 51 " ideal model delta harmonic sigma weight residual -180.00 -155.65 -24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LYS N 50 " pdb=" C LYS N 50 " pdb=" N VAL N 51 " pdb=" CA VAL N 51 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LYS L 50 " pdb=" C LYS L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta harmonic sigma weight residual -180.00 -155.74 -24.26 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 9291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1567 0.031 - 0.062: 579 0.062 - 0.093: 168 0.093 - 0.124: 122 0.124 - 0.155: 15 Chirality restraints: 2451 Sorted by residual: chirality pdb=" CA ILE M 48 " pdb=" N ILE M 48 " pdb=" C ILE M 48 " pdb=" CB ILE M 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ILE N 48 " pdb=" N ILE N 48 " pdb=" C ILE N 48 " pdb=" CB ILE N 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 2448 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 319 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 320 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 319 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO C 320 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 320 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 320 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 319 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO B 320 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 320 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 320 " 0.018 5.00e-02 4.00e+02 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1099 2.74 - 3.28: 14808 3.28 - 3.82: 25105 3.82 - 4.36: 32064 4.36 - 4.90: 55720 Nonbonded interactions: 128796 Sorted by model distance: nonbonded pdb=" OG SER A 46 " pdb=" OG1 THR A 311 " model vdw 2.200 2.440 nonbonded pdb=" OG SER C 46 " pdb=" OG1 THR C 311 " model vdw 2.200 2.440 nonbonded pdb=" OG SER B 46 " pdb=" OG1 THR B 311 " model vdw 2.200 2.440 nonbonded pdb=" O ARG B 49 " pdb=" OG1 THR B 369 " model vdw 2.203 2.440 nonbonded pdb=" O ARG C 49 " pdb=" OG1 THR C 369 " model vdw 2.203 2.440 ... (remaining 128791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.180 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 42.470 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.100 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:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15276 Z= 0.192 Angle : 0.492 4.341 20733 Z= 0.295 Chirality : 0.041 0.155 2451 Planarity : 0.003 0.032 2610 Dihedral : 10.430 89.217 5559 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.86 % Allowed : 5.24 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.33 (0.19), residues: 1911 helix: 1.00 (0.27), residues: 369 sheet: 0.31 (0.20), residues: 639 loop : -0.04 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 103 HIS 0.002 0.001 HIS B 317 PHE 0.009 0.001 PHE J 100C TYR 0.012 0.001 TYR M 49 ARG 0.002 0.000 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 351 time to evaluate : 1.888 Fit side-chains REVERT: A 289 MET cc_start: 0.8421 (tpt) cc_final: 0.7901 (tpt) REVERT: A 448 ASP cc_start: 0.7610 (m-30) cc_final: 0.7136 (m-30) REVERT: B 448 ASP cc_start: 0.7694 (m-30) cc_final: 0.7469 (t0) REVERT: B 489 ASP cc_start: 0.6830 (t0) cc_final: 0.6428 (m-30) REVERT: B 493 SER cc_start: 0.7668 (t) cc_final: 0.7338 (p) REVERT: B 501 GLN cc_start: 0.7824 (mt0) cc_final: 0.7479 (mt0) REVERT: C 172 LEU cc_start: 0.8968 (tp) cc_final: 0.8649 (tp) REVERT: C 489 ASP cc_start: 0.7140 (t0) cc_final: 0.6631 (m-30) REVERT: C 493 SER cc_start: 0.7544 (t) cc_final: 0.7207 (p) REVERT: H 19 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7622 (tttt) REVERT: H 83 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8081 (p) REVERT: I 83 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8212 (p) REVERT: L 107 LYS cc_start: 0.5695 (mtmt) cc_final: 0.5475 (mtmm) REVERT: M 107 LYS cc_start: 0.6027 (mtmt) cc_final: 0.5824 (mtmm) REVERT: N 27 SER cc_start: 0.8087 (p) cc_final: 0.7857 (m) outliers start: 15 outliers final: 2 residues processed: 360 average time/residue: 1.3075 time to fit residues: 518.1803 Evaluate side-chains 245 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 241 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 83 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 345 ASN A 426 ASN B 27 ASN B 63 ASN B 183 ASN B 302 GLN B 331 ASN C 27 ASN C 63 ASN C 183 ASN C 208 ASN C 302 GLN C 426 ASN M 17 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15276 Z= 0.276 Angle : 0.545 5.935 20733 Z= 0.297 Chirality : 0.045 0.159 2451 Planarity : 0.004 0.037 2610 Dihedral : 4.878 42.332 2076 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.82 % Allowed : 12.15 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.40 (0.19), residues: 1911 helix: 1.59 (0.26), residues: 369 sheet: 0.41 (0.21), residues: 600 loop : -0.29 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 314 HIS 0.005 0.001 HIS B 317 PHE 0.018 0.001 PHE H 100C TYR 0.022 0.002 TYR M 49 ARG 0.007 0.001 ARG H 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 251 time to evaluate : 1.706 Fit side-chains REVERT: A 77 LYS cc_start: 0.8015 (mmpt) cc_final: 0.7631 (mmtt) REVERT: A 289 MET cc_start: 0.8306 (tpt) cc_final: 0.7672 (tpt) REVERT: A 426 ASN cc_start: 0.7621 (t0) cc_final: 0.7392 (t0) REVERT: B 77 LYS cc_start: 0.8003 (mttm) cc_final: 0.7602 (mmmt) REVERT: B 84 ASP cc_start: 0.7133 (m-30) cc_final: 0.6903 (m-30) REVERT: B 91 THR cc_start: 0.8729 (m) cc_final: 0.8475 (m) REVERT: B 163 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7442 (mm-30) REVERT: B 235 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7969 (mtm-85) REVERT: B 289 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8114 (mmm) REVERT: B 493 SER cc_start: 0.7723 (t) cc_final: 0.7210 (p) REVERT: B 501 GLN cc_start: 0.7934 (mt0) cc_final: 0.7551 (mt0) REVERT: C 77 LYS cc_start: 0.8032 (mttp) cc_final: 0.7778 (mmtt) REVERT: C 163 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: C 259 SER cc_start: 0.8548 (p) cc_final: 0.8320 (m) REVERT: C 378 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: H 19 LYS cc_start: 0.7833 (ttmt) cc_final: 0.7559 (tttt) REVERT: H 51 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8706 (tt) REVERT: I 46 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7547 (tt0) REVERT: I 82 SER cc_start: 0.8535 (m) cc_final: 0.8029 (t) REVERT: M 7 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7753 (p) REVERT: M 107 LYS cc_start: 0.6123 (mtmt) cc_final: 0.5908 (mtmm) REVERT: N 7 SER cc_start: 0.8019 (OUTLIER) cc_final: 0.7769 (p) REVERT: N 24 ARG cc_start: 0.7708 (mtp-110) cc_final: 0.7476 (mtp-110) REVERT: N 100 GLN cc_start: 0.7610 (mp10) cc_final: 0.7244 (pm20) outliers start: 49 outliers final: 18 residues processed: 286 average time/residue: 1.2441 time to fit residues: 392.2648 Evaluate side-chains 249 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 224 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 54 ASN Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 27 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 174 optimal weight: 0.5980 chunk 188 optimal weight: 0.1980 chunk 155 optimal weight: 0.9990 chunk 173 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 202 GLN B 27 ASN B 63 ASN B 183 ASN C 27 ASN C 63 ASN H 39 GLN J 39 GLN L 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15276 Z= 0.163 Angle : 0.469 5.865 20733 Z= 0.255 Chirality : 0.043 0.153 2451 Planarity : 0.004 0.035 2610 Dihedral : 4.438 31.345 2073 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.86 % Allowed : 12.95 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.51 (0.19), residues: 1911 helix: 1.97 (0.26), residues: 369 sheet: 0.42 (0.21), residues: 600 loop : -0.32 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 314 HIS 0.004 0.001 HIS C 317 PHE 0.010 0.001 PHE H 100C TYR 0.015 0.001 TYR C 299 ARG 0.003 0.000 ARG N 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 261 time to evaluate : 1.702 Fit side-chains REVERT: A 77 LYS cc_start: 0.7987 (mmpt) cc_final: 0.7607 (mmtt) REVERT: A 394 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7423 (ptpt) REVERT: A 448 ASP cc_start: 0.7490 (m-30) cc_final: 0.7169 (m-30) REVERT: B 77 LYS cc_start: 0.7911 (mttm) cc_final: 0.7618 (mmtt) REVERT: B 84 ASP cc_start: 0.7068 (m-30) cc_final: 0.6634 (m-30) REVERT: B 91 THR cc_start: 0.8564 (m) cc_final: 0.8296 (m) REVERT: B 163 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7480 (mm-30) REVERT: B 235 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.7974 (mtm-85) REVERT: B 378 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: B 394 LYS cc_start: 0.7526 (mtmt) cc_final: 0.7235 (ptpt) REVERT: B 493 SER cc_start: 0.7629 (t) cc_final: 0.7226 (p) REVERT: B 501 GLN cc_start: 0.7960 (mt0) cc_final: 0.7607 (mt0) REVERT: C 163 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7543 (mm-30) REVERT: H 46 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7210 (tt0) REVERT: I 10 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6989 (mt-10) REVERT: J 46 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7437 (tt0) REVERT: J 80 MET cc_start: 0.7762 (ttp) cc_final: 0.7514 (ttp) REVERT: M 107 LYS cc_start: 0.6060 (mtmt) cc_final: 0.5564 (mtpm) REVERT: N 7 SER cc_start: 0.8183 (OUTLIER) cc_final: 0.7865 (p) REVERT: N 100 GLN cc_start: 0.7567 (mp10) cc_final: 0.7184 (pm20) outliers start: 67 outliers final: 29 residues processed: 308 average time/residue: 1.1683 time to fit residues: 398.5189 Evaluate side-chains 259 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 225 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 54 ASN Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 89 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 185 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 208 ASN A 345 ASN B 27 ASN B 63 ASN B 183 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15276 Z= 0.287 Angle : 0.540 8.241 20733 Z= 0.290 Chirality : 0.045 0.199 2451 Planarity : 0.004 0.036 2610 Dihedral : 4.627 32.201 2071 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.07 % Allowed : 12.95 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.15 (0.19), residues: 1911 helix: 1.44 (0.26), residues: 396 sheet: 0.33 (0.20), residues: 594 loop : -0.60 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 314 HIS 0.006 0.001 HIS B 317 PHE 0.017 0.001 PHE H 100C TYR 0.024 0.002 TYR L 49 ARG 0.009 0.001 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 229 time to evaluate : 1.746 Fit side-chains REVERT: A 77 LYS cc_start: 0.8012 (mmpt) cc_final: 0.7580 (mmtt) REVERT: B 163 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: B 235 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.8069 (mtm-85) REVERT: B 354 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6253 (mp-120) REVERT: B 493 SER cc_start: 0.7603 (t) cc_final: 0.7190 (p) REVERT: B 501 GLN cc_start: 0.7961 (mt0) cc_final: 0.7602 (mt0) REVERT: C 77 LYS cc_start: 0.7959 (mttp) cc_final: 0.7670 (mmtt) REVERT: C 163 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: C 272 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.6917 (ttmt) REVERT: C 405 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8363 (t) REVERT: H 10 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6840 (mm-30) REVERT: H 46 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7207 (tt0) REVERT: I 10 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7041 (mt-10) REVERT: J 46 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7405 (tt0) REVERT: L 50 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7631 (mttt) REVERT: M 107 LYS cc_start: 0.6191 (mtmt) cc_final: 0.5665 (mtpm) REVERT: N 100 GLN cc_start: 0.7666 (mp10) cc_final: 0.7243 (pm20) outliers start: 88 outliers final: 46 residues processed: 291 average time/residue: 1.1868 time to fit residues: 382.0088 Evaluate side-chains 274 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 220 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 74 LYS Chi-restraints excluded: chain N residue 89 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 128 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN B 63 ASN B 183 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN C 345 ASN I 39 GLN L 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15276 Z= 0.222 Angle : 0.504 7.768 20733 Z= 0.270 Chirality : 0.044 0.162 2451 Planarity : 0.004 0.037 2610 Dihedral : 4.541 32.275 2071 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.89 % Allowed : 13.70 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.18 (0.19), residues: 1911 helix: 1.58 (0.26), residues: 396 sheet: 0.32 (0.20), residues: 594 loop : -0.63 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 314 HIS 0.005 0.001 HIS A 317 PHE 0.014 0.001 PHE H 100C TYR 0.020 0.002 TYR M 49 ARG 0.009 0.001 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 233 time to evaluate : 1.735 Fit side-chains REVERT: A 394 LYS cc_start: 0.7575 (mtmt) cc_final: 0.7245 (ptpt) REVERT: A 426 ASN cc_start: 0.7653 (t0) cc_final: 0.7342 (t0) REVERT: B 77 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7540 (mmmt) REVERT: B 163 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7449 (mm-30) REVERT: B 235 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.7975 (mtm-85) REVERT: B 354 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.6378 (mp-120) REVERT: B 493 SER cc_start: 0.7590 (t) cc_final: 0.7203 (p) REVERT: B 501 GLN cc_start: 0.7940 (mt0) cc_final: 0.7591 (mt0) REVERT: C 77 LYS cc_start: 0.7859 (mttp) cc_final: 0.7622 (mmtt) REVERT: C 163 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: C 272 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.6896 (ttmt) REVERT: C 405 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8343 (t) REVERT: H 10 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6718 (mm-30) REVERT: H 46 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7194 (tt0) REVERT: I 10 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7045 (mt-10) REVERT: I 51 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8637 (tt) REVERT: J 46 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7400 (tt0) REVERT: L 45 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.6278 (ppp80) REVERT: L 50 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7400 (mttt) REVERT: M 107 LYS cc_start: 0.6141 (mtmt) cc_final: 0.5782 (mtpm) REVERT: N 100 GLN cc_start: 0.7638 (mp10) cc_final: 0.7213 (pm20) outliers start: 85 outliers final: 50 residues processed: 292 average time/residue: 1.2154 time to fit residues: 392.3560 Evaluate side-chains 283 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 223 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 74 LYS Chi-restraints excluded: chain N residue 89 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.8980 chunk 167 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 45 optimal weight: 0.1980 chunk 185 optimal weight: 0.1980 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN B 63 ASN B 183 ASN B 345 ASN C 63 ASN L 37 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15276 Z= 0.166 Angle : 0.473 7.412 20733 Z= 0.253 Chirality : 0.043 0.163 2451 Planarity : 0.004 0.043 2610 Dihedral : 4.384 31.979 2071 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.66 % Allowed : 14.28 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.45 (0.19), residues: 1911 helix: 2.20 (0.26), residues: 372 sheet: 0.39 (0.20), residues: 609 loop : -0.51 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 314 HIS 0.005 0.001 HIS A 317 PHE 0.010 0.001 PHE H 100C TYR 0.018 0.001 TYR L 49 ARG 0.010 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 231 time to evaluate : 1.874 Fit side-chains REVERT: A 77 LYS cc_start: 0.7958 (mmpt) cc_final: 0.7551 (mmtt) REVERT: A 354 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7004 (mp10) REVERT: A 394 LYS cc_start: 0.7770 (mtmt) cc_final: 0.7450 (ptpt) REVERT: A 426 ASN cc_start: 0.7634 (t0) cc_final: 0.7318 (t0) REVERT: B 77 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7556 (mmmt) REVERT: B 163 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: B 235 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.7998 (mtm-85) REVERT: B 354 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.6266 (mp-120) REVERT: B 394 LYS cc_start: 0.7507 (mtmt) cc_final: 0.7267 (ptpt) REVERT: B 493 SER cc_start: 0.7568 (t) cc_final: 0.7225 (p) REVERT: B 501 GLN cc_start: 0.7914 (mt0) cc_final: 0.7571 (mt0) REVERT: C 77 LYS cc_start: 0.7875 (mttp) cc_final: 0.7633 (mmtt) REVERT: C 163 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7555 (mm-30) REVERT: C 183 ASN cc_start: 0.7176 (m-40) cc_final: 0.6896 (m110) REVERT: C 405 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.8341 (t) REVERT: C 427 LYS cc_start: 0.7684 (tptm) cc_final: 0.7194 (ptpt) REVERT: H 46 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7181 (tt0) REVERT: I 10 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7066 (mt-10) REVERT: I 51 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8606 (tt) REVERT: J 46 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7355 (tt0) REVERT: L 45 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.6280 (ppp80) REVERT: M 38 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8636 (tt0) REVERT: M 107 LYS cc_start: 0.6133 (mtmt) cc_final: 0.5757 (mtpm) REVERT: N 54 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7654 (ttp-110) REVERT: N 100 GLN cc_start: 0.7593 (mp10) cc_final: 0.7153 (pm20) outliers start: 81 outliers final: 49 residues processed: 290 average time/residue: 1.1482 time to fit residues: 370.1729 Evaluate side-chains 286 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 228 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 89 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 156 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 185 optimal weight: 0.4980 chunk 115 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 331 ASN A 345 ASN B 27 ASN B 63 ASN B 183 ASN C 27 ASN C 63 ASN C 500 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15276 Z= 0.219 Angle : 0.497 7.751 20733 Z= 0.265 Chirality : 0.043 0.163 2451 Planarity : 0.004 0.034 2610 Dihedral : 4.453 32.316 2071 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.72 % Allowed : 14.34 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.25 (0.19), residues: 1911 helix: 1.80 (0.26), residues: 396 sheet: 0.32 (0.20), residues: 591 loop : -0.64 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 314 HIS 0.006 0.001 HIS A 317 PHE 0.013 0.001 PHE H 100C TYR 0.021 0.002 TYR M 49 ARG 0.004 0.000 ARG N 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 234 time to evaluate : 1.912 Fit side-chains REVERT: A 77 LYS cc_start: 0.7975 (mmpt) cc_final: 0.7537 (mmtt) REVERT: A 421 LYS cc_start: 0.7911 (ttpt) cc_final: 0.7704 (ttpt) REVERT: A 426 ASN cc_start: 0.7642 (t0) cc_final: 0.7317 (t0) REVERT: A 493 SER cc_start: 0.7006 (t) cc_final: 0.6625 (p) REVERT: B 163 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: B 235 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.8012 (mtm-85) REVERT: B 354 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.6300 (mp-120) REVERT: B 394 LYS cc_start: 0.7549 (mtmt) cc_final: 0.7275 (ptpt) REVERT: B 493 SER cc_start: 0.7633 (t) cc_final: 0.7305 (p) REVERT: B 501 GLN cc_start: 0.7904 (mt0) cc_final: 0.7554 (mt0) REVERT: C 77 LYS cc_start: 0.7894 (mttp) cc_final: 0.7641 (mmtt) REVERT: C 163 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7558 (mm-30) REVERT: C 183 ASN cc_start: 0.7126 (m-40) cc_final: 0.6851 (m110) REVERT: C 272 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.6853 (ttmt) REVERT: C 405 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8341 (t) REVERT: C 427 LYS cc_start: 0.7681 (tptm) cc_final: 0.7228 (ptpt) REVERT: C 493 SER cc_start: 0.7317 (t) cc_final: 0.7072 (p) REVERT: H 46 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7213 (tt0) REVERT: I 10 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: I 51 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8626 (tt) REVERT: J 46 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7371 (tt0) REVERT: L 7 SER cc_start: 0.7741 (OUTLIER) cc_final: 0.7513 (p) REVERT: L 45 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.6265 (ppp80) REVERT: M 107 LYS cc_start: 0.6139 (mtmt) cc_final: 0.5762 (mtpm) REVERT: N 100 GLN cc_start: 0.7620 (mp10) cc_final: 0.7150 (pm20) outliers start: 82 outliers final: 56 residues processed: 293 average time/residue: 1.1757 time to fit residues: 383.5351 Evaluate side-chains 290 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 225 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 74 LYS Chi-restraints excluded: chain N residue 89 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 35 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 331 ASN B 27 ASN B 63 ASN B 183 ASN B 426 ASN C 63 ASN C 371 ASN C 426 ASN C 500 ASN I 54 ASN M 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15276 Z= 0.333 Angle : 0.561 8.481 20733 Z= 0.299 Chirality : 0.046 0.175 2451 Planarity : 0.004 0.037 2610 Dihedral : 4.726 33.502 2071 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.66 % Allowed : 14.74 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.02 (0.19), residues: 1911 helix: 1.56 (0.25), residues: 396 sheet: 0.22 (0.20), residues: 594 loop : -0.78 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 314 HIS 0.006 0.001 HIS B 317 PHE 0.019 0.002 PHE H 100C TYR 0.026 0.002 TYR M 49 ARG 0.005 0.001 ARG M 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 223 time to evaluate : 1.825 Fit side-chains REVERT: A 272 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7264 (ttmt) REVERT: A 394 LYS cc_start: 0.7516 (mtmt) cc_final: 0.7165 (ptpt) REVERT: A 426 ASN cc_start: 0.7648 (t0) cc_final: 0.7358 (t0) REVERT: B 77 LYS cc_start: 0.7994 (mmtt) cc_final: 0.7545 (mmmt) REVERT: B 163 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: B 235 ARG cc_start: 0.8363 (ttm-80) cc_final: 0.8113 (mtm-85) REVERT: B 354 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.6365 (mp-120) REVERT: B 493 SER cc_start: 0.7593 (t) cc_final: 0.7211 (p) REVERT: B 501 GLN cc_start: 0.7925 (mt0) cc_final: 0.7576 (mt0) REVERT: C 77 LYS cc_start: 0.7966 (mttp) cc_final: 0.7688 (mmtt) REVERT: C 163 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: C 183 ASN cc_start: 0.7121 (m-40) cc_final: 0.6797 (m110) REVERT: C 272 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.6905 (ttmt) REVERT: H 10 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6796 (mm-30) REVERT: H 46 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7201 (tt0) REVERT: I 10 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7056 (mt-10) REVERT: I 51 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8687 (tt) REVERT: J 46 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7320 (tt0) REVERT: L 45 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6283 (ppp80) REVERT: M 107 LYS cc_start: 0.6166 (mtmt) cc_final: 0.5789 (mtpm) REVERT: N 54 ARG cc_start: 0.8043 (mtm-85) cc_final: 0.7814 (mtm-85) REVERT: N 100 GLN cc_start: 0.7685 (mp10) cc_final: 0.7219 (pm20) outliers start: 81 outliers final: 56 residues processed: 284 average time/residue: 1.1410 time to fit residues: 359.9193 Evaluate side-chains 284 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 219 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 54 ASN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 74 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 163 optimal weight: 0.4980 chunk 171 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 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 27 ASN A 371 ASN B 27 ASN B 63 ASN B 183 ASN C 63 ASN I 54 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15276 Z= 0.218 Angle : 0.506 8.329 20733 Z= 0.270 Chirality : 0.044 0.166 2451 Planarity : 0.004 0.037 2610 Dihedral : 4.584 33.195 2071 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.20 % Allowed : 15.54 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.09 (0.19), residues: 1911 helix: 1.67 (0.26), residues: 396 sheet: 0.21 (0.20), residues: 591 loop : -0.72 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 314 HIS 0.005 0.001 HIS A 317 PHE 0.013 0.001 PHE H 100C TYR 0.020 0.002 TYR M 49 ARG 0.004 0.000 ARG N 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 230 time to evaluate : 1.706 Fit side-chains REVERT: A 394 LYS cc_start: 0.7536 (mtmt) cc_final: 0.7203 (ptpt) REVERT: A 426 ASN cc_start: 0.7666 (t0) cc_final: 0.7346 (t0) REVERT: B 77 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7511 (mmmt) REVERT: B 163 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: B 235 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.8016 (mtm-85) REVERT: B 354 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.6364 (mp-120) REVERT: B 493 SER cc_start: 0.7648 (t) cc_final: 0.7305 (p) REVERT: B 501 GLN cc_start: 0.7917 (mt0) cc_final: 0.7575 (mt0) REVERT: C 77 LYS cc_start: 0.7951 (mttp) cc_final: 0.7677 (mmtt) REVERT: C 163 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: C 183 ASN cc_start: 0.7115 (m-40) cc_final: 0.6787 (m110) REVERT: C 405 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.8360 (t) REVERT: C 493 SER cc_start: 0.7395 (t) cc_final: 0.7142 (p) REVERT: H 46 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7203 (tt0) REVERT: I 10 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7052 (mt-10) REVERT: I 51 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8657 (tt) REVERT: J 46 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7391 (tt0) REVERT: L 45 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.6262 (ppp80) REVERT: M 107 LYS cc_start: 0.6140 (mtmt) cc_final: 0.5761 (mtpm) REVERT: N 100 GLN cc_start: 0.7642 (mp10) cc_final: 0.7190 (pm20) outliers start: 73 outliers final: 55 residues processed: 283 average time/residue: 1.1690 time to fit residues: 366.2056 Evaluate side-chains 286 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 224 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 54 ASN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 74 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.3980 chunk 111 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 176 optimal weight: 0.0020 chunk 152 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 331 ASN B 27 ASN B 63 ASN B 183 ASN C 63 ASN C 500 ASN I 39 GLN ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15276 Z= 0.175 Angle : 0.482 8.410 20733 Z= 0.257 Chirality : 0.043 0.166 2451 Planarity : 0.004 0.036 2610 Dihedral : 4.448 32.619 2071 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.86 % Allowed : 16.06 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.18 (0.19), residues: 1911 helix: 1.81 (0.26), residues: 396 sheet: 0.26 (0.20), residues: 591 loop : -0.69 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 314 HIS 0.005 0.001 HIS A 317 PHE 0.010 0.001 PHE I 100C TYR 0.018 0.001 TYR M 49 ARG 0.003 0.000 ARG M 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 228 time to evaluate : 1.608 Fit side-chains REVERT: A 394 LYS cc_start: 0.7775 (mtmt) cc_final: 0.7477 (ptpt) REVERT: A 426 ASN cc_start: 0.7649 (t0) cc_final: 0.7331 (t0) REVERT: A 493 SER cc_start: 0.7016 (t) cc_final: 0.6678 (p) REVERT: B 77 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7510 (mmmt) REVERT: B 163 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7462 (mm-30) REVERT: B 235 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.8025 (mtm-85) REVERT: B 354 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.6268 (mp-120) REVERT: B 394 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7455 (ptmt) REVERT: B 493 SER cc_start: 0.7589 (t) cc_final: 0.7263 (p) REVERT: B 501 GLN cc_start: 0.7895 (mt0) cc_final: 0.7551 (mt0) REVERT: C 163 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7534 (mm-30) REVERT: C 183 ASN cc_start: 0.7158 (m-40) cc_final: 0.6845 (m110) REVERT: C 405 SER cc_start: 0.8587 (OUTLIER) cc_final: 0.8339 (t) REVERT: C 493 SER cc_start: 0.7305 (t) cc_final: 0.7098 (p) REVERT: H 46 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7098 (tt0) REVERT: H 100 MET cc_start: 0.8225 (mtt) cc_final: 0.8001 (mtt) REVERT: I 10 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: I 51 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8580 (tt) REVERT: J 46 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7375 (tt0) REVERT: L 45 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.6247 (ppp80) REVERT: M 38 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8445 (tt0) REVERT: M 107 LYS cc_start: 0.6075 (mtmt) cc_final: 0.5704 (mtpm) REVERT: N 100 GLN cc_start: 0.7600 (mp10) cc_final: 0.7145 (pm20) outliers start: 67 outliers final: 52 residues processed: 280 average time/residue: 1.2109 time to fit residues: 376.4427 Evaluate side-chains 285 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 224 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 74 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 331 ASN B 27 ASN B 63 ASN B 183 ASN C 63 ASN C 500 ASN ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.110825 restraints weight = 16812.990| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.54 r_work: 0.3116 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15276 Z= 0.303 Angle : 0.549 8.920 20733 Z= 0.292 Chirality : 0.045 0.172 2451 Planarity : 0.004 0.038 2610 Dihedral : 4.675 33.204 2071 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.97 % Allowed : 16.00 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.02 (0.19), residues: 1911 helix: 1.61 (0.25), residues: 396 sheet: 0.21 (0.20), residues: 594 loop : -0.80 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 314 HIS 0.006 0.001 HIS B 317 PHE 0.017 0.001 PHE H 100C TYR 0.026 0.002 TYR M 49 ARG 0.003 0.000 ARG B 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6242.52 seconds wall clock time: 111 minutes 38.87 seconds (6698.87 seconds total)