Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 18:40:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9i_25758/04_2023/7t9i_25758_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9i_25758/04_2023/7t9i_25758.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/7t9i_25758/04_2023/7t9i_25758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9i_25758/04_2023/7t9i_25758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9i_25758/04_2023/7t9i_25758_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9i_25758/04_2023/7t9i_25758_trim.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.038 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: 5 Type Number sf(0) Gaussians S 100 5.16 5 C 7620 2.51 5 N 2028 2.21 5 O 2224 1.98 5 H 11557 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 50": "OD1" <-> "OD2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "R PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X ASP 33": "OD1" <-> "OD2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y GLU 10": "OE1" <-> "OE2" Residue "Y ASP 66": "OD1" <-> "OD2" Residue "Y ASP 322": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 23529 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1205 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1636 Classifications: {'peptide': 109} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "N" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1893 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "R" Number of atoms: 9416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 9416 Classifications: {'peptide': 596} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 568} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "X" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3286 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 102 Chain: "Y" Number of atoms: 5110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5110 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "Z" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 871 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.97, per 1000 atoms: 0.42 Number of scatterers: 23529 At special positions: 0 Unit cell: (103.272, 99.962, 202.572, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 O 2224 8.00 N 2028 7.00 C 7620 6.00 H 11557 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 31 " distance=2.03 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 60 " distance=2.04 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 82 " distance=2.03 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 87 " distance=2.02 Simple disulfide: pdb=" SG CYS B 2 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 105 " distance=2.04 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 83 " distance=2.03 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 85 " distance=2.04 Simple disulfide: pdb=" SG CYS B 88 " - pdb=" SG CYS B 95 " distance=2.04 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 31 " distance=2.03 Simple disulfide: pdb=" SG CYS R 29 " - pdb=" SG CYS R 41 " distance=2.03 Simple disulfide: pdb=" SG CYS R 283 " - pdb=" SG CYS R 398 " distance=2.03 Simple disulfide: pdb=" SG CYS R 301 " - pdb=" SG CYS R 390 " distance=2.04 Simple disulfide: pdb=" SG CYS R 494 " - pdb=" SG CYS R 569 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 101 " - " ASN A 78 " " NAG B 201 " - " ASN B 23 " " NAG C 1 " - " ASN A 52 " " NAG R 801 " - " ASN R 99 " " NAG R 802 " - " ASN R 77 " " NAG R 803 " - " ASN R 198 " " NAG R 804 " - " ASN R 177 " Time building additional restraints: 19.49 Conformation dependent library (CDL) restraints added in 2.1 seconds 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2902 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 19 sheets defined 32.2% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.625A pdb=" N SER B 48 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.688A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.507A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 172 through 176 removed outlier: 3.791A pdb=" N LEU R 175 " --> pdb=" O PHE R 172 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS R 176 " --> pdb=" O GLN R 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 172 through 176' Processing helix chain 'R' and resid 218 through 222 removed outlier: 4.464A pdb=" N PHE R 221 " --> pdb=" O LYS R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 287 removed outlier: 3.622A pdb=" N LYS R 287 " --> pdb=" O CYS R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 304 Processing helix chain 'R' and resid 381 through 391 Processing helix chain 'R' and resid 416 through 442 removed outlier: 4.834A pdb=" N TRP R 422 " --> pdb=" O ARG R 418 " (cutoff:3.500A) Processing helix chain 'R' and resid 447 through 477 Processing helix chain 'R' and resid 480 through 491 removed outlier: 3.731A pdb=" N HIS R 484 " --> pdb=" O GLU R 480 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE R 486 " --> pdb=" O TYR R 482 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASP R 487 " --> pdb=" O ASN R 483 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 525 removed outlier: 4.163A pdb=" N ASN R 495 " --> pdb=" O GLY R 491 " (cutoff:3.500A) Processing helix chain 'R' and resid 528 through 532 Processing helix chain 'R' and resid 534 through 559 removed outlier: 3.572A pdb=" N ALA R 538 " --> pdb=" O ARG R 534 " (cutoff:3.500A) Proline residue: R 556 - end of helix removed outlier: 3.511A pdb=" N GLY R 559 " --> pdb=" O LEU R 555 " (cutoff:3.500A) Processing helix chain 'R' and resid 576 through 609 Processing helix chain 'R' and resid 620 through 649 removed outlier: 3.902A pdb=" N LEU R 629 " --> pdb=" O ARG R 625 " (cutoff:3.500A) Proline residue: R 639 - end of helix Processing helix chain 'R' and resid 655 through 666 removed outlier: 3.776A pdb=" N LYS R 660 " --> pdb=" O VAL R 656 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE R 661 " --> pdb=" O SER R 657 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU R 662 " --> pdb=" O ASN R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 668 through 679 Proline residue: R 675 - end of helix Processing helix chain 'R' and resid 682 through 697 Processing helix chain 'X' and resid 15 through 39 Processing helix chain 'X' and resid 52 through 59 Processing helix chain 'X' and resid 233 through 239 removed outlier: 3.521A pdb=" N ASN X 239 " --> pdb=" O GLN X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 279 Processing helix chain 'X' and resid 293 through 304 removed outlier: 3.528A pdb=" N GLY X 304 " --> pdb=" O LYS X 300 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 317 Processing helix chain 'X' and resid 331 through 352 removed outlier: 3.947A pdb=" N THR X 335 " --> pdb=" O ASP X 331 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER X 352 " --> pdb=" O ILE X 348 " (cutoff:3.500A) Processing helix chain 'X' and resid 370 through 391 Processing helix chain 'Y' and resid 4 through 25 Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Z' and resid 8 through 24 removed outlier: 3.541A pdb=" N ASN Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 45 Processing helix chain 'Z' and resid 46 through 48 No H-bonds generated for 'chain 'Z' and resid 46 through 48' Processing helix chain 'Z' and resid 55 through 59 removed outlier: 3.670A pdb=" N GLU Z 58 " --> pdb=" O PRO Z 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 4.160A pdb=" N CYS A 32 " --> pdb=" O CYS B 31 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS B 31 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N THR B 25 " --> pdb=" O PRO A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 67 removed outlier: 6.129A pdb=" N ALA A 81 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR A 65 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N HIS A 79 " --> pdb=" O TYR A 65 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG A 67 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLU A 77 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 63 removed outlier: 6.759A pdb=" N SER B 82 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE B 57 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 80 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR B 59 " --> pdb=" O PRO B 78 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR B 61 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER B 76 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU B 63 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR B 74 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.535A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.549A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 30 through 33 removed outlier: 3.648A pdb=" N ARG R 38 " --> pdb=" O HIS R 32 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR R 56 " --> pdb=" O PHE R 37 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU R 57 " --> pdb=" O TYR R 82 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N SER R 84 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU R 59 " --> pdb=" O SER R 84 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE R 81 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ARG R 109 " --> pdb=" O ILE R 81 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL R 83 " --> pdb=" O ARG R 109 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR R 111 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE R 106 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N PHE R 134 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE R 108 " --> pdb=" O PHE R 134 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR R 136 " --> pdb=" O ILE R 108 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ASN R 110 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU R 131 " --> pdb=" O GLU R 157 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N THR R 159 " --> pdb=" O LEU R 131 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE R 133 " --> pdb=" O THR R 159 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU R 180 " --> pdb=" O LEU R 202 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA R 204 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP R 203 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ASP R 232 " --> pdb=" O ASP R 203 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL R 205 " --> pdb=" O ASP R 232 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU R 231 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU R 252 " --> pdb=" O ASP R 276 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA R 275 " --> pdb=" O THR R 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 66 through 67 Processing sheet with id=AA9, first strand: chain 'R' and resid 97 through 98 removed outlier: 6.320A pdb=" N PHE R 97 " --> pdb=" O LYS R 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'R' and resid 166 through 167 removed outlier: 3.573A pdb=" N ILE R 167 " --> pdb=" O SER R 191 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'X' and resid 210 through 214 removed outlier: 10.205A pdb=" N ALA X 243 " --> pdb=" O THR X 40 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ARG X 42 " --> pdb=" O ALA X 243 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE X 245 " --> pdb=" O ARG X 42 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU X 44 " --> pdb=" O ILE X 245 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL X 247 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU X 46 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASP X 249 " --> pdb=" O LEU X 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Y' and resid 46 through 51 removed outlier: 6.644A pdb=" N ILE Y 338 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR Y 50 " --> pdb=" O LEU Y 336 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU Y 336 " --> pdb=" O THR Y 50 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS Y 317 " --> pdb=" O GLY Y 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 58 through 63 removed outlier: 3.905A pdb=" N ALA Y 60 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Y 70 " --> pdb=" O TRP Y 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 58 through 63 removed outlier: 3.905A pdb=" N ALA Y 60 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Y 70 " --> pdb=" O TRP Y 82 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU Y 79 " --> pdb=" O ILE Y 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 100 through 105 removed outlier: 7.027A pdb=" N GLY Y 115 " --> pdb=" O MET Y 101 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS Y 103 " --> pdb=" O ALA Y 113 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA Y 113 " --> pdb=" O CYS Y 103 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR Y 105 " --> pdb=" O TYR Y 111 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR Y 111 " --> pdb=" O TYR Y 105 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY Y 116 " --> pdb=" O ILE Y 120 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE Y 120 " --> pdb=" O GLY Y 116 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU Y 139 " --> pdb=" O CYS Y 121 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN Y 125 " --> pdb=" O VAL Y 135 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL Y 135 " --> pdb=" O ASN Y 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Y' and resid 146 through 151 removed outlier: 3.724A pdb=" N CYS Y 148 " --> pdb=" O SER Y 160 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP Y 170 " --> pdb=" O GLN Y 176 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN Y 176 " --> pdb=" O ASP Y 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Y' and resid 187 through 192 removed outlier: 7.047A pdb=" N GLY Y 202 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU Y 190 " --> pdb=" O VAL Y 200 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL Y 200 " --> pdb=" O LEU Y 190 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU Y 192 " --> pdb=" O LEU Y 198 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU Y 198 " --> pdb=" O LEU Y 192 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA Y 203 " --> pdb=" O SER Y 207 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER Y 207 " --> pdb=" O ALA Y 203 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP Y 212 " --> pdb=" O CYS Y 218 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N CYS Y 218 " --> pdb=" O ASP Y 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 231 through 234 removed outlier: 3.735A pdb=" N ALA Y 231 " --> pdb=" O GLY Y 244 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N CYS Y 250 " --> pdb=" O THR Y 263 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR Y 263 " --> pdb=" O CYS Y 250 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU Y 252 " --> pdb=" O LEU Y 261 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN Y 259 " --> pdb=" O ASP Y 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 273 through 278 removed outlier: 3.597A pdb=" N SER Y 275 " --> pdb=" O GLY Y 288 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ASP Y 298 " --> pdb=" O ARG Y 304 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG Y 304 " --> pdb=" O ASP Y 298 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1398 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: 9.35 Time building geometry restraints manager: 19.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11523 1.02 - 1.23: 57 1.23 - 1.43: 5136 1.43 - 1.63: 6939 1.63 - 1.83: 132 Bond restraints: 23787 Sorted by residual: bond pdb=" ND2 ASN A 15 " pdb="HD21 ASN A 15 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN X 23 " pdb="HD22 ASN X 23 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN X 23 " pdb="HD21 ASN X 23 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN A 15 " pdb="HD22 ASN A 15 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" ND2 ASN A 52 " pdb="HD21 ASN A 52 " ideal model delta sigma weight residual 0.860 0.971 -0.111 2.00e-02 2.50e+03 3.11e+01 ... (remaining 23782 not shown) Histogram of bond angle deviations from ideal: 97.69 - 104.99: 207 104.99 - 112.29: 26666 112.29 - 119.59: 6478 119.59 - 126.89: 9263 126.89 - 134.19: 152 Bond angle restraints: 42766 Sorted by residual: angle pdb=" C ASN A 15 " pdb=" CA ASN A 15 " pdb=" CB ASN A 15 " ideal model delta sigma weight residual 108.86 99.99 8.87 1.44e+00 4.82e-01 3.79e+01 angle pdb=" N PHE A 74 " pdb=" CA PHE A 74 " pdb=" C PHE A 74 " ideal model delta sigma weight residual 110.41 117.56 -7.15 1.23e+00 6.61e-01 3.38e+01 angle pdb=" CA GLU X 21 " pdb=" C GLU X 21 " pdb=" N ALA X 22 " ideal model delta sigma weight residual 117.07 110.47 6.60 1.14e+00 7.69e-01 3.35e+01 angle pdb=" C PHE A 74 " pdb=" N LYS A 75 " pdb=" CA LYS A 75 " ideal model delta sigma weight residual 122.84 130.14 -7.30 1.30e+00 5.92e-01 3.16e+01 angle pdb=" C LYS X 24 " pdb=" N LYS X 25 " pdb=" CA LYS X 25 " ideal model delta sigma weight residual 120.28 127.35 -7.07 1.34e+00 5.57e-01 2.78e+01 ... (remaining 42761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8768 17.84 - 35.68: 722 35.68 - 53.52: 114 53.52 - 71.37: 37 71.37 - 89.21: 27 Dihedral angle restraints: 9668 sinusoidal: 4330 harmonic: 5338 Sorted by residual: dihedral pdb=" CB CYS R 494 " pdb=" SG CYS R 494 " pdb=" SG CYS R 569 " pdb=" CB CYS R 569 " ideal model delta sinusoidal sigma weight residual -86.00 -35.08 -50.92 1 1.00e+01 1.00e-02 3.55e+01 dihedral pdb=" CB CYS R 301 " pdb=" SG CYS R 301 " pdb=" SG CYS R 390 " pdb=" CB CYS R 390 " ideal model delta sinusoidal sigma weight residual -86.00 -130.41 44.41 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CA THR A 86 " pdb=" C THR A 86 " pdb=" N CYS A 87 " pdb=" CA CYS A 87 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 9665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1766 0.091 - 0.182: 159 0.182 - 0.273: 7 0.273 - 0.365: 1 0.365 - 0.456: 1 Chirality restraints: 1934 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.90e+01 chirality pdb=" C1 NAG A 101 " pdb=" ND2 ASN A 78 " pdb=" C2 NAG A 101 " pdb=" O5 NAG A 101 " both_signs ideal model delta sigma weight residual False -2.40 -2.86 0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 52 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1931 not shown) Planarity restraints: 3566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 15 " 0.265 2.00e-02 2.50e+03 4.54e-01 3.09e+03 pdb=" CG ASN A 15 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 15 " -0.258 2.00e-02 2.50e+03 pdb=" ND2 ASN A 15 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 15 " 0.749 2.00e-02 2.50e+03 pdb="HD22 ASN A 15 " -0.734 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN X 23 " 0.292 2.00e-02 2.50e+03 3.04e-01 1.38e+03 pdb=" CG ASN X 23 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN X 23 " -0.261 2.00e-02 2.50e+03 pdb=" ND2 ASN X 23 " -0.005 2.00e-02 2.50e+03 pdb="HD21 ASN X 23 " -0.434 2.00e-02 2.50e+03 pdb="HD22 ASN X 23 " 0.457 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.305 2.00e-02 2.50e+03 2.65e-01 8.81e+02 pdb=" C7 NAG C 1 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.027 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.464 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.198 2.00e-02 2.50e+03 ... (remaining 3563 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 2688 2.26 - 2.84: 51425 2.84 - 3.43: 59957 3.43 - 4.01: 82640 4.01 - 4.60: 125495 Nonbonded interactions: 322205 Sorted by model distance: nonbonded pdb=" O ALA R 380 " pdb=" HG SER R 383 " model vdw 1.670 1.850 nonbonded pdb=" H LYS R 291 " pdb=" O GLU R 394 " model vdw 1.694 1.850 nonbonded pdb=" HZ1 LYS X 233 " pdb=" OD2 ASP Y 228 " model vdw 1.696 1.850 nonbonded pdb=" O LYS R 250 " pdb=" H THR R 273 " model vdw 1.702 1.850 nonbonded pdb=" O ILE B 36 " pdb=" HZ2 LYS B 39 " model vdw 1.709 1.850 ... (remaining 322200 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 8.000 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: 0.360 Extract box with map and model: 29.680 Check model and map are aligned: 0.360 Set scattering table: 0.190 Process input model: 72.110 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 12230 Z= 0.350 Angle : 0.915 9.661 16612 Z= 0.522 Chirality : 0.052 0.456 1934 Planarity : 0.010 0.265 2096 Dihedral : 12.760 84.578 4314 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.16 (0.22), residues: 1510 helix: 1.51 (0.25), residues: 428 sheet: -1.14 (0.29), residues: 305 loop : -0.52 (0.22), residues: 777 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 269 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 271 average time/residue: 2.0640 time to fit residues: 621.4648 Evaluate side-chains 172 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.758 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.2669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN N 123 GLN R 113 ASN R 173 GLN Y 13 GLN Y 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 12230 Z= 0.307 Angle : 0.658 5.672 16612 Z= 0.352 Chirality : 0.044 0.179 1934 Planarity : 0.005 0.052 2096 Dihedral : 5.111 29.033 1663 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.21 (0.21), residues: 1510 helix: 1.73 (0.25), residues: 415 sheet: -1.17 (0.29), residues: 298 loop : -0.69 (0.22), residues: 797 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 197 average time/residue: 1.8550 time to fit residues: 410.8447 Evaluate side-chains 166 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 1.868 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.9387 time to fit residues: 4.6398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 120 optimal weight: 0.0070 chunk 134 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 90 HIS R 113 ASN Y 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 12230 Z= 0.227 Angle : 0.562 5.917 16612 Z= 0.301 Chirality : 0.042 0.144 1934 Planarity : 0.004 0.039 2096 Dihedral : 4.889 27.774 1663 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.19 (0.22), residues: 1510 helix: 1.97 (0.25), residues: 418 sheet: -1.19 (0.29), residues: 306 loop : -0.82 (0.21), residues: 786 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 182 average time/residue: 1.8359 time to fit residues: 381.7281 Evaluate side-chains 171 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 4 average time/residue: 0.7224 time to fit residues: 6.2215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 113 ASN R 173 GLN Y 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 12230 Z= 0.263 Angle : 0.577 9.045 16612 Z= 0.308 Chirality : 0.042 0.193 1934 Planarity : 0.004 0.045 2096 Dihedral : 4.911 29.780 1663 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.31 (0.22), residues: 1510 helix: 1.91 (0.25), residues: 424 sheet: -1.23 (0.29), residues: 309 loop : -0.95 (0.22), residues: 777 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 24 residues processed: 198 average time/residue: 1.7092 time to fit residues: 385.2502 Evaluate side-chains 180 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.862 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 5 average time/residue: 0.6487 time to fit residues: 6.8456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN Y 9 GLN Y 13 GLN Y 225 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 12230 Z= 0.355 Angle : 0.657 7.714 16612 Z= 0.353 Chirality : 0.044 0.240 1934 Planarity : 0.005 0.058 2096 Dihedral : 5.320 36.564 1663 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.69 (0.21), residues: 1510 helix: 1.53 (0.25), residues: 423 sheet: -1.41 (0.29), residues: 305 loop : -1.17 (0.21), residues: 782 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 162 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 27 residues processed: 193 average time/residue: 1.7698 time to fit residues: 387.1236 Evaluate side-chains 176 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.912 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 7 average time/residue: 1.0526 time to fit residues: 11.4587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 113 ASN ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 12230 Z= 0.281 Angle : 0.610 13.016 16612 Z= 0.325 Chirality : 0.042 0.172 1934 Planarity : 0.005 0.046 2096 Dihedral : 5.203 35.438 1663 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.52 (0.22), residues: 1510 helix: 1.79 (0.26), residues: 414 sheet: -1.22 (0.30), residues: 307 loop : -1.15 (0.21), residues: 789 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 154 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 33 residues processed: 189 average time/residue: 1.9319 time to fit residues: 411.7335 Evaluate side-chains 178 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 145 time to evaluate : 1.824 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 27 residues processed: 7 average time/residue: 1.2866 time to fit residues: 13.2552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 9 GLN ** Y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 12230 Z= 0.318 Angle : 0.628 11.503 16612 Z= 0.336 Chirality : 0.043 0.154 1934 Planarity : 0.005 0.051 2096 Dihedral : 5.293 35.202 1663 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.63 (0.22), residues: 1510 helix: 1.64 (0.25), residues: 420 sheet: -1.21 (0.30), residues: 302 loop : -1.24 (0.22), residues: 788 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 148 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 30 residues processed: 187 average time/residue: 1.8352 time to fit residues: 389.2395 Evaluate side-chains 175 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 2 average time/residue: 0.4351 time to fit residues: 3.8130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.0030 chunk 27 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 187 ASN Y 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 12230 Z= 0.192 Angle : 0.565 10.297 16612 Z= 0.299 Chirality : 0.041 0.178 1934 Planarity : 0.004 0.040 2096 Dihedral : 4.978 31.661 1663 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.36 (0.22), residues: 1510 helix: 2.01 (0.26), residues: 414 sheet: -1.10 (0.30), residues: 306 loop : -1.12 (0.22), residues: 790 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 147 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 30 residues processed: 189 average time/residue: 1.8044 time to fit residues: 384.8443 Evaluate side-chains 173 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 2.120 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 1 average time/residue: 0.2416 time to fit residues: 2.8249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 87 optimal weight: 0.3980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN Y 9 GLN ** Y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 12230 Z= 0.220 Angle : 0.572 9.554 16612 Z= 0.304 Chirality : 0.041 0.152 1934 Planarity : 0.004 0.041 2096 Dihedral : 4.941 30.056 1663 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.37 (0.22), residues: 1510 helix: 2.06 (0.26), residues: 414 sheet: -1.11 (0.30), residues: 314 loop : -1.15 (0.22), residues: 782 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 31 residues processed: 184 average time/residue: 1.7935 time to fit residues: 373.1652 Evaluate side-chains 179 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 1.862 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 30 residues processed: 2 average time/residue: 1.1899 time to fit residues: 5.3438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 148 optimal weight: 0.3980 chunk 136 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 113 ASN ** Y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 12230 Z= 0.273 Angle : 0.610 9.583 16612 Z= 0.324 Chirality : 0.042 0.160 1934 Planarity : 0.005 0.047 2096 Dihedral : 5.106 30.457 1663 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.52 (0.22), residues: 1510 helix: 1.89 (0.26), residues: 414 sheet: -1.15 (0.29), residues: 314 loop : -1.25 (0.21), residues: 782 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 45 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue ILE 295 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue SER 305 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 150 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 28 residues processed: 185 average time/residue: 1.8241 time to fit residues: 384.9514 Evaluate side-chains 170 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.865 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 0 time to fit residues: 2.4198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 9 GLN ** Y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.128199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.110537 restraints weight = 82522.565| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.34 r_work: 0.3908 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 12230 Z= 0.245 Angle : 0.588 8.739 16612 Z= 0.312 Chirality : 0.042 0.178 1934 Planarity : 0.004 0.043 2096 Dihedral : 5.023 29.183 1663 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.07 % 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: -0.52 (0.22), residues: 1510 helix: 1.96 (0.26), residues: 415 sheet: -1.21 (0.29), residues: 318 loop : -1.26 (0.21), residues: 777 =============================================================================== Job complete usr+sys time: 8520.72 seconds wall clock time: 150 minutes 26.26 seconds (9026.26 seconds total)