Starting phenix.real_space_refine on Sat Nov 18 17:54:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utz_26795/11_2023/7utz_26795_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utz_26795/11_2023/7utz_26795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utz_26795/11_2023/7utz_26795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utz_26795/11_2023/7utz_26795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utz_26795/11_2023/7utz_26795_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utz_26795/11_2023/7utz_26795_trim_updated.pdb" } resolution = 2.4 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= 0.026 sd= 0.080 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 7680 2.51 5 N 2039 2.21 5 O 2228 1.98 5 H 11632 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 474": "OD1" <-> "OD2" Residue "R PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ASP 170": "OD1" <-> "OD2" Residue "Y GLU 172": "OE1" <-> "OE2" Residue "Y ASP 267": "OD1" <-> "OD2" Residue "Y ASP 312": "OD1" <-> "OD2" Residue "Z TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 23679 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1273 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1648 Classifications: {'peptide': 109} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 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: 9460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 9460 Classifications: {'peptide': 600} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 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: "A" 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: "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: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'NAG': 4, 'Z41': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.53, per 1000 atoms: 0.44 Number of scatterers: 23679 At special positions: 0 Unit cell: (177.834, 133.791, 108.03, 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 2228 8.00 N 2039 7.00 C 7680 6.00 H 11632 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, 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=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 88 " - pdb=" SG CYS B 95 " distance=2.03 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 284 " - pdb=" SG CYS R 408 " distance=2.03 Simple disulfide: pdb=" SG CYS R 301 " - pdb=" SG CYS R 390 " distance=2.03 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 NAG-ASN " NAG A 101 " - " ASN A 78 " " NAG A 102 " - " ASN A 52 " " NAG B 201 " - " ASN B 23 " " 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: 20.24 Conformation dependent library (CDL) restraints added in 2.6 seconds 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 19 sheets defined 28.4% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 41 through 46 removed outlier: 3.975A pdb=" N THR A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'B' and resid 44 through 47 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 281 through 286 Processing helix chain 'R' and resid 295 through 303 Processing helix chain 'R' and resid 377 through 390 Processing helix chain 'R' and resid 416 through 441 removed outlier: 4.966A pdb=" N VAL R 421 " --> pdb=" O ARG R 418 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU R 430 " --> pdb=" O LEU R 427 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL R 433 " --> pdb=" O LEU R 430 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU R 440 " --> pdb=" O LEU R 437 " (cutoff:3.500A) Processing helix chain 'R' and resid 448 through 476 Processing helix chain 'R' and resid 481 through 490 removed outlier: 4.958A pdb=" N ILE R 486 " --> pdb=" O TYR R 482 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASP R 487 " --> pdb=" O ASN R 483 " (cutoff:3.500A) Processing helix chain 'R' and resid 492 through 524 Processing helix chain 'R' and resid 529 through 531 No H-bonds generated for 'chain 'R' and resid 529 through 531' Processing helix chain 'R' and resid 535 through 558 Proline residue: R 556 - end of helix Processing helix chain 'R' and resid 577 through 608 Processing helix chain 'R' and resid 620 through 648 removed outlier: 3.895A 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 656 through 665 removed outlier: 3.725A pdb=" N LYS R 660 " --> pdb=" O VAL R 656 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE R 661 " --> pdb=" O SER R 657 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU R 662 " --> pdb=" O ASN R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 669 through 679 Proline residue: R 675 - end of helix Processing helix chain 'R' and resid 683 through 696 Processing helix chain 'X' and resid 15 through 39 Processing helix chain 'X' and resid 53 through 58 Processing helix chain 'X' and resid 234 through 238 Processing helix chain 'X' and resid 266 through 278 Processing helix chain 'X' and resid 294 through 303 Processing helix chain 'X' and resid 313 through 316 Processing helix chain 'X' and resid 332 through 351 removed outlier: 3.516A pdb=" N PHE X 345 " --> pdb=" O ILE X 341 " (cutoff:3.500A) Processing helix chain 'X' and resid 371 through 390 Processing helix chain 'Y' and resid 4 through 24 Processing helix chain 'Y' and resid 30 through 35 Processing helix chain 'Z' and resid 8 through 23 Processing helix chain 'Z' and resid 30 through 47 removed outlier: 4.953A pdb=" N LYS Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLU Z 47 " --> pdb=" O ALA Z 43 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 11 through 14 Processing sheet with id= B, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 65 through 69 Processing sheet with id= D, first strand: chain 'A' and resid 59 through 64 removed outlier: 6.432A pdb=" N ALA A 81 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 3 through 11 removed outlier: 3.510A pdb=" N LEU B 20 " --> pdb=" O ILE B 11 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 57 through 63 Processing sheet with id= G, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.892A pdb=" N SER B 82 " --> pdb=" O ARG B 55 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.531A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.500A pdb=" N GLN N 39 " --> pdb=" O VAL N 93 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'R' and resid 30 through 33 removed outlier: 3.668A pdb=" N ARG R 38 " --> pdb=" O HIS R 32 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR R 56 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N CYS R 41 " --> pdb=" O THR R 56 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS R 58 " --> pdb=" O CYS R 41 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ARG R 80 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU R 59 " --> pdb=" O ARG R 80 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR R 82 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N HIS R 105 " --> pdb=" O ILE R 81 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N VAL R 83 " --> pdb=" O HIS R 105 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU R 107 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE R 130 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ILE R 108 " --> pdb=" O PHE R 130 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY R 132 " --> pdb=" O ILE R 108 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE R 155 " --> pdb=" O LEU R 131 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE R 133 " --> pdb=" O ILE R 155 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU R 157 " --> pdb=" O ILE R 133 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU R 182 " --> pdb=" O ASP R 203 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL R 205 " --> pdb=" O LEU R 182 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 230 through 232 removed outlier: 6.616A pdb=" N GLU R 251 " --> pdb=" O LEU R 231 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG R 274 " --> pdb=" O LEU R 252 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL R 397 " --> pdb=" O ALA R 275 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'X' and resid 359 through 363 removed outlier: 6.807A pdb=" N VAL X 287 " --> pdb=" O TYR X 360 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N HIS X 362 " --> pdb=" O VAL X 287 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU X 289 " --> pdb=" O HIS X 362 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE X 244 " --> pdb=" O ILE X 288 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE X 290 " --> pdb=" O ILE X 244 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE X 246 " --> pdb=" O PHE X 290 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN X 292 " --> pdb=" O PHE X 246 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL X 248 " --> pdb=" O ASN X 292 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA X 243 " --> pdb=" O ARG X 42 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'Y' and resid 78 through 83 removed outlier: 3.588A pdb=" N LYS Y 78 " --> pdb=" O SER Y 74 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU Y 70 " --> pdb=" O TRP Y 82 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA Y 60 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'Y' and resid 100 through 105 removed outlier: 6.733A pdb=" N GLY Y 115 " --> pdb=" O MET Y 101 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N CYS Y 103 " --> pdb=" O ALA Y 113 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA Y 113 " --> pdb=" O CYS Y 103 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TYR Y 105 " --> pdb=" O TYR Y 111 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N TYR Y 111 " --> pdb=" O TYR Y 105 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASN Y 125 " --> pdb=" O VAL Y 135 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL Y 135 " --> pdb=" O ASN Y 125 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'Y' and resid 156 through 160 removed outlier: 6.340A pdb=" N ASP Y 170 " --> pdb=" O GLN Y 176 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLN Y 176 " --> pdb=" O ASP Y 170 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'Y' and resid 187 through 192 removed outlier: 7.086A pdb=" N GLY Y 202 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU Y 190 " --> pdb=" O VAL Y 200 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL Y 200 " --> pdb=" O LEU Y 190 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU Y 192 " --> pdb=" O LEU Y 198 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU Y 198 " --> pdb=" O LEU Y 192 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP Y 212 " --> pdb=" O CYS Y 218 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N CYS Y 218 " --> pdb=" O ASP Y 212 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'Y' and resid 273 through 278 removed outlier: 6.488A pdb=" N GLY Y 288 " --> pdb=" O THR Y 274 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL Y 276 " --> pdb=" O LEU Y 286 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU Y 286 " --> pdb=" O VAL Y 276 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE Y 278 " --> pdb=" O LEU Y 284 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU Y 284 " --> pdb=" O PHE Y 278 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASP Y 298 " --> pdb=" O ARG Y 304 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ARG Y 304 " --> pdb=" O ASP Y 298 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'Y' and resid 317 through 320 removed outlier: 3.762A pdb=" N CYS Y 317 " --> pdb=" O GLY Y 330 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU Y 336 " --> pdb=" O LEU Y 51 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG Y 49 " --> pdb=" O ILE Y 338 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN Y 340 " --> pdb=" O THR Y 47 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N THR Y 47 " --> pdb=" O ASN Y 340 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Y' and resid 250 through 254 removed outlier: 3.655A pdb=" N MET Y 262 " --> pdb=" O LEU Y 252 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP Y 254 " --> pdb=" O GLU Y 260 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLU Y 260 " --> pdb=" O ASP Y 254 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1173 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: 9.37 Time building geometry restraints manager: 20.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11598 1.04 - 1.23: 822 1.23 - 1.43: 4503 1.43 - 1.63: 6882 1.63 - 1.83: 132 Bond restraints: 23937 Sorted by residual: bond pdb=" N GLY X 304 " pdb=" CA GLY X 304 " ideal model delta sigma weight residual 1.448 1.494 -0.045 1.43e-02 4.89e+03 1.00e+01 bond pdb=" N GLY R 21 " pdb=" CA GLY R 21 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.96e+00 bond pdb=" C ALA X 303 " pdb=" N GLY X 304 " ideal model delta sigma weight residual 1.331 1.359 -0.028 1.32e-02 5.74e+03 4.44e+00 bond pdb=" N GLY X 353 " pdb=" CA GLY X 353 " ideal model delta sigma weight residual 1.449 1.477 -0.027 1.45e-02 4.76e+03 3.56e+00 bond pdb=" C ALA B 72 " pdb=" N PRO B 73 " ideal model delta sigma weight residual 1.336 1.353 -0.018 9.80e-03 1.04e+04 3.21e+00 ... (remaining 23932 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.26: 362 106.26 - 113.24: 27561 113.24 - 120.22: 7780 120.22 - 127.20: 7181 127.20 - 134.18: 132 Bond angle restraints: 43016 Sorted by residual: angle pdb=" N SER R 26 " pdb=" CA SER R 26 " pdb=" C SER R 26 " ideal model delta sigma weight residual 108.13 111.50 -3.37 9.00e-01 1.23e+00 1.40e+01 angle pdb=" C30 Z41 R 805 " pdb=" C31 Z41 R 805 " pdb=" C32 Z41 R 805 " ideal model delta sigma weight residual 114.63 104.33 10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C ALA X 303 " pdb=" N GLY X 304 " pdb=" CA GLY X 304 " ideal model delta sigma weight residual 121.07 126.56 -5.49 1.79e+00 3.12e-01 9.40e+00 angle pdb=" C PRO N 102 " pdb=" N PHE N 103 " pdb=" CA PHE N 103 " ideal model delta sigma weight residual 121.70 126.96 -5.26 1.80e+00 3.09e-01 8.55e+00 angle pdb=" CA TRP X 234 " pdb=" CB TRP X 234 " pdb=" CG TRP X 234 " ideal model delta sigma weight residual 113.60 119.05 -5.45 1.90e+00 2.77e-01 8.21e+00 ... (remaining 43011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8888 17.94 - 35.88: 709 35.88 - 53.82: 102 53.82 - 71.76: 28 71.76 - 89.70: 22 Dihedral angle restraints: 9749 sinusoidal: 4389 harmonic: 5360 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 -35.35 -50.65 1 1.00e+01 1.00e-02 3.51e+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 -134.08 48.08 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA SER X 352 " pdb=" C SER X 352 " pdb=" N GLY X 353 " pdb=" CA GLY X 353 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 9746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1476 0.047 - 0.093: 349 0.093 - 0.140: 104 0.140 - 0.187: 6 0.187 - 0.233: 1 Chirality restraints: 1936 Sorted by residual: chirality pdb=" CA GLU X 27 " pdb=" N GLU X 27 " pdb=" C GLU X 27 " pdb=" CB GLU X 27 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA CYS A 7 " pdb=" N CYS A 7 " pdb=" C CYS A 7 " pdb=" CB CYS A 7 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE R 47 " pdb=" N ILE R 47 " pdb=" C ILE R 47 " pdb=" CB ILE R 47 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 1933 not shown) Planarity restraints: 3579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER X 352 " 0.035 2.00e-02 2.50e+03 6.98e-02 4.87e+01 pdb=" C SER X 352 " -0.121 2.00e-02 2.50e+03 pdb=" O SER X 352 " 0.046 2.00e-02 2.50e+03 pdb=" N GLY X 353 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA X 303 " 0.034 2.00e-02 2.50e+03 6.78e-02 4.60e+01 pdb=" C ALA X 303 " -0.117 2.00e-02 2.50e+03 pdb=" O ALA X 303 " 0.044 2.00e-02 2.50e+03 pdb=" N GLY X 304 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER X 352 " 0.016 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" N GLY X 353 " -0.050 2.00e-02 2.50e+03 pdb=" CA GLY X 353 " 0.013 2.00e-02 2.50e+03 pdb=" H GLY X 353 " 0.022 2.00e-02 2.50e+03 ... (remaining 3576 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 3892 2.28 - 2.86: 53677 2.86 - 3.44: 62485 3.44 - 4.02: 87361 4.02 - 4.60: 131286 Nonbonded interactions: 338701 Sorted by model distance: nonbonded pdb="HD21 ASN X 23 " pdb=" OE1 GLU X 27 " model vdw 1.704 1.850 nonbonded pdb="HD22 ASN Y 230 " pdb=" OD1 ASP Y 246 " model vdw 1.716 1.850 nonbonded pdb=" O ALA R 254 " pdb=" HG SER R 278 " model vdw 1.720 1.850 nonbonded pdb=" OD1 ASP R 160 " pdb="HD21 ASN R 186 " model vdw 1.723 1.850 nonbonded pdb=" O ALA X 48 " pdb=" HG SER X 51 " model vdw 1.726 1.850 ... (remaining 338696 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: 5.460 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: 0.370 Extract box with map and model: 16.430 Check model and map are aligned: 0.390 Set scattering table: 0.200 Process input model: 77.610 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 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 : 0.004 0.045 12305 Z= 0.261 Angle : 0.694 10.300 16698 Z= 0.361 Chirality : 0.044 0.233 1936 Planarity : 0.005 0.077 2104 Dihedral : 12.268 81.074 4364 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.08 % Allowed : 0.31 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.05 (0.21), residues: 1514 helix: 1.63 (0.25), residues: 431 sheet: -1.13 (0.28), residues: 322 loop : -0.43 (0.22), residues: 761 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 244 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 243 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 244 average time/residue: 2.4206 time to fit residues: 645.8900 Evaluate side-chains 154 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 1.805 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.3065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 0.0570 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 35 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 12305 Z= 0.309 Angle : 0.596 6.377 16698 Z= 0.320 Chirality : 0.043 0.267 1936 Planarity : 0.005 0.071 2104 Dihedral : 5.780 55.746 1700 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.87 % Allowed : 10.58 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.18 (0.21), residues: 1514 helix: 1.64 (0.25), residues: 422 sheet: -1.23 (0.27), residues: 329 loop : -0.53 (0.22), residues: 763 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 199 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 190 average time/residue: 2.5192 time to fit residues: 522.6988 Evaluate side-chains 169 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 1.823 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.8105 time to fit residues: 5.3253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 147 optimal weight: 0.0060 chunk 121 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN R 32 HIS ** Y 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12305 Z= 0.294 Angle : 0.571 5.017 16698 Z= 0.305 Chirality : 0.042 0.159 1936 Planarity : 0.005 0.072 2104 Dihedral : 5.823 52.231 1700 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.02 % Allowed : 11.51 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.24 (0.21), residues: 1514 helix: 1.63 (0.25), residues: 428 sheet: -1.31 (0.27), residues: 316 loop : -0.61 (0.21), residues: 770 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 179 average time/residue: 2.5288 time to fit residues: 498.5456 Evaluate side-chains 170 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 1.748 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.1024 time to fit residues: 4.9385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.0970 chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN ** Y 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12305 Z= 0.261 Angle : 0.544 5.280 16698 Z= 0.291 Chirality : 0.041 0.139 1936 Planarity : 0.005 0.075 2104 Dihedral : 5.661 44.536 1700 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.79 % Allowed : 12.44 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.21), residues: 1514 helix: 1.65 (0.25), residues: 429 sheet: -1.18 (0.28), residues: 310 loop : -0.64 (0.21), residues: 775 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 184 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 175 average time/residue: 2.4527 time to fit residues: 471.3458 Evaluate side-chains 162 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.857 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.7980 time to fit residues: 5.3985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 0.0270 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN X 29 GLN ** Y 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12305 Z= 0.351 Angle : 0.603 5.336 16698 Z= 0.323 Chirality : 0.043 0.139 1936 Planarity : 0.005 0.086 2104 Dihedral : 5.933 44.528 1700 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.33 % Allowed : 12.83 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.40 (0.21), residues: 1514 helix: 1.43 (0.25), residues: 430 sheet: -1.23 (0.28), residues: 321 loop : -0.76 (0.21), residues: 763 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 192 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 184 average time/residue: 2.3378 time to fit residues: 472.6898 Evaluate side-chains 178 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.949 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 5 average time/residue: 0.6095 time to fit residues: 6.5370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN ** Y 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12305 Z= 0.263 Angle : 0.551 5.030 16698 Z= 0.294 Chirality : 0.042 0.139 1936 Planarity : 0.005 0.085 2104 Dihedral : 5.765 48.415 1700 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.33 % Allowed : 14.00 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.32 (0.21), residues: 1514 helix: 1.60 (0.25), residues: 429 sheet: -1.26 (0.28), residues: 304 loop : -0.75 (0.21), residues: 781 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 192 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 1.896 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 outliers start: 30 outliers final: 20 residues processed: 182 average time/residue: 2.4486 time to fit residues: 488.8610 Evaluate side-chains 179 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.862 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.4193 time to fit residues: 4.2407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.0870 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN ** Y 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12305 Z= 0.220 Angle : 0.526 4.981 16698 Z= 0.280 Chirality : 0.041 0.141 1936 Planarity : 0.005 0.088 2104 Dihedral : 5.665 49.893 1700 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.18 % Allowed : 14.77 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.15 (0.21), residues: 1514 helix: 1.77 (0.26), residues: 429 sheet: -1.18 (0.28), residues: 302 loop : -0.68 (0.21), residues: 783 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 190 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 24 residues processed: 183 average time/residue: 2.5500 time to fit residues: 511.3700 Evaluate side-chains 178 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 5 average time/residue: 0.8795 time to fit residues: 7.7959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.0040 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN Z 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12305 Z= 0.296 Angle : 0.570 5.678 16698 Z= 0.303 Chirality : 0.042 0.144 1936 Planarity : 0.005 0.074 2104 Dihedral : 5.816 51.257 1700 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.64 % Allowed : 15.32 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.27 (0.21), residues: 1514 helix: 1.66 (0.25), residues: 429 sheet: -1.25 (0.28), residues: 304 loop : -0.74 (0.21), residues: 781 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 24 residues processed: 183 average time/residue: 2.4991 time to fit residues: 501.6146 Evaluate side-chains 181 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 4 average time/residue: 1.1621 time to fit residues: 7.8036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN Y 91 HIS Z 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12305 Z= 0.322 Angle : 0.588 5.588 16698 Z= 0.314 Chirality : 0.042 0.150 1936 Planarity : 0.005 0.070 2104 Dihedral : 5.938 54.393 1700 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.49 % Allowed : 15.86 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.35 (0.21), residues: 1514 helix: 1.54 (0.25), residues: 431 sheet: -1.24 (0.28), residues: 305 loop : -0.79 (0.21), residues: 778 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 24 residues processed: 185 average time/residue: 2.4433 time to fit residues: 496.2441 Evaluate side-chains 181 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 2.021 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 3 average time/residue: 1.3968 time to fit residues: 7.4685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 12305 Z= 0.390 Angle : 0.638 7.313 16698 Z= 0.340 Chirality : 0.044 0.150 1936 Planarity : 0.006 0.069 2104 Dihedral : 6.280 58.922 1700 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.02 % Allowed : 16.41 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.56 (0.21), residues: 1514 helix: 1.31 (0.25), residues: 431 sheet: -1.31 (0.28), residues: 305 loop : -0.90 (0.21), residues: 778 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 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 LYS 101 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 LEU 378 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 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 24 residues processed: 184 average time/residue: 2.5100 time to fit residues: 508.6870 Evaluate side-chains 184 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 1.844 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 23 residues processed: 3 average time/residue: 0.8729 time to fit residues: 5.7520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN N 120 GLN ** Z 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.134435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.118768 restraints weight = 58988.027| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.67 r_work: 0.3836 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12305 Z= 0.275 Angle : 0.574 5.869 16698 Z= 0.305 Chirality : 0.042 0.155 1936 Planarity : 0.005 0.060 2104 Dihedral : 5.994 55.882 1700 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.10 % Allowed : 16.49 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.39 (0.21), residues: 1514 helix: 1.51 (0.25), residues: 431 sheet: -1.27 (0.28), residues: 306 loop : -0.80 (0.21), residues: 777 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9604.19 seconds wall clock time: 169 minutes 22.51 seconds (10162.51 seconds total)