Starting phenix.real_space_refine on Fri Mar 15 11:48:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwh_17993/03_2024/8pwh_17993.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwh_17993/03_2024/8pwh_17993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwh_17993/03_2024/8pwh_17993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwh_17993/03_2024/8pwh_17993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwh_17993/03_2024/8pwh_17993.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwh_17993/03_2024/8pwh_17993.pdb" } resolution = 3.17 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= 0.002 sd= 1.172 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 7213 2.51 5 N 1969 2.21 5 O 2272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11535 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1649 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "B" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1650 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Chain: "C" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1657 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "D" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1665 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4794 Classifications: {'peptide': 624} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 579} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.62, per 1000 atoms: 0.57 Number of scatterers: 11535 At special positions: 0 Unit cell: (105.56, 131.08, 148.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2272 8.00 N 1969 7.00 C 7213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 194 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 140 " - pdb=" SG CYS E 170 " distance=2.03 Simple disulfide: pdb=" SG CYS E 173 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 177 " - pdb=" SG CYS E 190 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 202 " - pdb=" SG CYS E 213 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 222 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS E 233 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 246 " - pdb=" SG CYS E 273 " distance=2.03 Simple disulfide: pdb=" SG CYS E 277 " - pdb=" SG CYS E 289 " distance=2.03 Simple disulfide: pdb=" SG CYS E 293 " - pdb=" SG CYS E 309 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 316 " distance=2.03 Simple disulfide: pdb=" SG CYS E 320 " - pdb=" SG CYS E 345 " distance=2.03 Simple disulfide: pdb=" SG CYS E 453 " - pdb=" SG CYS E 482 " distance=2.03 Simple disulfide: pdb=" SG CYS E 489 " - pdb=" SG CYS E 498 " distance=2.03 Simple disulfide: pdb=" SG CYS E 493 " - pdb=" SG CYS E 506 " distance=2.03 Simple disulfide: pdb=" SG CYS E 509 " - pdb=" SG CYS E 518 " distance=2.03 Simple disulfide: pdb=" SG CYS E 522 " - pdb=" SG CYS E 538 " distance=2.03 Simple disulfide: pdb=" SG CYS E 541 " - pdb=" SG CYS E 554 " distance=2.03 Simple disulfide: pdb=" SG CYS E 545 " - pdb=" SG CYS E 562 " distance=2.03 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 574 " distance=2.03 Simple disulfide: pdb=" SG CYS E 578 " - pdb=" SG CYS E 601 " distance=2.03 Simple disulfide: pdb=" SG CYS E 604 " - pdb=" SG CYS E 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 608 " - pdb=" SG CYS E 612 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG E 701 " - " ASN E 46 " " NAG E 702 " - " ASN E 508 " " NAG E 703 " - " ASN E 549 " " NAG G 1 " - " ASN E 165 " " NAG J 1 " - " ASN E 237 " Time building additional restraints: 4.48 Conformation dependent library (CDL) restraints added in 2.3 seconds 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 32 sheets defined 9.2% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.969A pdb=" N GLY A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.636A pdb=" N GLU A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 183 through 187' Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.987A pdb=" N ASP B 31 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR B 32 " --> pdb=" O ILE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.849A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 183 through 187 removed outlier: 4.201A pdb=" N GLU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 187' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.769A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.830A pdb=" N THR D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 190 Processing helix chain 'E' and resid 16 through 28 removed outlier: 4.252A pdb=" N ASP E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 53 removed outlier: 3.569A pdb=" N LEU E 52 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 88 removed outlier: 3.548A pdb=" N ASP E 88 " --> pdb=" O LEU E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 88' Processing helix chain 'E' and resid 146 through 151 removed outlier: 3.982A pdb=" N ILE E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 190 removed outlier: 4.024A pdb=" N CYS E 190 " --> pdb=" O SER E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 213 removed outlier: 4.005A pdb=" N CYS E 213 " --> pdb=" O PRO E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 230 removed outlier: 4.062A pdb=" N CYS E 230 " --> pdb=" O HIS E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.592A pdb=" N ALA E 343 " --> pdb=" O GLN E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 371 through 378 removed outlier: 4.184A pdb=" N LEU E 375 " --> pdb=" O PRO E 372 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLN E 376 " --> pdb=" O GLU E 373 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL E 377 " --> pdb=" O GLN E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 486 Processing helix chain 'E' and resid 493 through 497 removed outlier: 3.639A pdb=" N GLY E 496 " --> pdb=" O CYS E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 562 removed outlier: 3.549A pdb=" N GLN E 561 " --> pdb=" O GLU E 558 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 6.624A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR A 49 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 33 " --> pdb=" O TYR A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 118 removed outlier: 5.921A pdb=" N TYR A 173 " --> pdb=" O ASN A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 150 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.781A pdb=" N THR B 117 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 131 removed outlier: 5.933A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 188 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 139 removed outlier: 5.933A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 184 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 176 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.772A pdb=" N TYR B 201 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 7 removed outlier: 4.066A pdb=" N THR C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C 63 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.252A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 117 Processing sheet with id=AB5, first strand: chain 'C' and resid 145 through 150 removed outlier: 3.915A pdb=" N LYS C 145 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.580A pdb=" N LEU D 78 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP D 72 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.562A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP D 101 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 57 through 59 Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 124 removed outlier: 5.572A pdb=" N ALA D 137 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL D 184 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY D 139 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL D 182 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU D 141 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER D 180 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS D 143 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU D 178 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 120 through 124 removed outlier: 5.572A pdb=" N ALA D 137 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL D 184 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY D 139 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL D 182 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU D 141 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER D 180 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS D 143 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU D 178 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AC4, first strand: chain 'E' and resid 38 through 41 removed outlier: 5.123A pdb=" N GLY E 130 " --> pdb=" O TYR E 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 236 through 238 Processing sheet with id=AC6, first strand: chain 'E' and resid 250 through 252 Processing sheet with id=AC7, first strand: chain 'E' and resid 267 through 269 Processing sheet with id=AC8, first strand: chain 'E' and resid 282 through 283 Processing sheet with id=AC9, first strand: chain 'E' and resid 297 through 301 Processing sheet with id=AD1, first strand: chain 'E' and resid 320 through 321 removed outlier: 7.005A pdb=" N CYS E 320 " --> pdb=" O PHE E 349 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 419 through 421 removed outlier: 6.887A pdb=" N LEU E 445 " --> pdb=" O SER E 420 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA E 444 " --> pdb=" O LEU E 472 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N THR E 474 " --> pdb=" O ALA E 444 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE E 446 " --> pdb=" O THR E 474 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 531 through 533 Processing sheet with id=AD4, first strand: chain 'E' and resid 568 through 570 Processing sheet with id=AD5, first strand: chain 'E' and resid 593 through 595 337 hydrogen bonds defined for protein. 807 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: 4.21 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3780 1.34 - 1.46: 2731 1.46 - 1.58: 5205 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 11809 Sorted by residual: bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C5 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.413 1.441 -0.028 2.00e-02 2.50e+03 2.00e+00 ... (remaining 11804 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.47: 431 106.47 - 113.35: 6460 113.35 - 120.23: 3926 120.23 - 127.10: 5103 127.10 - 133.98: 158 Bond angle restraints: 16078 Sorted by residual: angle pdb=" N GLY D 97 " pdb=" CA GLY D 97 " pdb=" C GLY D 97 " ideal model delta sigma weight residual 112.34 104.81 7.53 2.04e+00 2.40e-01 1.36e+01 angle pdb=" C LEU E 423 " pdb=" N GLN E 424 " pdb=" CA GLN E 424 " ideal model delta sigma weight residual 122.73 127.74 -5.01 1.62e+00 3.81e-01 9.55e+00 angle pdb=" C VAL D 48 " pdb=" N ALA D 49 " pdb=" CA ALA D 49 " ideal model delta sigma weight residual 121.80 116.93 4.87 1.71e+00 3.42e-01 8.10e+00 angle pdb=" N ILE B 29 " pdb=" CA ILE B 29 " pdb=" C ILE B 29 " ideal model delta sigma weight residual 112.98 109.67 3.31 1.25e+00 6.40e-01 7.01e+00 angle pdb=" C SER A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta sigma weight residual 121.54 126.45 -4.91 1.91e+00 2.74e-01 6.60e+00 ... (remaining 16073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.57: 6907 23.57 - 47.14: 281 47.14 - 70.70: 50 70.70 - 94.27: 16 94.27 - 117.84: 14 Dihedral angle restraints: 7268 sinusoidal: 2963 harmonic: 4305 Sorted by residual: dihedral pdb=" CA LEU D 96 " pdb=" C LEU D 96 " pdb=" N GLY D 97 " pdb=" CA GLY D 97 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA PHE D 99A" pdb=" C PHE D 99A" pdb=" N TYR D 99B" pdb=" CA TYR D 99B" ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" C1 NAG G 1 " pdb=" C5 NAG G 1 " pdb=" O5 NAG G 1 " pdb=" C4 NAG G 1 " ideal model delta sinusoidal sigma weight residual -64.11 53.73 -117.84 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 7265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1483 0.057 - 0.114: 300 0.114 - 0.171: 30 0.171 - 0.229: 1 0.229 - 0.286: 3 Chirality restraints: 1817 Sorted by residual: chirality pdb=" C1 NAG E 703 " pdb=" ND2 ASN E 549 " pdb=" C2 NAG E 703 " pdb=" O5 NAG E 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1814 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 124 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C LEU D 124 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU D 124 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA D 125 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 148 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO D 149 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 94 " -0.028 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO C 95 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " -0.021 5.00e-02 4.00e+02 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 254 2.65 - 3.21: 10787 3.21 - 3.77: 17438 3.77 - 4.34: 23751 4.34 - 4.90: 38509 Nonbonded interactions: 90739 Sorted by model distance: nonbonded pdb=" O LEU E 423 " pdb=" O HIS E 447 " model vdw 2.087 3.040 nonbonded pdb=" OD1 ASP A 82 " pdb=" OH TYR A 86 " model vdw 2.109 2.440 nonbonded pdb=" O LYS A 190 " pdb=" N ARG A 211 " model vdw 2.129 2.520 nonbonded pdb=" OG1 THR E 19 " pdb=" OG1 THR E 474 " model vdw 2.177 2.440 nonbonded pdb=" OG1 THR E 7 " pdb=" OE1 GLU E 39 " model vdw 2.179 2.440 ... (remaining 90734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 23 or resid 25 through 29 or resid 33 through 52 \ or resid 55 or resid 57 through 65 or resid 67 through 90 or resid 92 or resid \ 95 or resid 97 through 214)) selection = (chain 'C' and (resid 1 through 23 or resid 25 through 29 or resid 33 through 52 \ or resid 55 or resid 57 through 65 or resid 67 through 90 or resid 92 or resid \ 95 or resid 97 through 213 or (resid 214 and (name N or name CA or name C or nam \ e O or name CB or name SG )))) } ncs_group { reference = (chain 'B' and (resid 1 through 27 or resid 31 or resid 36 through 49 or resid 5 \ 3 or resid 56 or resid 60 or resid 65 through 69 or resid 71 or resid 73 or resi \ d 75 through 78 or resid 80 through 96 or resid 98 or resid 101 or resid 104 thr \ ough 105 or resid 108 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )))) selection = (chain 'D' and (resid 1 through 27 or resid 31 or resid 36 through 49 or resid 5 \ 2A or resid 55 or resid 59 or resid 64 through 68 or resid 70 or resid 72 or res \ id 74 through 77 or resid 79 through 92 or resid 94 or resid 97 or resid 99A thr \ ough 99B or resid 101 through 213)) } ncs_group { reference = chain 'G' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.180 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 34.420 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: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 0.084 11809 Z= 0.288 Angle : 0.641 8.686 16078 Z= 0.330 Chirality : 0.046 0.286 1817 Planarity : 0.005 0.047 2085 Dihedral : 14.685 117.837 4412 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.55 % Favored : 92.39 % Rotamer: Outliers : 4.29 % Allowed : 9.43 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.22), residues: 1484 helix: -1.67 (0.67), residues: 52 sheet: -0.53 (0.25), residues: 434 loop : -1.25 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 393 HIS 0.003 0.001 HIS A 189 PHE 0.012 0.002 PHE E 342 TYR 0.018 0.002 TYR D 99B ARG 0.004 0.000 ARG E 514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 141 time to evaluate : 1.275 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: A 4 MET cc_start: 0.8561 (mmm) cc_final: 0.8002 (mmm) REVERT: A 82 ASP cc_start: 0.7861 (t0) cc_final: 0.7447 (m-30) REVERT: A 189 HIS cc_start: 0.6237 (m-70) cc_final: 0.5863 (m-70) REVERT: B 30 LYS cc_start: 0.8818 (mttt) cc_final: 0.8495 (mtpp) REVERT: B 57 TYR cc_start: 0.8002 (m-10) cc_final: 0.7709 (m-80) REVERT: C 58 VAL cc_start: 0.8190 (t) cc_final: 0.7974 (p) REVERT: C 81 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7737 (mp0) REVERT: C 90 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7513 (pp30) REVERT: C 138 ASN cc_start: 0.8276 (m-40) cc_final: 0.7949 (m-40) REVERT: C 195 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7116 (mm-30) REVERT: D 138 LEU cc_start: 0.9036 (pp) cc_final: 0.8836 (pp) REVERT: D 195 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7548 (pt) REVERT: E 9 MET cc_start: 0.7165 (ptp) cc_final: 0.6836 (ptp) REVERT: E 260 MET cc_start: 0.8117 (mmt) cc_final: 0.7809 (mmt) REVERT: E 465 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8150 (mmt180) REVERT: E 593 LYS cc_start: 0.6869 (mttt) cc_final: 0.6360 (mmtp) outliers start: 55 outliers final: 28 residues processed: 189 average time/residue: 0.2757 time to fit residues: 70.9900 Evaluate side-chains 122 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 91 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Chi-restraints excluded: chain E residue 589 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 37 GLN A 147 GLN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN C 38 GLN D 39 GLN E 32 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 68 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS E 405 ASN ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 451 HIS E 462 GLN E 476 ASN E 526 GLN E 537 HIS E 624 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11809 Z= 0.413 Angle : 0.733 9.695 16078 Z= 0.372 Chirality : 0.049 0.274 1817 Planarity : 0.005 0.043 2085 Dihedral : 12.536 103.130 1856 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.96 % Favored : 90.97 % Rotamer: Outliers : 4.99 % Allowed : 12.08 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.22), residues: 1484 helix: -1.43 (0.66), residues: 52 sheet: -0.60 (0.25), residues: 440 loop : -1.34 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 148 HIS 0.004 0.001 HIS A 189 PHE 0.015 0.002 PHE B 129 TYR 0.021 0.002 TYR C 49 ARG 0.005 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 104 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8650 (mmm) cc_final: 0.8046 (mmm) REVERT: A 82 ASP cc_start: 0.7905 (t0) cc_final: 0.7347 (t0) REVERT: A 148 TRP cc_start: 0.5330 (m100) cc_final: 0.5082 (m100) REVERT: A 189 HIS cc_start: 0.6028 (m-70) cc_final: 0.5471 (m-70) REVERT: A 210 ASN cc_start: 0.2790 (OUTLIER) cc_final: 0.1579 (t0) REVERT: B 30 LYS cc_start: 0.8830 (mttt) cc_final: 0.8523 (mtpp) REVERT: B 57 TYR cc_start: 0.8002 (m-10) cc_final: 0.7762 (m-80) REVERT: B 124 LYS cc_start: 0.8272 (mttt) cc_final: 0.7823 (tttm) REVERT: B 213 LYS cc_start: 0.8051 (tmtt) cc_final: 0.7529 (tppt) REVERT: C 58 VAL cc_start: 0.8112 (t) cc_final: 0.7866 (p) REVERT: C 81 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7804 (mp0) REVERT: C 90 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7684 (pp30) REVERT: C 138 ASN cc_start: 0.8347 (m-40) cc_final: 0.8075 (m-40) REVERT: C 195 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7154 (mm-30) REVERT: D 66 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6536 (mtm180) REVERT: D 105 GLN cc_start: 0.8840 (mp10) cc_final: 0.8620 (mp10) REVERT: D 138 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8783 (pp) REVERT: D 171 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7449 (mp10) REVERT: E 260 MET cc_start: 0.8133 (mmt) cc_final: 0.7839 (mmt) REVERT: E 465 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8215 (mmt180) REVERT: E 570 ASP cc_start: 0.8737 (p0) cc_final: 0.8528 (p0) REVERT: E 593 LYS cc_start: 0.6913 (mttt) cc_final: 0.6652 (mmtp) outliers start: 64 outliers final: 38 residues processed: 157 average time/residue: 0.2509 time to fit residues: 56.5271 Evaluate side-chains 130 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 87 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Chi-restraints excluded: chain E residue 589 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.2980 chunk 41 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 0.0020 chunk 134 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN E 416 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11809 Z= 0.161 Angle : 0.617 10.409 16078 Z= 0.306 Chirality : 0.046 0.282 1817 Planarity : 0.005 0.044 2085 Dihedral : 10.846 100.008 1847 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.73 % Favored : 94.20 % Rotamer: Outliers : 3.59 % Allowed : 14.73 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1484 helix: -1.67 (0.62), residues: 59 sheet: -0.32 (0.25), residues: 428 loop : -1.14 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 148 HIS 0.004 0.001 HIS E 327 PHE 0.023 0.001 PHE D 122 TYR 0.020 0.001 TYR A 186 ARG 0.004 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 115 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8507 (mmm) cc_final: 0.8124 (mmm) REVERT: A 82 ASP cc_start: 0.7706 (t0) cc_final: 0.7457 (m-30) REVERT: A 92 TYR cc_start: 0.8317 (t80) cc_final: 0.7966 (m-80) REVERT: A 186 TYR cc_start: 0.8613 (t80) cc_final: 0.8364 (t80) REVERT: A 189 HIS cc_start: 0.6249 (m-70) cc_final: 0.5966 (m-70) REVERT: B 30 LYS cc_start: 0.8714 (mttt) cc_final: 0.8355 (mtpp) REVERT: B 216 LYS cc_start: 0.7731 (mmmt) cc_final: 0.7368 (ttpp) REVERT: C 58 VAL cc_start: 0.8205 (t) cc_final: 0.7973 (p) REVERT: C 81 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7697 (mp0) REVERT: C 138 ASN cc_start: 0.8288 (m-40) cc_final: 0.7996 (m-40) REVERT: C 195 GLU cc_start: 0.7447 (mm-30) cc_final: 0.6992 (mm-30) REVERT: D 35 ASP cc_start: 0.7631 (m-30) cc_final: 0.7214 (m-30) REVERT: D 59 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6673 (p90) REVERT: D 66 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.5616 (ptm160) REVERT: D 83 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.8110 (ttp-110) REVERT: D 210 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8373 (tppt) REVERT: E 260 MET cc_start: 0.8164 (mmt) cc_final: 0.7894 (mmt) REVERT: E 465 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8224 (mmt180) REVERT: E 519 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.7944 (p) REVERT: E 570 ASP cc_start: 0.8725 (p0) cc_final: 0.8285 (t70) REVERT: E 589 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6814 (mpp) outliers start: 46 outliers final: 30 residues processed: 153 average time/residue: 0.2286 time to fit residues: 50.6195 Evaluate side-chains 134 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 99 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Chi-restraints excluded: chain E residue 589 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 143 optimal weight: 0.2980 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN E 35 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11809 Z= 0.400 Angle : 0.720 11.206 16078 Z= 0.364 Chirality : 0.048 0.277 1817 Planarity : 0.005 0.042 2085 Dihedral : 10.436 97.195 1843 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.43 % Favored : 90.50 % Rotamer: Outliers : 4.44 % Allowed : 15.59 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.22), residues: 1484 helix: -1.38 (0.67), residues: 52 sheet: -0.61 (0.25), residues: 441 loop : -1.29 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 148 HIS 0.005 0.001 HIS A 189 PHE 0.014 0.002 PHE E 454 TYR 0.019 0.002 TYR C 49 ARG 0.003 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 91 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8690 (mmm) cc_final: 0.8020 (mmm) REVERT: A 82 ASP cc_start: 0.7866 (t0) cc_final: 0.7516 (m-30) REVERT: A 189 HIS cc_start: 0.6335 (m-70) cc_final: 0.5910 (m90) REVERT: B 89 GLU cc_start: 0.7985 (pm20) cc_final: 0.7714 (pm20) REVERT: B 152 TYR cc_start: 0.6325 (p90) cc_final: 0.5809 (p90) REVERT: C 81 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7814 (mp0) REVERT: C 195 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7250 (mm-30) REVERT: D 66 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6809 (mtm180) REVERT: D 83 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.8093 (ttm-80) REVERT: D 210 LYS cc_start: 0.8484 (mmmm) cc_final: 0.8270 (mmmm) REVERT: E 35 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8003 (mt0) REVERT: E 71 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7934 (pp30) REVERT: E 204 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.4149 (mpp-170) REVERT: E 260 MET cc_start: 0.8126 (mmt) cc_final: 0.7848 (mmt) REVERT: E 342 PHE cc_start: 0.7116 (m-80) cc_final: 0.6597 (m-80) REVERT: E 465 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8216 (mmt180) REVERT: E 570 ASP cc_start: 0.8776 (p0) cc_final: 0.8457 (p0) REVERT: E 589 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7806 (mpp) outliers start: 57 outliers final: 45 residues processed: 137 average time/residue: 0.2269 time to fit residues: 45.5585 Evaluate side-chains 136 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 85 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 549 ASN Chi-restraints excluded: chain E residue 589 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 0.0570 chunk 59 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN C 90 GLN C 138 ASN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11809 Z= 0.269 Angle : 0.654 11.881 16078 Z= 0.328 Chirality : 0.046 0.277 1817 Planarity : 0.005 0.043 2085 Dihedral : 9.957 93.841 1843 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.21 % Favored : 92.72 % Rotamer: Outliers : 4.44 % Allowed : 16.84 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.22), residues: 1484 helix: -1.51 (0.64), residues: 52 sheet: -0.43 (0.25), residues: 430 loop : -1.23 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 148 HIS 0.004 0.001 HIS E 327 PHE 0.016 0.002 PHE D 122 TYR 0.018 0.002 TYR A 186 ARG 0.003 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 93 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8629 (mmm) cc_final: 0.7970 (mmm) REVERT: A 82 ASP cc_start: 0.7865 (t0) cc_final: 0.7501 (m-30) REVERT: A 189 HIS cc_start: 0.6255 (m-70) cc_final: 0.5863 (m90) REVERT: B 89 GLU cc_start: 0.8029 (pm20) cc_final: 0.7681 (pm20) REVERT: B 216 LYS cc_start: 0.7698 (mmmt) cc_final: 0.7330 (ttpp) REVERT: C 81 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7721 (mp0) REVERT: C 195 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7186 (mm-30) REVERT: D 35 ASP cc_start: 0.7701 (m-30) cc_final: 0.7157 (m-30) REVERT: D 66 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6545 (mtm180) REVERT: E 71 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7910 (pp30) REVERT: E 260 MET cc_start: 0.8153 (mmt) cc_final: 0.7872 (mmt) REVERT: E 465 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8146 (mmt180) REVERT: E 519 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.7975 (p) REVERT: E 570 ASP cc_start: 0.8697 (p0) cc_final: 0.8341 (p0) REVERT: E 589 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7729 (mpp) outliers start: 57 outliers final: 41 residues processed: 140 average time/residue: 0.2435 time to fit residues: 50.9501 Evaluate side-chains 133 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 87 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Chi-restraints excluded: chain E residue 589 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 3.9990 chunk 128 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 143 optimal weight: 0.4980 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11809 Z= 0.162 Angle : 0.605 11.119 16078 Z= 0.301 Chirality : 0.045 0.283 1817 Planarity : 0.005 0.044 2085 Dihedral : 8.912 81.414 1842 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 3.74 % Allowed : 17.54 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.22), residues: 1484 helix: -1.52 (0.66), residues: 55 sheet: -0.15 (0.26), residues: 425 loop : -1.13 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 148 HIS 0.004 0.001 HIS E 327 PHE 0.018 0.001 PHE D 122 TYR 0.031 0.001 TYR B 57 ARG 0.003 0.000 ARG E 577 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 100 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8555 (mmm) cc_final: 0.8152 (mmm) REVERT: A 92 TYR cc_start: 0.8379 (t80) cc_final: 0.8075 (m-80) REVERT: A 189 HIS cc_start: 0.6267 (m-70) cc_final: 0.6005 (m90) REVERT: B 30 LYS cc_start: 0.8652 (mttt) cc_final: 0.8338 (mtpp) REVERT: B 80 TYR cc_start: 0.8852 (m-10) cc_final: 0.8626 (m-10) REVERT: B 124 LYS cc_start: 0.8159 (mttt) cc_final: 0.7862 (tptt) REVERT: B 213 LYS cc_start: 0.8094 (tmtt) cc_final: 0.7605 (tppt) REVERT: B 216 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7285 (ttpp) REVERT: C 81 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7711 (mp0) REVERT: C 195 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7098 (mm-30) REVERT: D 35 ASP cc_start: 0.7615 (m-30) cc_final: 0.7182 (m-30) REVERT: D 66 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6897 (mtm180) REVERT: E 161 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8675 (tt) REVERT: E 260 MET cc_start: 0.8153 (mmt) cc_final: 0.7885 (mmt) REVERT: E 465 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8204 (mmt180) REVERT: E 519 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8039 (p) REVERT: E 570 ASP cc_start: 0.8734 (p0) cc_final: 0.8508 (p0) outliers start: 48 outliers final: 35 residues processed: 138 average time/residue: 0.2421 time to fit residues: 48.2103 Evaluate side-chains 130 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 91 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11809 Z= 0.273 Angle : 0.642 11.801 16078 Z= 0.323 Chirality : 0.045 0.282 1817 Planarity : 0.005 0.043 2085 Dihedral : 8.294 61.321 1833 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.68 % Favored : 92.25 % Rotamer: Outliers : 4.44 % Allowed : 17.30 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1484 helix: -1.17 (0.72), residues: 49 sheet: -0.30 (0.25), residues: 435 loop : -1.16 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 161 HIS 0.003 0.001 HIS E 327 PHE 0.013 0.002 PHE D 122 TYR 0.017 0.002 TYR A 186 ARG 0.003 0.000 ARG E 577 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 87 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8691 (mmm) cc_final: 0.8124 (mmm) REVERT: A 189 HIS cc_start: 0.6209 (m-70) cc_final: 0.5876 (m90) REVERT: C 81 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7739 (mp0) REVERT: C 195 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7211 (mm-30) REVERT: D 66 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6896 (mtm180) REVERT: D 83 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.8081 (ttm-80) REVERT: D 210 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8475 (mmmt) REVERT: E 71 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7966 (pp30) REVERT: E 260 MET cc_start: 0.8136 (mmt) cc_final: 0.7903 (mmt) REVERT: E 323 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8254 (mp) REVERT: E 465 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8174 (mmt180) REVERT: E 519 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8094 (p) REVERT: E 589 MET cc_start: 0.8384 (mpp) cc_final: 0.8120 (mpp) outliers start: 57 outliers final: 43 residues processed: 133 average time/residue: 0.2204 time to fit residues: 43.1895 Evaluate side-chains 133 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 85 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 70 optimal weight: 0.0470 chunk 13 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 11809 Z= 0.369 Angle : 0.697 11.245 16078 Z= 0.356 Chirality : 0.047 0.277 1817 Planarity : 0.005 0.043 2085 Dihedral : 8.265 59.085 1833 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.76 % Favored : 91.17 % Rotamer: Outliers : 4.52 % Allowed : 17.61 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.22), residues: 1484 helix: -0.91 (0.73), residues: 46 sheet: -0.48 (0.26), residues: 430 loop : -1.28 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 161 HIS 0.004 0.001 HIS A 189 PHE 0.014 0.002 PHE D 122 TYR 0.022 0.002 TYR A 186 ARG 0.002 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 95 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8680 (mmm) cc_final: 0.7957 (mmm) REVERT: B 30 LYS cc_start: 0.8800 (mttt) cc_final: 0.8538 (mtpp) REVERT: B 213 LYS cc_start: 0.8110 (tmtt) cc_final: 0.7600 (tppt) REVERT: C 81 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7742 (mp0) REVERT: C 195 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7251 (mm-30) REVERT: D 66 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6896 (mtm180) REVERT: D 83 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8065 (ttm-80) REVERT: D 210 LYS cc_start: 0.8783 (ttmm) cc_final: 0.8504 (tptm) REVERT: E 71 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8040 (pp30) REVERT: E 161 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8765 (tt) REVERT: E 260 MET cc_start: 0.8145 (mmt) cc_final: 0.7902 (mmt) REVERT: E 323 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8350 (mp) REVERT: E 465 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8119 (mmt180) REVERT: E 519 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8078 (p) REVERT: E 589 MET cc_start: 0.8548 (mpp) cc_final: 0.8303 (mpp) outliers start: 58 outliers final: 46 residues processed: 142 average time/residue: 0.2407 time to fit residues: 50.1268 Evaluate side-chains 139 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 87 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 549 ASN Chi-restraints excluded: chain E residue 588 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 80 optimal weight: 0.0040 chunk 57 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 120 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11809 Z= 0.182 Angle : 0.616 9.805 16078 Z= 0.309 Chirality : 0.045 0.321 1817 Planarity : 0.005 0.044 2085 Dihedral : 7.547 59.656 1832 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.00 % Favored : 93.94 % Rotamer: Outliers : 3.74 % Allowed : 18.78 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.22), residues: 1484 helix: -1.66 (0.63), residues: 55 sheet: -0.24 (0.26), residues: 429 loop : -1.14 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 148 HIS 0.004 0.001 HIS E 327 PHE 0.020 0.001 PHE A 83 TYR 0.018 0.001 TYR B 80 ARG 0.004 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 88 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8635 (mmm) cc_final: 0.8093 (mmm) REVERT: A 189 HIS cc_start: 0.5914 (m-70) cc_final: 0.5684 (m90) REVERT: C 81 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7708 (mp0) REVERT: C 195 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7133 (mm-30) REVERT: D 35 ASP cc_start: 0.7615 (m-30) cc_final: 0.7174 (m-30) REVERT: D 66 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6894 (mtm180) REVERT: D 82 MET cc_start: 0.8756 (ttm) cc_final: 0.8539 (ttm) REVERT: D 83 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8117 (ttm-80) REVERT: D 210 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8520 (tptm) REVERT: E 161 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8664 (tt) REVERT: E 260 MET cc_start: 0.8148 (mmt) cc_final: 0.7888 (mmt) REVERT: E 323 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8206 (mp) REVERT: E 465 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8196 (mmt180) REVERT: E 519 VAL cc_start: 0.8409 (OUTLIER) cc_final: 0.8092 (p) REVERT: E 589 MET cc_start: 0.8422 (mpp) cc_final: 0.8186 (mpp) outliers start: 48 outliers final: 40 residues processed: 126 average time/residue: 0.2161 time to fit residues: 40.7603 Evaluate side-chains 131 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 86 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 97 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 125 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11809 Z= 0.234 Angle : 0.625 9.630 16078 Z= 0.316 Chirality : 0.045 0.327 1817 Planarity : 0.005 0.042 2085 Dihedral : 7.455 59.960 1832 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.48 % Favored : 92.45 % Rotamer: Outliers : 3.59 % Allowed : 18.94 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.22), residues: 1484 helix: -1.23 (0.71), residues: 49 sheet: -0.28 (0.26), residues: 432 loop : -1.13 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 148 HIS 0.004 0.001 HIS E 327 PHE 0.037 0.002 PHE A 83 TYR 0.026 0.002 TYR B 152 ARG 0.004 0.000 ARG A 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 84 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8649 (mmm) cc_final: 0.8088 (mmm) REVERT: A 82 ASP cc_start: 0.8039 (t0) cc_final: 0.7677 (m-30) REVERT: A 173 TYR cc_start: 0.7199 (m-80) cc_final: 0.6177 (m-80) REVERT: C 81 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7731 (mp0) REVERT: C 195 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7205 (mm-30) REVERT: D 35 ASP cc_start: 0.7700 (m-30) cc_final: 0.7206 (m-30) REVERT: D 66 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6384 (mtm180) REVERT: D 82 MET cc_start: 0.8805 (ttm) cc_final: 0.8600 (ttm) REVERT: D 210 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8536 (tptm) REVERT: E 161 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8700 (tt) REVERT: E 260 MET cc_start: 0.8139 (mmt) cc_final: 0.7909 (mmt) REVERT: E 323 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8262 (mp) REVERT: E 465 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8174 (mmt180) REVERT: E 519 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8131 (p) REVERT: E 589 MET cc_start: 0.8527 (mpp) cc_final: 0.8284 (mpp) outliers start: 46 outliers final: 38 residues processed: 123 average time/residue: 0.2308 time to fit residues: 42.8968 Evaluate side-chains 127 residues out of total 1283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 84 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN ** E 546 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 = 0.4137 r_free = 0.4137 target = 0.116381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.090756 restraints weight = 33121.264| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 4.38 r_work: 0.3535 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11809 Z= 0.290 Angle : 0.653 9.556 16078 Z= 0.332 Chirality : 0.046 0.315 1817 Planarity : 0.005 0.042 2085 Dihedral : 7.587 59.500 1832 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.02 % Favored : 91.91 % Rotamer: Outliers : 3.74 % Allowed : 18.86 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.22), residues: 1484 helix: -1.15 (0.72), residues: 49 sheet: -0.30 (0.26), residues: 430 loop : -1.22 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 148 HIS 0.004 0.001 HIS E 327 PHE 0.042 0.002 PHE A 83 TYR 0.025 0.002 TYR B 57 ARG 0.004 0.000 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2577.63 seconds wall clock time: 47 minutes 31.45 seconds (2851.45 seconds total)