Starting phenix.real_space_refine on Sat Nov 16 17:18:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwh_17993/11_2024/8pwh_17993.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwh_17993/11_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_17993/11_2024/8pwh_17993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwh_17993/11_2024/8pwh_17993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwh_17993/11_2024/8pwh_17993.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pwh_17993/11_2024/8pwh_17993.cif" } 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. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 7.10, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 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: 2.88 Conformation dependent library (CDL) restraints added in 1.6 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: 1.61 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: 3.98 Time building geometry restraints manager: 3.36 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: 0.00 - 1.74: 15684 1.74 - 3.47: 337 3.47 - 5.21: 45 5.21 - 6.95: 10 6.95 - 8.69: 2 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 3.040 nonbonded pdb=" O LYS A 190 " pdb=" N ARG A 211 " model vdw 2.129 3.120 nonbonded pdb=" OG1 THR E 19 " pdb=" OG1 THR E 474 " model vdw 2.177 3.040 nonbonded pdb=" OG1 THR E 7 " pdb=" OE1 GLU E 39 " model vdw 2.179 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.930 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.820 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.760 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 55 poor density : 141 time to evaluate : 1.433 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: 0.2810 time to fit residues: 72.6033 Evaluate side-chains 122 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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: 0.9980 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 C 90 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 416 ASN E 451 HIS E 462 GLN 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: 0.7581 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11809 Z= 0.349 Angle : 0.701 9.816 16078 Z= 0.357 Chirality : 0.048 0.280 1817 Planarity : 0.005 0.048 2085 Dihedral : 12.582 102.621 1856 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.09 % Favored : 91.85 % Rotamer: Outliers : 3.82 % Allowed : 12.55 % Favored : 83.63 % 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: -1.51 (0.22), residues: 1484 helix: -1.39 (0.66), residues: 52 sheet: -0.52 (0.25), residues: 430 loop : -1.24 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 148 HIS 0.003 0.001 HIS E 327 PHE 0.013 0.002 PHE A 139 TYR 0.018 0.002 TYR C 49 ARG 0.007 0.001 ARG E 577 *********************** 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 160 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 111 time to evaluate : 1.412 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: 0.8656 (mmm) cc_final: 0.7989 (mmm) REVERT: A 92 TYR cc_start: 0.8178 (t80) cc_final: 0.7821 (m-80) REVERT: A 189 HIS cc_start: 0.6351 (m-70) cc_final: 0.5845 (m90) REVERT: B 30 LYS cc_start: 0.8862 (mttt) cc_final: 0.8594 (mtpp) REVERT: B 57 TYR cc_start: 0.8155 (m-10) cc_final: 0.7894 (m-80) REVERT: C 58 VAL cc_start: 0.8152 (t) cc_final: 0.7892 (p) REVERT: C 81 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7856 (mp0) REVERT: C 90 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7677 (pp30) REVERT: C 138 ASN cc_start: 0.8363 (m-40) cc_final: 0.8025 (m-40) REVERT: D 35 ASP cc_start: 0.7847 (m-30) cc_final: 0.7523 (m-30) REVERT: D 66 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6334 (mtm180) REVERT: D 138 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8856 (pp) REVERT: D 171 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7321 (mp10) REVERT: D 210 LYS cc_start: 0.8534 (mmmm) cc_final: 0.8271 (tppt) REVERT: E 260 MET cc_start: 0.8139 (mmt) cc_final: 0.7851 (mmt) REVERT: E 465 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8018 (mmt-90) REVERT: E 519 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.7858 (p) REVERT: E 570 ASP cc_start: 0.8639 (p0) cc_final: 0.8365 (t70) outliers start: 49 outliers final: 31 residues processed: 152 average time/residue: 0.2714 time to fit residues: 58.0017 Evaluate side-chains 127 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 B residue 83 MET Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 128 VAL 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 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 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 465 ARG 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.4980 chunk 41 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 134 optimal weight: 10.0000 chunk 145 optimal weight: 0.0010 chunk 119 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 0.0170 overall best weight: 0.5226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 166 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN E 466 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11809 Z= 0.168 Angle : 0.627 10.263 16078 Z= 0.311 Chirality : 0.047 0.282 1817 Planarity : 0.005 0.045 2085 Dihedral : 10.747 95.727 1842 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.59 % Favored : 94.34 % Rotamer: Outliers : 3.35 % Allowed : 13.48 % Favored : 83.16 % 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: -1.25 (0.22), residues: 1484 helix: -1.67 (0.66), residues: 54 sheet: -0.25 (0.25), residues: 440 loop : -1.08 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 148 HIS 0.004 0.001 HIS E 327 PHE 0.023 0.001 PHE D 122 TYR 0.019 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 to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 1.494 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: 0.8578 (mmm) cc_final: 0.8226 (mmm) REVERT: A 92 TYR cc_start: 0.8139 (t80) cc_final: 0.7835 (m-80) REVERT: B 30 LYS cc_start: 0.8787 (mttt) cc_final: 0.8422 (mtpp) REVERT: B 155 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6898 (mm-30) REVERT: B 213 LYS cc_start: 0.8013 (tmtt) cc_final: 0.7715 (tmtt) REVERT: B 216 LYS cc_start: 0.7701 (mmmt) cc_final: 0.7361 (ttpp) REVERT: C 81 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7842 (mp0) REVERT: C 138 ASN cc_start: 0.8354 (m-40) cc_final: 0.7897 (m-40) REVERT: D 210 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8395 (tppt) REVERT: E 260 MET cc_start: 0.8117 (mmt) cc_final: 0.7829 (mmt) REVERT: E 465 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8305 (mmt-90) REVERT: E 466 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8460 (p0) REVERT: E 570 ASP cc_start: 0.8597 (p0) cc_final: 0.8288 (t70) REVERT: E 593 LYS cc_start: 0.5984 (mmtp) cc_final: 0.5774 (mmtt) outliers start: 43 outliers final: 28 residues processed: 155 average time/residue: 0.2498 time to fit residues: 55.7497 Evaluate side-chains 130 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR 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 91 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 203 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 59 TYR 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 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 549 ASN 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: 0.5980 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1881 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= 0.282 Angle : 0.660 11.101 16078 Z= 0.330 Chirality : 0.047 0.280 1817 Planarity : 0.005 0.042 2085 Dihedral : 9.942 89.302 1830 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.67 % Favored : 93.26 % Rotamer: Outliers : 3.90 % Allowed : 14.73 % Favored : 81.37 % 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: -1.61 (0.67), residues: 54 sheet: -0.37 (0.25), residues: 431 loop : -1.13 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 148 HIS 0.003 0.001 HIS E 327 PHE 0.020 0.002 PHE D 122 TYR 0.019 0.002 TYR A 186 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 151 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 101 time to evaluate : 1.385 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: 0.8672 (mmm) cc_final: 0.8146 (mmm) REVERT: B 1 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7963 (tm-30) REVERT: B 30 LYS cc_start: 0.8866 (mttt) cc_final: 0.8500 (mtpp) REVERT: B 152 TYR cc_start: 0.6131 (p90) cc_final: 0.5498 (p90) REVERT: C 81 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7752 (mp0) REVERT: C 138 ASN cc_start: 0.8382 (m-40) cc_final: 0.8049 (m-40) REVERT: D 66 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.5633 (ptm160) REVERT: D 83 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.8016 (ttm-80) REVERT: D 210 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8348 (tppt) REVERT: E 260 MET cc_start: 0.8104 (mmt) cc_final: 0.7824 (mmt) REVERT: E 466 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8684 (p0) REVERT: E 519 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.7971 (p) REVERT: E 570 ASP cc_start: 0.8692 (p0) cc_final: 0.8319 (t70) outliers start: 50 outliers final: 37 residues processed: 142 average time/residue: 0.2515 time to fit residues: 51.4873 Evaluate side-chains 130 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 91 THR Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 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 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 106 ILE Chi-restraints excluded: chain C residue 109 THR 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 C residue 196 VAL Chi-restraints excluded: chain D residue 12 VAL 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 95 LEU Chi-restraints excluded: chain E residue 107 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 106 optimal weight: 0.0570 chunk 59 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 158 ASN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN E 466 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11809 Z= 0.310 Angle : 0.672 11.909 16078 Z= 0.338 Chirality : 0.047 0.279 1817 Planarity : 0.005 0.043 2085 Dihedral : 9.250 77.995 1826 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.55 % Favored : 92.39 % Rotamer: Outliers : 4.05 % Allowed : 15.43 % Favored : 80.51 % 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: -1.32 (0.22), residues: 1484 helix: -1.16 (0.72), residues: 46 sheet: -0.37 (0.25), residues: 432 loop : -1.13 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 148 HIS 0.003 0.001 HIS E 327 PHE 0.017 0.002 PHE D 122 TYR 0.018 0.002 TYR A 186 ARG 0.003 0.000 ARG E 116 *********************** 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 147 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 95 time to evaluate : 1.190 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: 0.8662 (mmm) cc_final: 0.8063 (mmm) REVERT: B 1 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 3 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7202 (mp10) REVERT: B 89 GLU cc_start: 0.8105 (pm20) cc_final: 0.7841 (pm20) REVERT: B 152 TYR cc_start: 0.6154 (p90) cc_final: 0.5538 (p90) REVERT: B 216 LYS cc_start: 0.7696 (mmmt) cc_final: 0.7341 (ttpp) REVERT: C 81 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7863 (mp0) REVERT: D 66 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.5971 (ptm160) REVERT: D 210 LYS cc_start: 0.8593 (mmmm) cc_final: 0.8169 (mmmm) REVERT: E 71 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7925 (pp30) REVERT: E 260 MET cc_start: 0.8122 (mmt) cc_final: 0.7878 (mmt) REVERT: E 342 PHE cc_start: 0.7155 (m-80) cc_final: 0.6626 (m-80) REVERT: E 466 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8652 (p0) REVERT: E 519 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.7985 (p) REVERT: E 570 ASP cc_start: 0.8700 (p0) cc_final: 0.8497 (p0) outliers start: 52 outliers final: 40 residues processed: 138 average time/residue: 0.2244 time to fit residues: 45.5536 Evaluate side-chains 138 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 94 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 B residue 83 MET Chi-restraints excluded: chain B residue 98 ARG 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 30 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 6 GLU 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 175 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 19 THR 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 420 SER 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 504 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 ASN C 158 ASN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 466 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11809 Z= 0.216 Angle : 0.638 11.680 16078 Z= 0.318 Chirality : 0.045 0.281 1817 Planarity : 0.005 0.045 2085 Dihedral : 8.407 59.204 1824 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.47 % Favored : 93.46 % Rotamer: Outliers : 3.74 % Allowed : 15.43 % Favored : 80.83 % 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: -1.21 (0.22), residues: 1484 helix: -1.26 (0.73), residues: 48 sheet: -0.21 (0.25), residues: 435 loop : -1.09 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 148 HIS 0.004 0.001 HIS E 327 PHE 0.017 0.001 PHE D 122 TYR 0.033 0.002 TYR B 57 ARG 0.002 0.000 ARG E 116 *********************** 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 146 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 98 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8886 (mm) cc_final: 0.8583 (mm) REVERT: A 4 MET cc_start: 0.8675 (mmm) cc_final: 0.8115 (mmm) REVERT: A 173 TYR cc_start: 0.6772 (m-80) cc_final: 0.5994 (m-80) REVERT: B 1 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7777 (tm-30) REVERT: B 3 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7187 (mp10) REVERT: B 152 TYR cc_start: 0.6047 (p90) cc_final: 0.5387 (p90) REVERT: B 216 LYS cc_start: 0.7758 (mmmt) cc_final: 0.7408 (ttpp) REVERT: C 81 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7852 (mp0) REVERT: D 66 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.5357 (ptm160) REVERT: D 83 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.8047 (ttp-110) REVERT: D 85 GLU cc_start: 0.6907 (pp20) cc_final: 0.6552 (pp20) REVERT: D 210 LYS cc_start: 0.8564 (mmmm) cc_final: 0.8280 (mmmm) REVERT: E 35 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8101 (mt0) REVERT: E 71 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7927 (pp30) REVERT: E 260 MET cc_start: 0.8147 (mmt) cc_final: 0.7873 (mmt) REVERT: E 466 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.8800 (p0) REVERT: E 519 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8169 (p) REVERT: E 570 ASP cc_start: 0.8684 (p0) cc_final: 0.8446 (p0) outliers start: 48 outliers final: 38 residues processed: 142 average time/residue: 0.2257 time to fit residues: 48.4392 Evaluate side-chains 133 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 90 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL 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 91 THR Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 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 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 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 6 GLU 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 175 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 19 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 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 493 CYS 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 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: 7.9990 chunk 81 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN E 35 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 ASN ** E 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11809 Z= 0.387 Angle : 0.704 9.627 16078 Z= 0.357 Chirality : 0.047 0.280 1817 Planarity : 0.005 0.044 2085 Dihedral : 8.020 57.877 1824 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.42 % Favored : 91.51 % Rotamer: Outliers : 4.52 % Allowed : 15.43 % Favored : 80.05 % 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: -1.43 (0.22), residues: 1484 helix: -1.38 (0.68), residues: 52 sheet: -0.44 (0.25), residues: 429 loop : -1.20 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 161 HIS 0.003 0.001 HIS E 227 PHE 0.017 0.002 PHE D 122 TYR 0.027 0.002 TYR B 57 ARG 0.002 0.000 ARG A 211 *********************** 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 150 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 92 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8788 (mmm) cc_final: 0.8073 (mmm) REVERT: B 152 TYR cc_start: 0.6229 (p90) cc_final: 0.5690 (p90) REVERT: B 155 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7037 (mm-30) REVERT: C 81 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7855 (mp0) REVERT: D 192 GLN cc_start: 0.9205 (tp40) cc_final: 0.8971 (tp-100) REVERT: D 210 LYS cc_start: 0.8555 (mmmm) cc_final: 0.8264 (mmmm) REVERT: E 71 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8026 (pp30) REVERT: E 171 HIS cc_start: 0.7745 (t-90) cc_final: 0.7418 (t-90) REVERT: E 260 MET cc_start: 0.8112 (mmt) cc_final: 0.7880 (mmt) REVERT: E 323 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8293 (mp) REVERT: E 466 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8778 (p0) REVERT: E 519 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8272 (p) REVERT: E 570 ASP cc_start: 0.8671 (p0) cc_final: 0.8420 (p0) outliers start: 58 outliers final: 49 residues processed: 141 average time/residue: 0.2274 time to fit residues: 47.4453 Evaluate side-chains 141 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 88 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 B residue 34 ILE Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 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 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 58 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR 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 6 GLU 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 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 19 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 323 LEU Chi-restraints excluded: chain E residue 420 SER 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 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 578 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN E 466 ASN ** E 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11809 Z= 0.367 Angle : 0.695 9.550 16078 Z= 0.356 Chirality : 0.047 0.279 1817 Planarity : 0.005 0.043 2085 Dihedral : 7.920 59.643 1824 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.69 % Favored : 91.24 % Rotamer: Outliers : 4.52 % Allowed : 15.51 % 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: -1.50 (0.22), residues: 1484 helix: -1.43 (0.67), residues: 52 sheet: -0.52 (0.25), residues: 428 loop : -1.23 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 161 HIS 0.003 0.001 HIS E 327 PHE 0.020 0.002 PHE D 122 TYR 0.027 0.002 TYR B 57 ARG 0.004 0.000 ARG D 83 *********************** 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 149 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 91 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8845 (mmm) cc_final: 0.8087 (mmm) REVERT: B 152 TYR cc_start: 0.6243 (p90) cc_final: 0.5746 (p90) REVERT: B 155 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7031 (mm-30) REVERT: C 81 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7861 (mp0) REVERT: D 210 LYS cc_start: 0.8590 (mmmm) cc_final: 0.8330 (mmmm) REVERT: E 71 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8050 (pp30) REVERT: E 260 MET cc_start: 0.8143 (mmt) cc_final: 0.7898 (mmt) REVERT: E 519 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8289 (p) REVERT: E 570 ASP cc_start: 0.8679 (p0) cc_final: 0.8425 (p0) REVERT: E 593 LYS cc_start: 0.6319 (mmtp) cc_final: 0.5777 (mmmt) outliers start: 58 outliers final: 50 residues processed: 138 average time/residue: 0.2235 time to fit residues: 45.7073 Evaluate side-chains 142 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 90 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 B residue 34 ILE Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 98 ARG 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 21 ILE Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR 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 6 GLU 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 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 19 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 420 SER 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 578 CYS 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: 0.4980 chunk 124 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 80 optimal weight: 0.0570 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11809 Z= 0.181 Angle : 0.629 9.630 16078 Z= 0.317 Chirality : 0.045 0.285 1817 Planarity : 0.005 0.045 2085 Dihedral : 7.405 59.708 1823 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.93 % Favored : 94.00 % Rotamer: Outliers : 3.35 % Allowed : 16.52 % Favored : 80.12 % 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: -1.27 (0.22), residues: 1484 helix: -1.51 (0.68), residues: 56 sheet: -0.30 (0.25), residues: 441 loop : -1.09 (0.21), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 148 HIS 0.004 0.001 HIS E 327 PHE 0.020 0.001 PHE D 122 TYR 0.025 0.001 TYR B 57 ARG 0.005 0.000 ARG D 83 *********************** 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 140 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8705 (mmm) cc_final: 0.8119 (mmm) REVERT: A 173 TYR cc_start: 0.6937 (m-80) cc_final: 0.6076 (m-80) REVERT: B 1 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8290 (tm-30) REVERT: B 216 LYS cc_start: 0.7687 (mmmt) cc_final: 0.7361 (ttpp) REVERT: C 81 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7852 (mp0) REVERT: D 66 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.5495 (ptm160) REVERT: D 83 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8140 (ttp-110) REVERT: D 210 LYS cc_start: 0.8572 (mmmm) cc_final: 0.8325 (mmmm) REVERT: E 71 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7970 (pp30) REVERT: E 171 HIS cc_start: 0.7703 (t-90) cc_final: 0.7383 (t-90) REVERT: E 260 MET cc_start: 0.8144 (mmt) cc_final: 0.7879 (mmt) REVERT: E 570 ASP cc_start: 0.8607 (p0) cc_final: 0.8373 (p0) REVERT: E 593 LYS cc_start: 0.6193 (mmtp) cc_final: 0.5789 (mmmt) outliers start: 43 outliers final: 37 residues processed: 134 average time/residue: 0.2256 time to fit residues: 45.3049 Evaluate side-chains 129 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 B residue 83 MET Chi-restraints excluded: chain B residue 98 ARG 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 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 6 GLU 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 110 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 19 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 480 ASP Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 549 ASN Chi-restraints excluded: chain E residue 578 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2483 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= 0.262 Angle : 0.646 9.547 16078 Z= 0.328 Chirality : 0.046 0.284 1817 Planarity : 0.005 0.045 2085 Dihedral : 7.363 59.627 1821 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.94 % Favored : 92.99 % Rotamer: Outliers : 3.35 % Allowed : 16.76 % Favored : 79.89 % 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: -1.62 (0.66), residues: 55 sheet: -0.27 (0.25), residues: 440 loop : -1.14 (0.21), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 148 HIS 0.004 0.001 HIS E 327 PHE 0.031 0.002 PHE D 122 TYR 0.027 0.002 TYR A 186 ARG 0.005 0.000 ARG D 83 ********************** 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 134 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 91 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8706 (mmm) cc_final: 0.8100 (mmm) REVERT: A 173 TYR cc_start: 0.6972 (m-80) cc_final: 0.6067 (m-80) REVERT: B 1 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8297 (tm-30) REVERT: C 81 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7864 (mp0) REVERT: D 66 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.5443 (ptm160) REVERT: E 71 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8058 (pp30) REVERT: E 260 MET cc_start: 0.8108 (mmt) cc_final: 0.7864 (mmt) outliers start: 43 outliers final: 37 residues processed: 127 average time/residue: 0.2478 time to fit residues: 46.9524 Evaluate side-chains 125 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 B residue 83 MET Chi-restraints excluded: chain B residue 98 ARG 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 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 6 GLU 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 110 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 19 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 480 ASP Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 549 ASN Chi-restraints excluded: chain E residue 578 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 10.0000 chunk 108 optimal weight: 0.0270 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 GLN 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 = 0.116464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.090769 restraints weight = 32842.529| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 4.42 r_work: 0.3539 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2539 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= 0.275 Angle : 0.667 10.155 16078 Z= 0.338 Chirality : 0.046 0.282 1817 Planarity : 0.005 0.051 2085 Dihedral : 7.382 59.097 1821 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.01 % Favored : 92.92 % Rotamer: Outliers : 3.12 % Allowed : 17.30 % Favored : 79.58 % 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: -1.33 (0.22), residues: 1484 helix: -1.56 (0.67), residues: 55 sheet: -0.28 (0.25), residues: 440 loop : -1.16 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 148 HIS 0.003 0.001 HIS E 327 PHE 0.029 0.002 PHE D 122 TYR 0.024 0.002 TYR A 186 ARG 0.005 0.000 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2598.53 seconds wall clock time: 48 minutes 43.79 seconds (2923.79 seconds total)