Starting phenix.real_space_refine on Fri Dec 8 14:10:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1r_33571/12_2023/7y1r_33571.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1r_33571/12_2023/7y1r_33571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1r_33571/12_2023/7y1r_33571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1r_33571/12_2023/7y1r_33571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1r_33571/12_2023/7y1r_33571.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1r_33571/12_2023/7y1r_33571.pdb" } resolution = 4.01 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= 0.001 sd= 0.025 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 55 5.16 5 C 5432 2.51 5 N 1469 2.21 5 O 1609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 311": "OD1" <-> "OD2" Residue "E ASP 414": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8565 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2474 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 283} Chain breaks: 4 Chain: "B" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2494 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 286} Chain breaks: 3 Chain: "E" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3332 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 23, 'TRANS': 404} Chain breaks: 2 Chain: "L" 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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: 6 Unresolved non-hydrogen chiralities: 3 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.43, per 1000 atoms: 0.52 Number of scatterers: 8565 At special positions: 0 Unit cell: (98.115, 99.17, 132.93, 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 55 16.00 O 1609 8.00 N 1469 7.00 C 5432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 256 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS E 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 256 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 327 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 297 " - pdb=" SG CYS B 360 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG D 1 " - " NAG D 2 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG B 401 " - " ASN B 53 " " NAG C 1 " - " ASN A 53 " " NAG D 1 " - " ASN B 107 " " NAG F 1 " - " ASN E 56 " " NAG G 1 " - " ASN E 137 " " NAG H 1 " - " ASN E 390 " " NAG I 1 " - " ASN E 214 " " NAG L 1 " - " ASN A 107 " Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 2.0 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1986 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 19 sheets defined 16.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 15 through 29 Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.687A pdb=" N ASP A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 removed outlier: 3.518A pdb=" N TYR A 92 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 93 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.908A pdb=" N GLY A 173 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 4.394A pdb=" N CYS A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.507A pdb=" N ALA A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'B' and resid 5 through 28 removed outlier: 4.101A pdb=" N MET B 9 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 10 " --> pdb=" O THR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.714A pdb=" N ASP B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 95 removed outlier: 4.183A pdb=" N LYS B 94 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 171 through 181 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 308 through 318 removed outlier: 4.264A pdb=" N ALA B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 86 removed outlier: 3.751A pdb=" N GLN E 84 " --> pdb=" O GLY E 81 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 135 Processing helix chain 'E' and resid 326 through 332 removed outlier: 3.885A pdb=" N LEU E 330 " --> pdb=" O PRO E 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 78 removed outlier: 4.180A pdb=" N LYS A 77 " --> pdb=" O GLN B 349 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS B 344 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL B 341 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS B 346 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR B 339 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASN B 352 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU B 333 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 82 removed outlier: 3.579A pdb=" N MET A 232 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG A 123 " --> pdb=" O MET A 232 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 143 removed outlier: 4.557A pdb=" N SER A 154 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLN A 143 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR A 152 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 267 removed outlier: 4.297A pdb=" N CYS A 265 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 292 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 272 removed outlier: 3.627A pdb=" N ILE A 271 " --> pdb=" O TYR A 288 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 288 " --> pdb=" O ILE A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 338 removed outlier: 8.038A pdb=" N CYS A 327 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N CYS A 358 " --> pdb=" O CYS A 327 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ARG A 356 " --> pdb=" O PRO A 329 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ALA A 331 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 354 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU A 333 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN A 352 " --> pdb=" O GLU A 333 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 78 through 81 removed outlier: 3.642A pdb=" N LEU B 231 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 128 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 167 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 107 removed outlier: 4.038A pdb=" N PHE B 106 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU B 186 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 267 removed outlier: 3.906A pdb=" N CYS B 265 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 294 " --> pdb=" O CYS B 265 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 267 " --> pdb=" O PHE B 292 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B 292 " --> pdb=" O ARG B 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 271 through 272 removed outlier: 3.835A pdb=" N ILE B 271 " --> pdb=" O TYR B 288 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 288 " --> pdb=" O ILE B 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 328 through 329 removed outlier: 3.905A pdb=" N VAL B 328 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 46 through 47 removed outlier: 6.494A pdb=" N LEU E 46 " --> pdb=" O HIS E 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 93 through 94 removed outlier: 6.992A pdb=" N VAL E 144 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 153 through 154 removed outlier: 3.862A pdb=" N LEU E 154 " --> pdb=" O GLU E 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 189 through 192 removed outlier: 6.698A pdb=" N ARG E 190 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU E 237 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 201 through 202 removed outlier: 4.176A pdb=" N ILE E 202 " --> pdb=" O TRP E 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 349 through 350 removed outlier: 7.387A pdb=" N LEU E 349 " --> pdb=" O HIS E 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 364 through 366 removed outlier: 3.519A pdb=" N SER E 392 " --> pdb=" O LEU E 365 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP E 414 " --> pdb=" O PHE E 389 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU E 391 " --> pdb=" O ASP E 414 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER E 450 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET E 415 " --> pdb=" O SER E 450 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 471 through 473 removed outlier: 6.279A pdb=" N LEU E 472 " --> pdb=" O SER E 499 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 130 hydrogen bonds defined for protein. 351 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: 1.98 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2757 1.35 - 1.46: 2003 1.46 - 1.58: 3917 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 8754 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NAG B 401 " pdb=" O5 NAG B 401 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.31e+00 ... (remaining 8749 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.89: 334 106.89 - 113.73: 4885 113.73 - 120.57: 3195 120.57 - 127.41: 3359 127.41 - 134.26: 101 Bond angle restraints: 11874 Sorted by residual: angle pdb=" C LYS A 280 " pdb=" N TRP A 281 " pdb=" CA TRP A 281 " ideal model delta sigma weight residual 121.58 115.05 6.53 1.95e+00 2.63e-01 1.12e+01 angle pdb=" CA ARG A 29 " pdb=" CB ARG A 29 " pdb=" CG ARG A 29 " ideal model delta sigma weight residual 114.10 119.80 -5.70 2.00e+00 2.50e-01 8.11e+00 angle pdb=" CA MET E 443 " pdb=" CB MET E 443 " pdb=" CG MET E 443 " ideal model delta sigma weight residual 114.10 119.43 -5.33 2.00e+00 2.50e-01 7.11e+00 angle pdb=" CA TRP A 281 " pdb=" CB TRP A 281 " pdb=" CG TRP A 281 " ideal model delta sigma weight residual 113.60 118.60 -5.00 1.90e+00 2.77e-01 6.92e+00 angle pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " pdb=" CD LYS B 15 " ideal model delta sigma weight residual 111.30 117.18 -5.88 2.30e+00 1.89e-01 6.54e+00 ... (remaining 11869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.59: 5131 22.59 - 45.17: 338 45.17 - 67.76: 26 67.76 - 90.34: 24 90.34 - 112.93: 3 Dihedral angle restraints: 5522 sinusoidal: 2467 harmonic: 3055 Sorted by residual: dihedral pdb=" CB CYS A 4 " pdb=" SG CYS A 4 " pdb=" SG CYS E 201 " pdb=" CB CYS E 201 " ideal model delta sinusoidal sigma weight residual 93.00 177.78 -84.78 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS A 264 " pdb=" SG CYS A 264 " pdb=" SG CYS A 327 " pdb=" CB CYS A 327 " ideal model delta sinusoidal sigma weight residual 93.00 170.99 -77.99 1 1.00e+01 1.00e-02 7.60e+01 dihedral pdb=" CB CYS B 293 " pdb=" SG CYS B 293 " pdb=" SG CYS B 358 " pdb=" CB CYS B 358 " ideal model delta sinusoidal sigma weight residual 93.00 153.93 -60.93 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 5519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1161 0.054 - 0.109: 195 0.109 - 0.163: 20 0.163 - 0.217: 2 0.217 - 0.272: 6 Chirality restraints: 1384 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1381 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 159 " -0.064 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO B 160 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " -0.020 2.00e-02 2.50e+03 1.93e-02 9.31e+00 pdb=" CG TRP A 281 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 279 " -0.016 2.00e-02 2.50e+03 1.27e-02 4.03e+00 pdb=" CG TRP A 279 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 279 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 279 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 279 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 279 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 279 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 279 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 279 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 279 " -0.002 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1126 2.76 - 3.30: 7937 3.30 - 3.83: 13107 3.83 - 4.37: 14297 4.37 - 4.90: 24519 Nonbonded interactions: 60986 Sorted by model distance: nonbonded pdb=" OG SER E 100 " pdb=" OE1 GLU E 101 " model vdw 2.227 2.440 nonbonded pdb=" O ALA B 76 " pdb=" OG1 THR B 234 " model vdw 2.270 2.440 nonbonded pdb=" OE1 GLU B 125 " pdb=" OG SER B 168 " model vdw 2.273 2.440 nonbonded pdb=" O SER E 337 " pdb=" OG1 THR E 361 " model vdw 2.291 2.440 nonbonded pdb=" ND2 ASN A 155 " pdb=" OH TYR B 152 " model vdw 2.322 2.520 ... (remaining 60981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 196 or resid 225 through 240 or resid 255 throug \ h 361)) selection = (chain 'B' and (resid 4 through 60 or resid 73 through 180 or resid 188 through \ 196 or resid 225 through 240 or resid 255 through 361)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' } 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 group one per residue 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: 2.630 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: 0.000 Extract box with map and model: 8.570 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.320 Find NCS groups from input model: 0.410 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5420 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8754 Z= 0.206 Angle : 0.704 7.482 11874 Z= 0.303 Chirality : 0.044 0.272 1384 Planarity : 0.005 0.099 1497 Dihedral : 14.463 112.926 3497 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.79 (0.24), residues: 1017 helix: 0.25 (0.46), residues: 130 sheet: -1.23 (0.49), residues: 125 loop : -2.57 (0.19), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 281 HIS 0.006 0.001 HIS A 138 PHE 0.012 0.001 PHE A 257 TYR 0.023 0.001 TYR B 74 ARG 0.006 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2304 time to fit residues: 51.5933 Evaluate side-chains 157 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8754 Z= 0.257 Angle : 0.729 8.881 11874 Z= 0.342 Chirality : 0.047 0.342 1384 Planarity : 0.006 0.084 1497 Dihedral : 9.495 93.480 1454 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.85 (0.24), residues: 1017 helix: -0.09 (0.43), residues: 140 sheet: -1.62 (0.42), residues: 160 loop : -2.53 (0.20), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 279 HIS 0.012 0.001 HIS B 138 PHE 0.016 0.002 PHE A 106 TYR 0.021 0.002 TYR B 314 ARG 0.004 0.001 ARG E 501 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.877 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2252 time to fit residues: 54.9899 Evaluate side-chains 161 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8754 Z= 0.181 Angle : 0.651 9.405 11874 Z= 0.294 Chirality : 0.042 0.245 1384 Planarity : 0.004 0.069 1497 Dihedral : 9.201 89.617 1454 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.31 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.73 (0.24), residues: 1017 helix: 0.19 (0.44), residues: 139 sheet: -1.67 (0.42), residues: 165 loop : -2.44 (0.20), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 281 HIS 0.005 0.001 HIS A 289 PHE 0.011 0.001 PHE B 228 TYR 0.021 0.001 TYR A 52 ARG 0.004 0.000 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.793 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2311 time to fit residues: 54.5253 Evaluate side-chains 160 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0570 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 0.0170 chunk 88 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8754 Z= 0.160 Angle : 0.643 9.728 11874 Z= 0.288 Chirality : 0.042 0.264 1384 Planarity : 0.004 0.061 1497 Dihedral : 8.513 85.841 1454 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.49 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.70 (0.24), residues: 1017 helix: 0.32 (0.45), residues: 138 sheet: -1.62 (0.43), residues: 163 loop : -2.45 (0.20), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 301 HIS 0.008 0.001 HIS A 283 PHE 0.009 0.001 PHE A 106 TYR 0.012 0.001 TYR B 74 ARG 0.006 0.000 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2199 time to fit residues: 54.0197 Evaluate side-chains 164 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 0.0040 chunk 40 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 0.0870 chunk 88 optimal weight: 0.6980 chunk 24 optimal weight: 0.0030 chunk 33 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 overall best weight: 0.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN E 88 HIS ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5825 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8754 Z= 0.136 Angle : 0.630 9.636 11874 Z= 0.280 Chirality : 0.041 0.241 1384 Planarity : 0.004 0.051 1497 Dihedral : 8.044 82.751 1454 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.65 (0.25), residues: 1017 helix: 0.62 (0.46), residues: 132 sheet: -1.69 (0.42), residues: 163 loop : -2.42 (0.20), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 281 HIS 0.003 0.001 HIS E 40 PHE 0.011 0.001 PHE E 389 TYR 0.010 0.001 TYR B 270 ARG 0.003 0.000 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2317 time to fit residues: 55.4995 Evaluate side-chains 164 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.0270 chunk 24 optimal weight: 0.0030 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 32 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 95 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.1826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8754 Z= 0.132 Angle : 0.624 9.607 11874 Z= 0.275 Chirality : 0.040 0.246 1384 Planarity : 0.004 0.046 1497 Dihedral : 7.604 80.015 1454 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.61 (0.24), residues: 1017 helix: 0.61 (0.45), residues: 138 sheet: -1.62 (0.45), residues: 152 loop : -2.42 (0.20), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 301 HIS 0.003 0.001 HIS E 40 PHE 0.017 0.001 PHE E 322 TYR 0.024 0.001 TYR A 52 ARG 0.005 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2403 time to fit residues: 58.5149 Evaluate side-chains 162 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8754 Z= 0.247 Angle : 0.762 11.464 11874 Z= 0.347 Chirality : 0.046 0.272 1384 Planarity : 0.005 0.044 1497 Dihedral : 7.568 76.505 1454 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.77 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.73 (0.24), residues: 1017 helix: 0.43 (0.45), residues: 134 sheet: -1.55 (0.40), residues: 182 loop : -2.53 (0.21), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 301 HIS 0.007 0.001 HIS A 283 PHE 0.023 0.002 PHE E 389 TYR 0.023 0.002 TYR B 270 ARG 0.005 0.001 ARG E 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.993 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2369 time to fit residues: 59.4167 Evaluate side-chains 174 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 0.2980 chunk 94 optimal weight: 0.0980 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8754 Z= 0.172 Angle : 0.682 11.842 11874 Z= 0.308 Chirality : 0.044 0.385 1384 Planarity : 0.004 0.043 1497 Dihedral : 7.134 73.131 1454 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.73 (0.24), residues: 1017 helix: 0.80 (0.47), residues: 128 sheet: -1.81 (0.40), residues: 170 loop : -2.49 (0.20), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 301 HIS 0.007 0.001 HIS E 342 PHE 0.013 0.001 PHE E 389 TYR 0.027 0.002 TYR B 74 ARG 0.005 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.899 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2258 time to fit residues: 56.1272 Evaluate side-chains 177 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.0570 chunk 59 optimal weight: 0.0370 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8754 Z= 0.165 Angle : 0.686 10.825 11874 Z= 0.308 Chirality : 0.043 0.307 1384 Planarity : 0.005 0.048 1497 Dihedral : 6.859 69.569 1454 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.70 (0.24), residues: 1017 helix: 0.71 (0.46), residues: 134 sheet: -1.67 (0.42), residues: 161 loop : -2.52 (0.20), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 279 HIS 0.004 0.001 HIS E 40 PHE 0.019 0.001 PHE E 322 TYR 0.013 0.001 TYR B 270 ARG 0.005 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.882 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2392 time to fit residues: 56.0669 Evaluate side-chains 166 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 chunk 80 optimal weight: 0.0470 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 49 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 0.0370 chunk 74 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN E 102 ASN E 198 ASN ** E 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8754 Z= 0.157 Angle : 0.692 10.730 11874 Z= 0.312 Chirality : 0.043 0.265 1384 Planarity : 0.004 0.052 1497 Dihedral : 6.697 66.261 1454 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.11 % Allowed : 0.65 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.66 (0.24), residues: 1017 helix: 0.66 (0.46), residues: 128 sheet: -1.57 (0.41), residues: 168 loop : -2.46 (0.20), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 279 HIS 0.007 0.001 HIS E 342 PHE 0.016 0.001 PHE E 389 TYR 0.019 0.001 TYR B 314 ARG 0.005 0.000 ARG A 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 0.886 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 0.2529 time to fit residues: 58.5784 Evaluate side-chains 163 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0849 time to fit residues: 1.5726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 0.0070 chunk 83 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 0.0770 chunk 58 optimal weight: 0.0170 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 143 GLN E 102 ASN ** E 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.185014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.164721 restraints weight = 14960.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.168647 restraints weight = 9219.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.171402 restraints weight = 6438.754| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8754 Z= 0.154 Angle : 0.676 10.698 11874 Z= 0.305 Chirality : 0.042 0.250 1384 Planarity : 0.004 0.053 1497 Dihedral : 6.435 60.796 1454 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.11 % Allowed : 0.54 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.65 (0.24), residues: 1017 helix: 0.59 (0.46), residues: 127 sheet: -1.69 (0.40), residues: 177 loop : -2.40 (0.20), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 279 HIS 0.008 0.001 HIS E 342 PHE 0.021 0.001 PHE E 322 TYR 0.041 0.001 TYR A 52 ARG 0.007 0.000 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2165.26 seconds wall clock time: 40 minutes 0.92 seconds (2400.92 seconds total)