Starting phenix.real_space_refine on Wed Nov 15 20:20:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbi_21590/11_2023/6wbi_21590_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbi_21590/11_2023/6wbi_21590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbi_21590/11_2023/6wbi_21590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbi_21590/11_2023/6wbi_21590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbi_21590/11_2023/6wbi_21590_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbi_21590/11_2023/6wbi_21590_updated.pdb" } resolution = 4.39 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= 0.000 sd= 0.003 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 35 5.16 5 C 8139 2.51 5 N 2392 2.21 5 O 2452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 243": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 13018 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 1835 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 13, 'TRANS': 309} Chain breaks: 3 Unresolved non-hydrogen bonds: 777 Unresolved non-hydrogen angles: 991 Unresolved non-hydrogen dihedrals: 634 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 373 Chain: "B" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 1835 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 13, 'TRANS': 309} Chain breaks: 2 Unresolved non-hydrogen bonds: 777 Unresolved non-hydrogen angles: 991 Unresolved non-hydrogen dihedrals: 634 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 373 Chain: "C" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1860 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 223} Link IDs: {'PTRANS': 13, 'TRANS': 313} Chain breaks: 2 Unresolved non-hydrogen bonds: 784 Unresolved non-hydrogen angles: 1000 Unresolved non-hydrogen dihedrals: 639 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 377 Chain: "D" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 1846 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 223} Link IDs: {'PTRANS': 13, 'TRANS': 311} Chain breaks: 2 Unresolved non-hydrogen bonds: 787 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 643 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 382 Chain: "E" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 1870 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain breaks: 2 Unresolved non-hydrogen bonds: 793 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 646 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 382 Chain: "F" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 1870 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain breaks: 2 Unresolved non-hydrogen bonds: 793 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 646 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 382 Chain: "G" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 1861 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PTRANS': 13, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 799 Unresolved non-hydrogen angles: 1019 Unresolved non-hydrogen dihedrals: 652 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 387 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'CBO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.04, per 1000 atoms: 0.62 Number of scatterers: 13018 At special positions: 0 Unit cell: (109.782, 105.678, 123.12, 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 35 16.00 O 2452 8.00 N 2392 7.00 C 8139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.06 Simple disulfide: pdb=" SG CYS C 246 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.02 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.05 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 Time building additional restraints: 6.84 Conformation dependent library (CDL) restraints added in 3.1 seconds 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4436 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 7 sheets defined 68.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 33 through 54 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 100 through 161 Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix removed outlier: 3.974A pdb=" N ALA A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 195 through 203 Processing helix chain 'A' and resid 208 through 235 Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 270 through 295 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 297 through 300 No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 327 through 336 removed outlier: 4.835A pdb=" N LEU A 335 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU A 336 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 343 through 357 Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 33 through 54 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 100 through 161 Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Proline residue: B 133 - end of helix Processing helix chain 'B' and resid 195 through 203 Processing helix chain 'B' and resid 208 through 236 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 270 through 295 Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 297 through 300 No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 327 through 336 removed outlier: 4.525A pdb=" N LEU B 335 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU B 336 " --> pdb=" O TYR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.506A pdb=" N SER B 357 " --> pdb=" O ASN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 33 through 54 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 74 through 88 removed outlier: 3.546A pdb=" N VAL C 88 " --> pdb=" O CYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 109 through 161 Proline residue: C 123 - end of helix removed outlier: 4.915A pdb=" N ALA C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Proline residue: C 133 - end of helix Processing helix chain 'C' and resid 195 through 203 Processing helix chain 'C' and resid 208 through 236 Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 270 through 295 Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 297 through 300 No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 305 through 311 removed outlier: 3.542A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 removed outlier: 5.025A pdb=" N SER C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 357 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'D' and resid 4 through 13 Processing helix chain 'D' and resid 33 through 53 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 74 through 87 Processing helix chain 'D' and resid 100 through 130 Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 133 through 161 Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.570A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 235 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 270 through 295 Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 306 through 311 removed outlier: 3.935A pdb=" N ILE D 311 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 337 Processing helix chain 'D' and resid 339 through 341 No H-bonds generated for 'chain 'D' and resid 339 through 341' Processing helix chain 'D' and resid 343 through 357 Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 33 through 54 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 74 through 87 Processing helix chain 'E' and resid 100 through 129 Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 161 removed outlier: 3.668A pdb=" N ILE E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 208 through 236 Processing helix chain 'E' and resid 251 through 254 Processing helix chain 'E' and resid 270 through 295 Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 305 through 311 removed outlier: 3.971A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 341 removed outlier: 5.689A pdb=" N SER E 340 " --> pdb=" O GLU E 336 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU E 341 " --> pdb=" O GLU E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 357 Processing helix chain 'E' and resid 362 through 369 Processing helix chain 'F' and resid 3 through 13 removed outlier: 3.739A pdb=" N SER F 13 " --> pdb=" O GLU F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 54 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 74 through 88 Processing helix chain 'F' and resid 100 through 130 Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 132 through 161 Processing helix chain 'F' and resid 195 through 203 Processing helix chain 'F' and resid 208 through 235 Processing helix chain 'F' and resid 251 through 253 No H-bonds generated for 'chain 'F' and resid 251 through 253' Processing helix chain 'F' and resid 270 through 295 Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 297 through 300 No H-bonds generated for 'chain 'F' and resid 297 through 300' Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'F' and resid 327 through 341 removed outlier: 5.213A pdb=" N SER F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLU F 341 " --> pdb=" O GLU F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 362 through 369 Processing helix chain 'G' and resid 3 through 13 Processing helix chain 'G' and resid 33 through 53 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 74 through 88 Processing helix chain 'G' and resid 100 through 129 Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 133 through 161 Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.700A pdb=" N ASN G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 236 Processing helix chain 'G' and resid 251 through 253 No H-bonds generated for 'chain 'G' and resid 251 through 253' Processing helix chain 'G' and resid 270 through 295 Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 297 through 300 No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 305 through 311 removed outlier: 3.947A pdb=" N ILE G 311 " --> pdb=" O LYS G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 341 removed outlier: 4.816A pdb=" N SER G 340 " --> pdb=" O GLU G 336 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 357 Processing helix chain 'G' and resid 362 through 369 Processing sheet with id= A, first strand: chain 'A' and resid 243 through 246 Processing sheet with id= B, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= C, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= D, first strand: chain 'D' and resid 244 through 246 Processing sheet with id= E, first strand: chain 'E' and resid 243 through 246 Processing sheet with id= F, first strand: chain 'F' and resid 243 through 246 Processing sheet with id= G, first strand: chain 'G' and resid 243 through 246 1093 hydrogen bonds defined for protein. 3201 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 6.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 13191 1.57 - 1.93: 35 1.93 - 2.28: 0 2.28 - 2.64: 0 2.64 - 3.00: 1 Bond restraints: 13227 Sorted by residual: bond pdb=" C LEU B 333 " pdb=" N LEU B 335 " ideal model delta sigma weight residual 1.332 2.996 -1.663 1.40e-02 5.10e+03 1.41e+04 bond pdb=" CA ALA C 131 " pdb=" C ALA C 131 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.37e-02 5.33e+03 9.50e+00 bond pdb=" CA PHE A 244 " pdb=" CB PHE A 244 " ideal model delta sigma weight residual 1.535 1.502 0.034 2.09e-02 2.29e+03 2.60e+00 bond pdb=" CA PHE G 244 " pdb=" CB PHE G 244 " ideal model delta sigma weight residual 1.535 1.505 0.030 1.90e-02 2.77e+03 2.50e+00 bond pdb=" CA GLY C 360 " pdb=" C GLY C 360 " ideal model delta sigma weight residual 1.516 1.528 -0.012 8.20e-03 1.49e+04 2.08e+00 ... (remaining 13222 not shown) Histogram of bond angle deviations from ideal: 44.24 - 62.28: 1 62.28 - 80.32: 0 80.32 - 98.36: 0 98.36 - 116.41: 8562 116.41 - 134.45: 9866 Bond angle restraints: 18429 Sorted by residual: angle pdb=" O LEU B 333 " pdb=" C LEU B 333 " pdb=" N LEU B 335 " ideal model delta sigma weight residual 122.59 44.24 78.35 1.33e+00 5.65e-01 3.47e+03 angle pdb=" C LEU B 333 " pdb=" N LEU B 335 " pdb=" CA LEU B 335 " ideal model delta sigma weight residual 121.54 134.45 -12.91 1.91e+00 2.74e-01 4.57e+01 angle pdb=" N ILE A 311 " pdb=" CA ILE A 311 " pdb=" C ILE A 311 " ideal model delta sigma weight residual 112.80 108.01 4.79 1.15e+00 7.56e-01 1.73e+01 angle pdb=" CA CYS C 265 " pdb=" CB CYS C 265 " pdb=" SG CYS C 265 " ideal model delta sigma weight residual 114.40 122.79 -8.39 2.30e+00 1.89e-01 1.33e+01 angle pdb=" N SER F 239 " pdb=" CA SER F 239 " pdb=" C SER F 239 " ideal model delta sigma weight residual 113.72 108.71 5.01 1.52e+00 4.33e-01 1.09e+01 ... (remaining 18424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.53: 7641 25.53 - 51.05: 89 51.05 - 76.58: 15 76.58 - 102.11: 6 102.11 - 127.63: 5 Dihedral angle restraints: 7756 sinusoidal: 1030 harmonic: 6726 Sorted by residual: dihedral pdb=" CA LEU B 333 " pdb=" C LEU B 333 " pdb=" N LEU B 335 " pdb=" CA LEU B 335 " ideal model delta harmonic sigma weight residual 180.00 83.00 97.00 0 5.00e+00 4.00e-02 3.76e+02 dihedral pdb=" CB CYS B 66 " pdb=" SG CYS B 66 " pdb=" SG CYS B 265 " pdb=" CB CYS B 265 " ideal model delta sinusoidal sigma weight residual 93.00 19.03 73.97 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS C 66 " pdb=" SG CYS C 66 " pdb=" SG CYS C 265 " pdb=" CB CYS C 265 " ideal model delta sinusoidal sigma weight residual 93.00 38.56 54.44 1 1.00e+01 1.00e-02 4.02e+01 ... (remaining 7753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2298 0.092 - 0.184: 70 0.184 - 0.276: 5 0.276 - 0.368: 1 0.368 - 0.460: 1 Chirality restraints: 2375 Sorted by residual: chirality pdb=" C9 CBO A 401 " pdb=" C10 CBO A 401 " pdb=" C11 CBO A 401 " pdb=" C8 CBO A 401 " both_signs ideal model delta sigma weight residual True 2.68 -2.22 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" C10 CBO A 401 " pdb=" C1 CBO A 401 " pdb=" C5 CBO A 401 " pdb=" C9 CBO A 401 " both_signs ideal model delta sigma weight residual True 2.56 -2.84 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA CYS C 66 " pdb=" N CYS C 66 " pdb=" C CYS C 66 " pdb=" CB CYS C 66 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2372 not shown) Planarity restraints: 2522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 333 " -0.147 2.00e-02 2.50e+03 2.58e-01 6.64e+02 pdb=" C LEU B 333 " 0.395 2.00e-02 2.50e+03 pdb=" O LEU B 333 " -0.294 2.00e-02 2.50e+03 pdb=" N LEU B 335 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 74 " 0.016 2.00e-02 2.50e+03 1.24e-02 3.83e+00 pdb=" CG TRP C 74 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP C 74 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 74 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 74 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 74 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 74 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 74 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 74 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 74 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 123 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO B 124 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.021 5.00e-02 4.00e+02 ... (remaining 2519 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 259 2.67 - 3.23: 15439 3.23 - 3.79: 21874 3.79 - 4.34: 23890 4.34 - 4.90: 37013 Nonbonded interactions: 98475 Sorted by model distance: nonbonded pdb=" O TYR A 331 " pdb=" N LEU A 335 " model vdw 2.117 2.520 nonbonded pdb=" OG SER D 247 " pdb=" O ASP D 261 " model vdw 2.144 2.440 nonbonded pdb=" O TYR C 233 " pdb=" OG SER C 236 " model vdw 2.167 2.440 nonbonded pdb=" OG SER F 247 " pdb=" O ASP F 261 " model vdw 2.172 2.440 nonbonded pdb=" O SER C 65 " pdb=" N LYS C 266 " model vdw 2.190 2.520 ... (remaining 98470 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 2 through 133 or (resid 134 through 135 and (name N or nam \ e CA or name C or name O or name CB )) or resid 136 through 370)) selection = (chain 'B' and (resid 2 through 133 or (resid 134 through 135 and (name N or nam \ e CA or name C or name O or name CB )) or resid 136 through 370)) selection = (chain 'C' and (resid 2 through 30 or resid 33 through 133 or (resid 134 through \ 135 and (name N or name CA or name C or name O or name CB )) or resid 136 throu \ gh 333 or resid 335 through 370)) selection = (chain 'D' and (resid 2 through 14 or resid 32 through 333 or resid 335 through \ 370)) selection = (chain 'E' and (resid 2 through 28 or resid 33 through 133 or (resid 134 through \ 135 and (name N or name CA or name C or name O or name CB )) or resid 136 throu \ gh 333 or resid 335 through 370)) selection = (chain 'F' and (resid 2 through 28 or resid 33 through 133 or (resid 134 through \ 135 and (name N or name CA or name C or name O or name CB )) or resid 136 throu \ gh 333 or resid 335 through 370)) selection = (chain 'G' and (resid 2 through 28 or resid 33 through 333 or resid 335 through \ 370)) } 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: 0.680 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: 3.640 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 40.030 Find NCS groups from input model: 1.120 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.015 1.663 13227 Z= 0.452 Angle : 0.907 78.352 18429 Z= 0.588 Chirality : 0.043 0.460 2375 Planarity : 0.007 0.258 2522 Dihedral : 10.975 127.634 3296 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 1.00 % Allowed : 7.80 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.17), residues: 2238 helix: 0.15 (0.12), residues: 1548 sheet: None (None), residues: 0 loop : -2.04 (0.23), residues: 690 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 114 average time/residue: 0.1956 time to fit residues: 35.8542 Evaluate side-chains 74 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 1.575 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.1048 time to fit residues: 2.4524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 40.0000 chunk 114 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS C 76 GLN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS E 264 GLN ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13227 Z= 0.177 Angle : 0.544 8.111 18429 Z= 0.272 Chirality : 0.042 0.451 2375 Planarity : 0.004 0.043 2522 Dihedral : 7.949 132.793 2324 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.79 % Rotamer: Outliers : 0.60 % Allowed : 4.60 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.54 (0.18), residues: 2240 helix: 2.01 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : -1.56 (0.25), residues: 652 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 114 average time/residue: 0.1739 time to fit residues: 33.1598 Evaluate side-chains 73 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.519 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1068 time to fit residues: 2.1631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 138 optimal weight: 30.0000 chunk 56 optimal weight: 0.9990 chunk 203 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 181 optimal weight: 0.0040 chunk 202 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13227 Z= 0.146 Angle : 0.528 8.323 18429 Z= 0.255 Chirality : 0.042 0.455 2375 Planarity : 0.004 0.047 2522 Dihedral : 7.759 134.745 2324 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.20 % Allowed : 3.40 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.41 (0.19), residues: 2240 helix: 2.66 (0.13), residues: 1598 sheet: None (None), residues: 0 loop : -1.32 (0.25), residues: 642 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 113 average time/residue: 0.1803 time to fit residues: 34.0119 Evaluate side-chains 80 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.443 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1116 time to fit residues: 2.1113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.9990 chunk 153 optimal weight: 0.0770 chunk 105 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 97 optimal weight: 30.0000 chunk 136 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 58 optimal weight: 0.0060 overall best weight: 2.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13227 Z= 0.147 Angle : 0.516 8.153 18429 Z= 0.249 Chirality : 0.041 0.458 2375 Planarity : 0.004 0.046 2522 Dihedral : 7.652 133.724 2324 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.77 (0.19), residues: 2240 helix: 2.92 (0.13), residues: 1594 sheet: -2.42 (1.21), residues: 19 loop : -1.07 (0.26), residues: 627 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1830 time to fit residues: 32.1561 Evaluate side-chains 78 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.3980 chunk 122 optimal weight: 4.9990 chunk 3 optimal weight: 30.0000 chunk 161 optimal weight: 50.0000 chunk 89 optimal weight: 40.0000 chunk 184 optimal weight: 10.0000 chunk 149 optimal weight: 40.0000 chunk 0 optimal weight: 60.0000 chunk 110 optimal weight: 40.0000 chunk 194 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 overall best weight: 5.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13227 Z= 0.214 Angle : 0.551 7.635 18429 Z= 0.276 Chirality : 0.042 0.467 2375 Planarity : 0.004 0.044 2522 Dihedral : 7.761 130.315 2324 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.20 % Allowed : 2.60 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.88 (0.19), residues: 2240 helix: 2.98 (0.13), residues: 1588 sheet: -4.20 (0.89), residues: 5 loop : -0.94 (0.26), residues: 647 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.583 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.1763 time to fit residues: 29.4675 Evaluate side-chains 73 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.529 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 127 optimal weight: 20.0000 chunk 53 optimal weight: 40.0000 chunk 216 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 100 optimal weight: 0.0030 chunk 18 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 overall best weight: 4.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13227 Z= 0.174 Angle : 0.535 8.211 18429 Z= 0.262 Chirality : 0.041 0.458 2375 Planarity : 0.004 0.045 2522 Dihedral : 7.735 132.965 2324 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.06 (0.19), residues: 2240 helix: 3.11 (0.13), residues: 1585 sheet: -2.15 (1.32), residues: 19 loop : -0.79 (0.26), residues: 636 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1913 time to fit residues: 31.6779 Evaluate side-chains 72 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 50.0000 chunk 24 optimal weight: 40.0000 chunk 123 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 182 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 135 optimal weight: 9.9990 chunk 131 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13227 Z= 0.269 Angle : 0.590 9.311 18429 Z= 0.304 Chirality : 0.042 0.466 2375 Planarity : 0.004 0.043 2522 Dihedral : 7.878 129.319 2324 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.91 (0.19), residues: 2240 helix: 2.95 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : -0.80 (0.26), residues: 652 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.506 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1968 time to fit residues: 32.9571 Evaluate side-chains 68 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.509 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 128 optimal weight: 50.0000 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 169 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13227 Z= 0.239 Angle : 0.576 8.874 18429 Z= 0.294 Chirality : 0.042 0.464 2375 Planarity : 0.004 0.043 2522 Dihedral : 7.889 131.110 2324 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.90 (0.19), residues: 2240 helix: 2.96 (0.13), residues: 1584 sheet: None (None), residues: 0 loop : -0.80 (0.26), residues: 656 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.657 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1779 time to fit residues: 27.9832 Evaluate side-chains 72 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.584 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.5980 chunk 206 optimal weight: 70.0000 chunk 188 optimal weight: 20.0000 chunk 201 optimal weight: 0.9980 chunk 121 optimal weight: 40.0000 chunk 87 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 61 optimal weight: 0.0670 chunk 181 optimal weight: 20.0000 chunk 190 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 overall best weight: 2.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13227 Z= 0.150 Angle : 0.541 8.683 18429 Z= 0.263 Chirality : 0.042 0.457 2375 Planarity : 0.004 0.045 2522 Dihedral : 7.745 135.721 2324 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.27 (0.19), residues: 2240 helix: 3.24 (0.13), residues: 1582 sheet: None (None), residues: 0 loop : -0.70 (0.26), residues: 658 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1589 time to fit residues: 27.4819 Evaluate side-chains 75 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 223 optimal weight: 50.0000 chunk 205 optimal weight: 40.0000 chunk 177 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13227 Z= 0.243 Angle : 0.576 7.893 18429 Z= 0.294 Chirality : 0.042 0.470 2375 Planarity : 0.004 0.044 2522 Dihedral : 7.842 130.570 2324 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.12 (0.19), residues: 2240 helix: 3.09 (0.13), residues: 1587 sheet: None (None), residues: 0 loop : -0.67 (0.27), residues: 653 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1667 time to fit residues: 27.2001 Evaluate side-chains 72 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 40.0000 chunk 189 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 26 optimal weight: 0.0070 chunk 49 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 182 optimal weight: 0.3980 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 50.0000 overall best weight: 2.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.037227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.029170 restraints weight = 164811.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.029670 restraints weight = 126682.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.030061 restraints weight = 103380.493| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13227 Z= 0.150 Angle : 0.539 8.309 18429 Z= 0.263 Chirality : 0.042 0.458 2375 Planarity : 0.004 0.045 2522 Dihedral : 7.732 136.089 2324 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.37 (0.19), residues: 2240 helix: 3.28 (0.13), residues: 1579 sheet: -1.45 (1.63), residues: 14 loop : -0.50 (0.27), residues: 647 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1983.64 seconds wall clock time: 36 minutes 54.35 seconds (2214.35 seconds total)