Starting phenix.real_space_refine on Tue Sep 24 08:21:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/09_2024/8jv5_36668.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/09_2024/8jv5_36668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/09_2024/8jv5_36668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/09_2024/8jv5_36668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/09_2024/8jv5_36668.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/09_2024/8jv5_36668.cif" } resolution = 3.23 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= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Br 6 7.06 5 S 51 5.16 5 C 4733 2.51 5 N 1249 2.21 5 O 1441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7480 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2428 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 297} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2428 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 297} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2435 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 298} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'NAG': 3, 'P73': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'NAG': 3, 'P73': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'NAG': 3, 'P73': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.18, per 1000 atoms: 0.69 Number of scatterers: 7480 At special positions: 0 Unit cell: (91.3, 85.49, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 6 34.99 S 51 16.00 O 1441 8.00 N 1249 7.00 C 4733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 273 " distance=2.02 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 220 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 264 " - pdb=" SG CYS C 273 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 502 " - " ASN A 213 " " NAG A 503 " - " ASN A 187 " " NAG A 504 " - " ASN A 78 " " NAG B 502 " - " ASN B 213 " " NAG B 503 " - " ASN B 187 " " NAG B 504 " - " ASN B 78 " " NAG C 502 " - " ASN C 213 " " NAG C 503 " - " ASN C 187 " " NAG C 504 " - " ASN C 78 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 15 sheets defined 20.8% alpha, 47.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 43 through 50 removed outlier: 3.702A pdb=" N ILE A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 213 through 219 removed outlier: 3.910A pdb=" N HIS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 Processing helix chain 'A' and resid 245 through 253 removed outlier: 4.102A pdb=" N ARG A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 335 through 358 Processing helix chain 'B' and resid 44 through 50 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 213 through 219 removed outlier: 3.905A pdb=" N HIS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 241 Processing helix chain 'B' and resid 245 through 253 removed outlier: 4.105A pdb=" N ARG B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 335 through 358 Processing helix chain 'C' and resid 43 through 50 removed outlier: 3.803A pdb=" N ILE C 47 " --> pdb=" O ILE C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 213 through 219 removed outlier: 3.902A pdb=" N HIS C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'C' and resid 245 through 253 removed outlier: 4.110A pdb=" N ARG C 252 " --> pdb=" O ILE C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 335 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.784A pdb=" N GLY A 254 " --> pdb=" O ARG A 321 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ASP A 323 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET A 256 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET A 325 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL A 258 " --> pdb=" O MET A 325 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE A 327 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE A 260 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N GLN A 329 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP A 262 " --> pdb=" O GLN A 329 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY A 331 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N CYS A 264 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N PHE A 333 " --> pdb=" O CYS A 264 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 153 removed outlier: 10.061A pdb=" N VAL A 147 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N TRP A 167 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N THR A 149 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N LEU A 165 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ARG A 151 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N SER A 101 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL A 324 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE A 103 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHE A 322 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU A 105 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 320 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 113 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ARG A 312 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR A 115 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLU A 310 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 64 through 72 Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 77 Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.784A pdb=" N GLY B 254 " --> pdb=" O ARG B 321 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASP B 323 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET B 256 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N MET B 325 " --> pdb=" O MET B 256 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 258 " --> pdb=" O MET B 325 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE B 327 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE B 260 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLN B 329 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP B 262 " --> pdb=" O GLN B 329 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLY B 331 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N CYS B 264 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N PHE B 333 " --> pdb=" O CYS B 264 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 153 removed outlier: 10.057A pdb=" N VAL B 147 " --> pdb=" O TRP B 167 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N TRP B 167 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N THR B 149 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N LEU B 165 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG B 151 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER B 101 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL B 324 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N PHE B 103 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE B 322 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU B 105 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 320 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 113 " --> pdb=" O ARG B 312 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ARG B 312 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR B 115 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N GLU B 310 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 64 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 75 through 77 Processing sheet with id=AB2, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.769A pdb=" N GLY C 254 " --> pdb=" O ARG C 321 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ASP C 323 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET C 256 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET C 325 " --> pdb=" O MET C 256 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 258 " --> pdb=" O MET C 325 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE C 327 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE C 260 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLN C 329 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP C 262 " --> pdb=" O GLN C 329 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY C 331 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N CYS C 264 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N PHE C 333 " --> pdb=" O CYS C 264 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 147 through 153 removed outlier: 10.058A pdb=" N VAL C 147 " --> pdb=" O TRP C 167 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N TRP C 167 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N THR C 149 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N LEU C 165 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG C 151 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N SER C 101 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL C 324 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE C 103 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE C 322 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU C 105 " --> pdb=" O ILE C 320 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE C 320 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN C 113 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ARG C 312 " --> pdb=" O ASN C 113 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR C 115 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU C 310 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 64 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 64 through 72 Processing sheet with id=AB6, first strand: chain 'C' and resid 75 through 77 300 hydrogen bonds defined for protein. 774 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: 2.09 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2065 1.33 - 1.48: 2359 1.48 - 1.63: 3155 1.63 - 1.79: 7 1.79 - 1.94: 65 Bond restraints: 7651 Sorted by residual: bond pdb=" C10 P73 A 501 " pdb=" N11 P73 A 501 " ideal model delta sigma weight residual 1.373 1.454 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C10 P73 B 501 " pdb=" N11 P73 B 501 " ideal model delta sigma weight residual 1.373 1.453 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C10 P73 C 501 " pdb=" N11 P73 C 501 " ideal model delta sigma weight residual 1.373 1.452 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C10 P73 B 501 " pdb=" N09 P73 B 501 " ideal model delta sigma weight residual 1.377 1.454 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C10 P73 C 501 " pdb=" N09 P73 C 501 " ideal model delta sigma weight residual 1.377 1.453 -0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 7646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 10043 1.41 - 2.81: 314 2.81 - 4.22: 65 4.22 - 5.62: 10 5.62 - 7.03: 6 Bond angle restraints: 10438 Sorted by residual: angle pdb=" C ASP B 229 " pdb=" N CYS B 230 " pdb=" CA CYS B 230 " ideal model delta sigma weight residual 120.67 117.43 3.24 1.34e+00 5.57e-01 5.84e+00 angle pdb=" C ASP C 229 " pdb=" N CYS C 230 " pdb=" CA CYS C 230 " ideal model delta sigma weight residual 120.67 117.48 3.19 1.34e+00 5.57e-01 5.68e+00 angle pdb=" CA CYS B 220 " pdb=" CB CYS B 220 " pdb=" SG CYS B 220 " ideal model delta sigma weight residual 114.40 119.86 -5.46 2.30e+00 1.89e-01 5.64e+00 angle pdb=" CA CYS C 220 " pdb=" CB CYS C 220 " pdb=" SG CYS C 220 " ideal model delta sigma weight residual 114.40 119.85 -5.45 2.30e+00 1.89e-01 5.61e+00 angle pdb=" N09 P73 C 501 " pdb=" C10 P73 C 501 " pdb=" N11 P73 C 501 " ideal model delta sigma weight residual 113.26 120.29 -7.03 3.00e+00 1.11e-01 5.48e+00 ... (remaining 10433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.23: 4215 15.23 - 30.47: 341 30.47 - 45.70: 80 45.70 - 60.94: 24 60.94 - 76.17: 12 Dihedral angle restraints: 4672 sinusoidal: 1927 harmonic: 2745 Sorted by residual: dihedral pdb=" CB CYS C 220 " pdb=" SG CYS C 220 " pdb=" SG CYS C 230 " pdb=" CB CYS C 230 " ideal model delta sinusoidal sigma weight residual 93.00 157.49 -64.49 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 230 " pdb=" CB CYS A 230 " ideal model delta sinusoidal sigma weight residual 93.00 157.43 -64.43 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" CB CYS B 220 " pdb=" SG CYS B 220 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual 93.00 157.33 -64.33 1 1.00e+01 1.00e-02 5.44e+01 ... (remaining 4669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 638 0.026 - 0.053: 315 0.053 - 0.079: 106 0.079 - 0.106: 85 0.106 - 0.132: 46 Chirality restraints: 1190 Sorted by residual: chirality pdb=" CA ILE B 94 " pdb=" N ILE B 94 " pdb=" C ILE B 94 " pdb=" CB ILE B 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" C1 NAG A 504 " pdb=" ND2 ASN A 78 " pdb=" C2 NAG A 504 " pdb=" O5 NAG A 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE C 94 " pdb=" N ILE C 94 " pdb=" C ILE C 94 " pdb=" CB ILE C 94 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1187 not shown) Planarity restraints: 1363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 198 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO C 199 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 199 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 199 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 198 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO A 199 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 198 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO B 199 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 199 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 199 " 0.023 5.00e-02 4.00e+02 ... (remaining 1360 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2290 2.83 - 3.35: 6419 3.35 - 3.86: 11685 3.86 - 4.38: 13688 4.38 - 4.90: 24128 Nonbonded interactions: 58210 Sorted by model distance: nonbonded pdb=" NE ARG B 281 " pdb=" OD1 ASP B 283 " model vdw 2.312 3.120 nonbonded pdb=" NE ARG A 281 " pdb=" OD1 ASP A 283 " model vdw 2.318 3.120 nonbonded pdb=" OD2 ASP B 99 " pdb=" OH TYR C 295 " model vdw 2.322 3.040 nonbonded pdb=" NE ARG C 281 " pdb=" OD1 ASP C 283 " model vdw 2.322 3.120 nonbonded pdb=" OD2 ASP A 99 " pdb=" OH TYR B 295 " model vdw 2.326 3.040 ... (remaining 58205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 43 through 358 or resid 501 through 504)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.270 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.005 0.081 7651 Z= 0.340 Angle : 0.629 7.026 10438 Z= 0.320 Chirality : 0.045 0.132 1190 Planarity : 0.005 0.044 1354 Dihedral : 12.601 76.169 2867 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.76 % Allowed : 3.29 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.88 (0.27), residues: 943 helix: 1.17 (0.44), residues: 174 sheet: 1.29 (0.29), residues: 330 loop : -0.16 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 262 HIS 0.000 0.000 HIS B 132 PHE 0.011 0.001 PHE B 327 TYR 0.008 0.001 TYR C 318 ARG 0.003 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ARG cc_start: 0.6841 (mtp85) cc_final: 0.6515 (mtm180) REVERT: B 72 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7578 (mtpp) outliers start: 6 outliers final: 0 residues processed: 155 average time/residue: 0.2378 time to fit residues: 46.9578 Evaluate side-chains 95 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 30.0000 chunk 24 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 247 GLN B 247 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7651 Z= 0.261 Angle : 0.577 6.217 10438 Z= 0.304 Chirality : 0.045 0.152 1190 Planarity : 0.004 0.038 1354 Dihedral : 7.106 53.858 1231 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.63 % Allowed : 10.38 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.74 (0.27), residues: 943 helix: 0.97 (0.42), residues: 194 sheet: 1.30 (0.29), residues: 335 loop : -0.39 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 262 HIS 0.000 0.000 HIS A 132 PHE 0.011 0.002 PHE B 103 TYR 0.008 0.001 TYR C 318 ARG 0.003 0.001 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7860 (t0) cc_final: 0.7656 (t0) REVERT: A 200 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8336 (ttmm) REVERT: A 276 ARG cc_start: 0.6868 (mtp85) cc_final: 0.6436 (mtm-85) REVERT: B 72 LYS cc_start: 0.7812 (mtmm) cc_final: 0.7538 (mtpp) REVERT: C 261 ARG cc_start: 0.8345 (ttt-90) cc_final: 0.8123 (ttt-90) outliers start: 5 outliers final: 4 residues processed: 103 average time/residue: 0.2221 time to fit residues: 30.0057 Evaluate side-chains 96 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 221 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.4980 chunk 26 optimal weight: 0.2980 chunk 70 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 0.0470 chunk 75 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7651 Z= 0.151 Angle : 0.515 6.962 10438 Z= 0.271 Chirality : 0.044 0.149 1190 Planarity : 0.004 0.035 1354 Dihedral : 6.847 59.013 1231 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.03 % Allowed : 11.39 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.27), residues: 943 helix: 1.44 (0.43), residues: 183 sheet: 1.55 (0.29), residues: 318 loop : -0.61 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 167 HIS 0.000 0.000 HIS C 132 PHE 0.007 0.001 PHE C 103 TYR 0.007 0.001 TYR C 92 ARG 0.002 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7753 (t0) cc_final: 0.7545 (t0) REVERT: A 200 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8275 (ttmm) REVERT: A 276 ARG cc_start: 0.6851 (mtp85) cc_final: 0.6355 (mtm-85) REVERT: B 72 LYS cc_start: 0.7743 (mtmm) cc_final: 0.7513 (mtpp) REVERT: B 261 ARG cc_start: 0.8264 (ttt-90) cc_final: 0.7975 (ttt-90) REVERT: C 268 MET cc_start: 0.7637 (mmm) cc_final: 0.7423 (mmm) outliers start: 16 outliers final: 12 residues processed: 98 average time/residue: 0.2431 time to fit residues: 30.6183 Evaluate side-chains 99 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7651 Z= 0.283 Angle : 0.578 10.040 10438 Z= 0.302 Chirality : 0.045 0.147 1190 Planarity : 0.004 0.033 1354 Dihedral : 6.611 57.897 1231 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.66 % Allowed : 12.28 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.56 (0.27), residues: 943 helix: 1.23 (0.42), residues: 185 sheet: 1.00 (0.29), residues: 336 loop : -0.50 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 167 HIS 0.001 0.000 HIS C 132 PHE 0.015 0.002 PHE B 103 TYR 0.011 0.001 TYR A 318 ARG 0.003 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.745 Fit side-chains REVERT: A 61 ASP cc_start: 0.7895 (t0) cc_final: 0.7694 (t0) REVERT: A 164 VAL cc_start: 0.6463 (m) cc_final: 0.6107 (m) REVERT: A 276 ARG cc_start: 0.7008 (mtp85) cc_final: 0.6569 (mtm-85) REVERT: B 261 ARG cc_start: 0.8330 (ttt-90) cc_final: 0.8073 (ttt-90) REVERT: C 79 THR cc_start: 0.7885 (t) cc_final: 0.7479 (p) REVERT: C 268 MET cc_start: 0.7777 (mmm) cc_final: 0.7557 (mmm) REVERT: C 285 LYS cc_start: 0.7508 (mtpt) cc_final: 0.7301 (ttmm) outliers start: 21 outliers final: 17 residues processed: 102 average time/residue: 0.2228 time to fit residues: 29.8190 Evaluate side-chains 107 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7651 Z= 0.236 Angle : 0.558 9.243 10438 Z= 0.293 Chirality : 0.045 0.153 1190 Planarity : 0.004 0.033 1354 Dihedral : 6.228 50.886 1231 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.04 % Allowed : 12.91 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.60 (0.27), residues: 943 helix: 1.28 (0.42), residues: 185 sheet: 1.03 (0.29), residues: 328 loop : -0.47 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 167 HIS 0.000 0.000 HIS B 132 PHE 0.010 0.001 PHE B 103 TYR 0.011 0.001 TYR C 318 ARG 0.003 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 0.744 Fit side-chains REVERT: A 108 MET cc_start: 0.8647 (ptp) cc_final: 0.8434 (ptp) REVERT: A 164 VAL cc_start: 0.6293 (m) cc_final: 0.6057 (m) REVERT: A 276 ARG cc_start: 0.7018 (mtp85) cc_final: 0.6544 (mtm-85) REVERT: A 286 ASP cc_start: 0.7107 (t70) cc_final: 0.6834 (t0) REVERT: B 276 ARG cc_start: 0.7712 (mpp80) cc_final: 0.7485 (mtm-85) REVERT: B 286 ASP cc_start: 0.7246 (t70) cc_final: 0.6945 (t0) REVERT: C 79 THR cc_start: 0.7797 (t) cc_final: 0.7327 (p) REVERT: C 268 MET cc_start: 0.7783 (mmm) cc_final: 0.7477 (mtt) REVERT: C 285 LYS cc_start: 0.7517 (mtpt) cc_final: 0.7296 (ttmm) outliers start: 24 outliers final: 17 residues processed: 106 average time/residue: 0.2217 time to fit residues: 30.6741 Evaluate side-chains 107 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7651 Z= 0.342 Angle : 0.614 8.698 10438 Z= 0.323 Chirality : 0.046 0.148 1190 Planarity : 0.005 0.035 1354 Dihedral : 6.158 46.726 1231 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.29 % Allowed : 13.92 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.42 (0.27), residues: 943 helix: 1.10 (0.42), residues: 185 sheet: 0.83 (0.28), residues: 330 loop : -0.47 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 272 HIS 0.000 0.000 HIS C 132 PHE 0.015 0.002 PHE B 103 TYR 0.011 0.002 TYR C 318 ARG 0.006 0.001 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.741 Fit side-chains REVERT: A 79 THR cc_start: 0.7855 (t) cc_final: 0.7290 (p) REVERT: A 276 ARG cc_start: 0.7088 (mtp85) cc_final: 0.6655 (mtm-85) REVERT: A 286 ASP cc_start: 0.7215 (t70) cc_final: 0.6931 (t0) REVERT: B 191 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8125 (tp) REVERT: B 261 ARG cc_start: 0.8407 (ttt-90) cc_final: 0.8204 (ttt-90) REVERT: B 276 ARG cc_start: 0.7789 (mpp80) cc_final: 0.7585 (mtm-85) REVERT: B 286 ASP cc_start: 0.7426 (t70) cc_final: 0.7119 (t0) REVERT: C 79 THR cc_start: 0.7699 (t) cc_final: 0.7235 (p) REVERT: C 191 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8098 (tp) REVERT: C 268 MET cc_start: 0.7828 (mmm) cc_final: 0.7491 (mtt) REVERT: C 285 LYS cc_start: 0.7632 (mtpt) cc_final: 0.7408 (ttmm) REVERT: C 286 ASP cc_start: 0.7168 (t70) cc_final: 0.6928 (t0) outliers start: 26 outliers final: 16 residues processed: 107 average time/residue: 0.2186 time to fit residues: 30.6540 Evaluate side-chains 108 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 0.0020 chunk 89 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7651 Z= 0.179 Angle : 0.542 7.872 10438 Z= 0.286 Chirality : 0.044 0.162 1190 Planarity : 0.004 0.035 1354 Dihedral : 5.534 34.998 1231 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.78 % Allowed : 14.81 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.84 (0.27), residues: 943 helix: 1.90 (0.44), residues: 167 sheet: 1.29 (0.29), residues: 310 loop : -0.45 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 167 HIS 0.000 0.000 HIS A 132 PHE 0.011 0.001 PHE C 103 TYR 0.008 0.001 TYR B 92 ARG 0.006 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 79 THR cc_start: 0.7841 (t) cc_final: 0.7256 (p) REVERT: A 276 ARG cc_start: 0.7023 (mtp85) cc_final: 0.6540 (mtm-85) REVERT: A 286 ASP cc_start: 0.7188 (t70) cc_final: 0.6914 (t0) REVERT: B 276 ARG cc_start: 0.7682 (mpp80) cc_final: 0.7475 (mtm-85) REVERT: B 286 ASP cc_start: 0.7386 (t70) cc_final: 0.7097 (t0) REVERT: C 79 THR cc_start: 0.7704 (t) cc_final: 0.7197 (p) REVERT: C 268 MET cc_start: 0.7810 (mmm) cc_final: 0.7470 (mtt) REVERT: C 286 ASP cc_start: 0.7119 (t70) cc_final: 0.6872 (t0) outliers start: 22 outliers final: 15 residues processed: 107 average time/residue: 0.2162 time to fit residues: 30.5657 Evaluate side-chains 104 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 8.9990 chunk 70 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7651 Z= 0.188 Angle : 0.553 11.120 10438 Z= 0.288 Chirality : 0.044 0.160 1190 Planarity : 0.004 0.033 1354 Dihedral : 5.187 25.852 1231 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.78 % Allowed : 15.06 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.83 (0.27), residues: 943 helix: 1.84 (0.44), residues: 167 sheet: 1.19 (0.29), residues: 317 loop : -0.38 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 167 HIS 0.000 0.000 HIS A 132 PHE 0.010 0.001 PHE C 103 TYR 0.009 0.001 TYR C 318 ARG 0.005 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 79 THR cc_start: 0.7851 (t) cc_final: 0.7268 (p) REVERT: A 276 ARG cc_start: 0.7015 (mtp85) cc_final: 0.6540 (mtm-85) REVERT: A 286 ASP cc_start: 0.7150 (t70) cc_final: 0.6889 (t0) REVERT: B 164 VAL cc_start: 0.6688 (m) cc_final: 0.6476 (m) REVERT: B 286 ASP cc_start: 0.7365 (t70) cc_final: 0.7090 (t0) REVERT: C 79 THR cc_start: 0.7692 (t) cc_final: 0.7202 (p) REVERT: C 268 MET cc_start: 0.7839 (mmm) cc_final: 0.7484 (mtt) REVERT: C 286 ASP cc_start: 0.7114 (t70) cc_final: 0.6873 (t0) outliers start: 22 outliers final: 20 residues processed: 104 average time/residue: 0.2153 time to fit residues: 29.4566 Evaluate side-chains 109 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7651 Z= 0.316 Angle : 0.607 7.738 10438 Z= 0.319 Chirality : 0.046 0.148 1190 Planarity : 0.004 0.033 1354 Dihedral : 5.277 29.632 1231 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.16 % Allowed : 15.06 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.46 (0.27), residues: 943 helix: 1.25 (0.42), residues: 179 sheet: 0.83 (0.29), residues: 330 loop : -0.46 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 272 HIS 0.000 0.000 HIS C 132 PHE 0.016 0.002 PHE B 103 TYR 0.010 0.001 TYR C 216 ARG 0.007 0.001 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 79 THR cc_start: 0.7823 (t) cc_final: 0.7237 (p) REVERT: A 276 ARG cc_start: 0.7093 (mtp85) cc_final: 0.6667 (mtm-85) REVERT: A 286 ASP cc_start: 0.7346 (t70) cc_final: 0.7099 (t0) REVERT: B 164 VAL cc_start: 0.6873 (m) cc_final: 0.6628 (m) REVERT: B 286 ASP cc_start: 0.7437 (t70) cc_final: 0.7145 (t0) REVERT: C 79 THR cc_start: 0.7703 (t) cc_final: 0.7185 (p) REVERT: C 268 MET cc_start: 0.7835 (mmm) cc_final: 0.7611 (mmm) REVERT: C 286 ASP cc_start: 0.7292 (t70) cc_final: 0.7073 (t0) REVERT: C 288 ASP cc_start: 0.7869 (m-30) cc_final: 0.7500 (t70) outliers start: 25 outliers final: 21 residues processed: 103 average time/residue: 0.2163 time to fit residues: 29.5431 Evaluate side-chains 107 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7651 Z= 0.283 Angle : 0.588 8.006 10438 Z= 0.308 Chirality : 0.045 0.146 1190 Planarity : 0.004 0.034 1354 Dihedral : 5.128 28.438 1231 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.41 % Allowed : 15.82 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.48 (0.27), residues: 943 helix: 1.24 (0.42), residues: 179 sheet: 0.89 (0.29), residues: 322 loop : -0.47 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 272 HIS 0.000 0.000 HIS C 132 PHE 0.013 0.002 PHE B 103 TYR 0.011 0.001 TYR C 318 ARG 0.006 0.001 ARG C 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 79 THR cc_start: 0.7801 (t) cc_final: 0.7212 (p) REVERT: A 276 ARG cc_start: 0.7062 (mtp85) cc_final: 0.6634 (mtm-85) REVERT: A 286 ASP cc_start: 0.7428 (t70) cc_final: 0.7204 (t0) REVERT: A 288 ASP cc_start: 0.7835 (m-30) cc_final: 0.7612 (t70) REVERT: B 164 VAL cc_start: 0.6912 (m) cc_final: 0.6676 (m) REVERT: B 286 ASP cc_start: 0.7450 (t70) cc_final: 0.7192 (t0) REVERT: B 288 ASP cc_start: 0.7805 (m-30) cc_final: 0.7495 (t70) REVERT: C 79 THR cc_start: 0.7719 (t) cc_final: 0.7170 (p) REVERT: C 268 MET cc_start: 0.7841 (mmm) cc_final: 0.7594 (mmm) REVERT: C 286 ASP cc_start: 0.7285 (t70) cc_final: 0.7058 (t0) REVERT: C 288 ASP cc_start: 0.7912 (m-30) cc_final: 0.7536 (t70) outliers start: 19 outliers final: 19 residues processed: 101 average time/residue: 0.2087 time to fit residues: 28.1507 Evaluate side-chains 108 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.189246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127891 restraints weight = 6709.461| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.59 r_work: 0.3258 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7651 Z= 0.167 Angle : 0.548 7.721 10438 Z= 0.285 Chirality : 0.044 0.150 1190 Planarity : 0.004 0.034 1354 Dihedral : 4.849 28.571 1231 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.15 % Allowed : 15.95 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.86 (0.27), residues: 943 helix: 1.82 (0.44), residues: 167 sheet: 1.29 (0.29), residues: 310 loop : -0.38 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 167 HIS 0.000 0.000 HIS A 132 PHE 0.011 0.001 PHE C 103 TYR 0.011 0.001 TYR C 318 ARG 0.005 0.000 ARG B 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1933.13 seconds wall clock time: 34 minutes 47.59 seconds (2087.59 seconds total)