Starting phenix.real_space_refine on Sun Dec 29 00:17:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bog_44735/12_2024/9bog_44735.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bog_44735/12_2024/9bog_44735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bog_44735/12_2024/9bog_44735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bog_44735/12_2024/9bog_44735.map" model { file = "/net/cci-nas-00/data/ceres_data/9bog_44735/12_2024/9bog_44735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bog_44735/12_2024/9bog_44735.cif" } resolution = 3.99 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= 0.026 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 20 5.16 5 C 5838 2.51 5 N 1705 2.21 5 O 1807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9370 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 5496 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 204} Link IDs: {'PTRANS': 31, 'TRANS': 768} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 714 Unresolved non-hydrogen angles: 913 Unresolved non-hydrogen dihedrals: 575 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 18, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 439 Chain: "F" Number of atoms: 884 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 154, 884 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 145} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 12, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "C" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1356 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 14, 'TRANS': 190} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 8, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "H" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 1634 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 262} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 448 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 4, 'TYR:plan': 10, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 251 Time building chain proxies: 5.91, per 1000 atoms: 0.63 Number of scatterers: 9370 At special positions: 0 Unit cell: (81.6, 92.4, 163.2, 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 20 16.00 O 1807 8.00 N 1705 7.00 C 5838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 810 " - pdb=" SG CYS D 832 " distance=2.04 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 56 " distance=2.03 Simple disulfide: pdb=" SG CYS H 3 " - pdb=" SG CYS H 44 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 187 " distance=2.04 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 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 25 sheets defined 5.3% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'D' and resid 5 through 10 removed outlier: 4.200A pdb=" N LEU D 9 " --> pdb=" O ASN D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 removed outlier: 4.177A pdb=" N ASN D 24 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 73 Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.752A pdb=" N ARG D 250 " --> pdb=" O ASP D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 448 removed outlier: 3.563A pdb=" N THR D 447 " --> pdb=" O ASN D 443 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR D 448 " --> pdb=" O PHE D 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 443 through 448' Processing helix chain 'D' and resid 817 through 822 removed outlier: 3.655A pdb=" N GLN D 821 " --> pdb=" O PRO D 818 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 36 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 125 through 129 removed outlier: 4.188A pdb=" N ALA C 128 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 69 Processing sheet with id=AA1, first strand: chain 'D' and resid 42 through 46 removed outlier: 5.002A pdb=" N TYR D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU D 39 " --> pdb=" O TYR D 43 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA D 45 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP D 36 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU D 113 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR D 38 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'D' and resid 152 through 153 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 152 through 153 current: chain 'D' and resid 161 through 170 removed outlier: 4.308A pdb=" N ASN D 202 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR D 182 " --> pdb=" O HIS D 200 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N HIS D 200 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER D 184 " --> pdb=" O TRP D 198 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TRP D 198 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 15.876A pdb=" N ILE D 201 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 10.076A pdb=" N TYR D 222 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR D 203 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR D 331 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG D 376 " --> pdb=" O ASN D 400 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ILE D 429 " --> pdb=" O THR D 489 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR D 489 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 431 " --> pdb=" O THR D 487 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ARG D 481 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY D 482 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D 647 " --> pdb=" O SER D 640 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 256 through 260 Processing sheet with id=AA5, first strand: chain 'D' and resid 273 through 280 removed outlier: 6.877A pdb=" N ILE D 268 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 266 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR D 279 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA D 264 " --> pdb=" O THR D 279 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 700 through 701 Processing sheet with id=AA7, first strand: chain 'D' and resid 711 through 714 Processing sheet with id=AA8, first strand: chain 'D' and resid 725 through 726 Processing sheet with id=AA9, first strand: chain 'D' and resid 762 through 763 removed outlier: 6.935A pdb=" N LEU D 753 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N SER D 790 " --> pdb=" O LEU D 753 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET D 755 " --> pdb=" O TYR D 788 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR D 788 " --> pdb=" O MET D 755 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU D 757 " --> pdb=" O GLN D 786 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLN D 786 " --> pdb=" O LEU D 757 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 762 through 763 Processing sheet with id=AB2, first strand: chain 'D' and resid 778 through 780 Processing sheet with id=AB3, first strand: chain 'H' and resid 168 through 171 removed outlier: 3.541A pdb=" N VAL H 170 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER F 3 " --> pdb=" O VAL H 274 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY F 9 " --> pdb=" O VAL H 268 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN H 191 " --> pdb=" O ALA H 242 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA H 242 " --> pdb=" O GLN H 191 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU H 193 " --> pdb=" O LEU H 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 18 through 20 removed outlier: 3.561A pdb=" N ALA F 19 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU F 52 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 23 through 24 removed outlier: 7.305A pdb=" N VAL C 9 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ARG C 116 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR C 11 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 114 through 116 removed outlier: 4.075A pdb=" N ALA F 145 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 104 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA F 147 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE F 149 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE C 108 " --> pdb=" O PHE F 149 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 110 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AB8, first strand: chain 'C' and resid 132 through 135 Processing sheet with id=AB9, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.626A pdb=" N ARG C 160 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 152 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 165 " --> pdb=" O VAL C 152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.626A pdb=" N ARG C 160 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL C 152 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE C 190 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU C 154 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG C 188 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 187 " --> pdb=" O MET C 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AC3, first strand: chain 'H' and resid 16 through 22 removed outlier: 6.459A pdb=" N PHE H 142 " --> pdb=" O ARG H 132 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG H 132 " --> pdb=" O PHE H 142 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE H 144 " --> pdb=" O ILE H 130 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE H 130 " --> pdb=" O PHE H 144 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP H 146 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL H 128 " --> pdb=" O TRP H 146 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE H 148 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE H 126 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ALA H 63 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL H 128 " --> pdb=" O GLY H 61 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY H 61 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE H 130 " --> pdb=" O GLN H 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 34 through 37 Processing sheet with id=AC5, first strand: chain 'H' and resid 117 through 120 removed outlier: 3.786A pdb=" N GLY H 117 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL H 154 " --> pdb=" O ALA H 119 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 178 through 181 removed outlier: 4.517A pdb=" N LEU H 252 " --> pdb=" O ILE H 181 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 184 through 185 422 hydrogen bonds defined for protein. 1083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3285 1.34 - 1.46: 2211 1.46 - 1.58: 3996 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 9522 Sorted by residual: bond pdb=" CB ASP C 78 " pdb=" CG ASP C 78 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.52e+00 bond pdb=" CB ASP D 134 " pdb=" CG ASP D 134 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.12e+00 bond pdb=" CB TRP D 183 " pdb=" CG TRP D 183 " ideal model delta sigma weight residual 1.498 1.527 -0.029 3.10e-02 1.04e+03 8.47e-01 bond pdb=" CB ASP C 192 " pdb=" CG ASP C 192 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.23e-01 bond pdb=" CA VAL D 16 " pdb=" CB VAL D 16 " ideal model delta sigma weight residual 1.548 1.538 0.010 1.13e-02 7.83e+03 7.24e-01 ... (remaining 9517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 12886 1.79 - 3.57: 161 3.57 - 5.36: 25 5.36 - 7.14: 3 7.14 - 8.93: 4 Bond angle restraints: 13079 Sorted by residual: angle pdb=" N ILE D 275 " pdb=" CA ILE D 275 " pdb=" C ILE D 275 " ideal model delta sigma weight residual 112.96 109.38 3.58 1.00e+00 1.00e+00 1.28e+01 angle pdb=" CB MET C 57 " pdb=" CG MET C 57 " pdb=" SD MET C 57 " ideal model delta sigma weight residual 112.70 120.67 -7.97 3.00e+00 1.11e-01 7.05e+00 angle pdb=" CA CYS D 810 " pdb=" CB CYS D 810 " pdb=" SG CYS D 810 " ideal model delta sigma weight residual 114.40 120.34 -5.94 2.30e+00 1.89e-01 6.67e+00 angle pdb=" CA LEU D 582 " pdb=" CB LEU D 582 " pdb=" CG LEU D 582 " ideal model delta sigma weight residual 116.30 125.23 -8.93 3.50e+00 8.16e-02 6.51e+00 angle pdb=" CA LEU H 172 " pdb=" CB LEU H 172 " pdb=" CG LEU H 172 " ideal model delta sigma weight residual 116.30 124.56 -8.26 3.50e+00 8.16e-02 5.56e+00 ... (remaining 13074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4950 17.91 - 35.82: 463 35.82 - 53.73: 97 53.73 - 71.64: 14 71.64 - 89.55: 4 Dihedral angle restraints: 5528 sinusoidal: 1431 harmonic: 4097 Sorted by residual: dihedral pdb=" CB CYS D 63 " pdb=" SG CYS D 63 " pdb=" SG CYS D 90 " pdb=" CB CYS D 90 " ideal model delta sinusoidal sigma weight residual 93.00 163.99 -70.99 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" CB CYS H 161 " pdb=" SG CYS H 161 " pdb=" SG CYS H 187 " pdb=" CB CYS H 187 " ideal model delta sinusoidal sigma weight residual 93.00 52.93 40.07 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA PHE D 525 " pdb=" C PHE D 525 " pdb=" N GLU D 526 " pdb=" CA GLU D 526 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 5525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 948 0.030 - 0.059: 395 0.059 - 0.089: 98 0.089 - 0.119: 112 0.119 - 0.148: 16 Chirality restraints: 1569 Sorted by residual: chirality pdb=" CA VAL D 320 " pdb=" N VAL D 320 " pdb=" C VAL D 320 " pdb=" CB VAL D 320 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CG LEU H 172 " pdb=" CB LEU H 172 " pdb=" CD1 LEU H 172 " pdb=" CD2 LEU H 172 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE D 259 " pdb=" N ILE D 259 " pdb=" C ILE D 259 " pdb=" CB ILE D 259 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 1566 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 320 " 0.039 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO D 321 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 52 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO C 53 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 167 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" CG ASP H 167 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP H 167 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP H 167 " 0.009 2.00e-02 2.50e+03 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 918 2.75 - 3.29: 8369 3.29 - 3.83: 14033 3.83 - 4.36: 14405 4.36 - 4.90: 27039 Nonbonded interactions: 64764 Sorted by model distance: nonbonded pdb=" O THR C 189 " pdb=" OG1 THR C 197 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR H 226 " pdb=" OG1 THR H 253 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR D 375 " pdb=" O PHE D 442 " model vdw 2.245 3.040 nonbonded pdb=" O SER H 216 " pdb=" OG SER H 216 " model vdw 2.264 3.040 nonbonded pdb=" OD1 ASN C 39 " pdb=" N ALA C 40 " model vdw 2.309 3.120 ... (remaining 64759 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 0.830 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.320 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 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 : 0.002 0.036 9522 Z= 0.133 Angle : 0.536 8.927 13079 Z= 0.286 Chirality : 0.043 0.148 1569 Planarity : 0.003 0.060 1758 Dihedral : 14.608 89.553 2897 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.29 % Allowed : 32.65 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.13 (0.22), residues: 1424 helix: -1.56 (0.77), residues: 49 sheet: 0.83 (0.21), residues: 625 loop : -0.40 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 508 HIS 0.007 0.001 HIS D 809 PHE 0.008 0.001 PHE D 525 TYR 0.014 0.001 TYR D 593 ARG 0.006 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 310 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 257 HIS cc_start: 0.6899 (m-70) cc_final: 0.6330 (m90) REVERT: D 324 GLN cc_start: 0.5958 (mm-40) cc_final: 0.5685 (mm110) REVERT: D 332 SER cc_start: 0.7158 (t) cc_final: 0.6879 (p) REVERT: D 379 ASN cc_start: 0.7299 (t0) cc_final: 0.7097 (m-40) REVERT: D 400 ASN cc_start: 0.8167 (m-40) cc_final: 0.7937 (t0) REVERT: D 416 PHE cc_start: 0.6806 (m-80) cc_final: 0.6591 (m-80) REVERT: D 484 LEU cc_start: 0.8478 (tp) cc_final: 0.8277 (tp) REVERT: D 518 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7817 (tm-30) REVERT: D 531 THR cc_start: 0.7266 (t) cc_final: 0.6974 (p) REVERT: D 537 THR cc_start: 0.7912 (m) cc_final: 0.7663 (p) REVERT: D 553 VAL cc_start: 0.8645 (t) cc_final: 0.8438 (m) REVERT: D 599 ASP cc_start: 0.7532 (t0) cc_final: 0.6978 (t0) REVERT: D 608 THR cc_start: 0.7986 (t) cc_final: 0.7493 (p) REVERT: D 636 ASN cc_start: 0.7805 (p0) cc_final: 0.7544 (p0) REVERT: D 669 LEU cc_start: 0.8051 (mp) cc_final: 0.7797 (mt) REVERT: D 688 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.7169 (m110) REVERT: D 756 THR cc_start: 0.8757 (m) cc_final: 0.8533 (p) REVERT: D 786 GLN cc_start: 0.7250 (mt0) cc_final: 0.6990 (mt0) REVERT: D 829 SER cc_start: 0.8534 (t) cc_final: 0.8167 (p) REVERT: F 4 THR cc_start: 0.8555 (m) cc_final: 0.8203 (p) REVERT: F 123 ASN cc_start: 0.7878 (t0) cc_final: 0.7514 (t0) REVERT: C 4 LEU cc_start: 0.8468 (mt) cc_final: 0.8191 (mp) REVERT: C 19 GLN cc_start: 0.7992 (mt0) cc_final: 0.7723 (mt0) REVERT: C 22 VAL cc_start: 0.8537 (t) cc_final: 0.8194 (p) REVERT: C 44 LYS cc_start: 0.9198 (tppp) cc_final: 0.8962 (mttm) REVERT: H 191 GLN cc_start: 0.8074 (pt0) cc_final: 0.7866 (pt0) outliers start: 2 outliers final: 0 residues processed: 310 average time/residue: 0.2118 time to fit residues: 91.5299 Evaluate side-chains 284 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 688 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 111 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 0.0570 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 30.0000 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 711 ASN D 809 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9522 Z= 0.167 Angle : 0.562 10.091 13079 Z= 0.287 Chirality : 0.044 0.162 1569 Planarity : 0.004 0.060 1758 Dihedral : 3.296 16.957 1521 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 8.16 % Allowed : 29.01 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.25 (0.23), residues: 1424 helix: -1.75 (0.80), residues: 44 sheet: 0.85 (0.20), residues: 642 loop : -0.29 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 183 HIS 0.004 0.001 HIS D 504 PHE 0.011 0.001 PHE D 4 TYR 0.016 0.001 TYR D 650 ARG 0.006 0.001 ARG H 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 283 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: D 257 HIS cc_start: 0.7174 (m-70) cc_final: 0.6771 (m90) REVERT: D 324 GLN cc_start: 0.6095 (mm-40) cc_final: 0.5814 (mm110) REVERT: D 379 ASN cc_start: 0.7574 (t0) cc_final: 0.7320 (t0) REVERT: D 489 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.7860 (p) REVERT: D 531 THR cc_start: 0.7343 (t) cc_final: 0.6968 (p) REVERT: D 537 THR cc_start: 0.7918 (m) cc_final: 0.7623 (p) REVERT: D 588 ASN cc_start: 0.8368 (m-40) cc_final: 0.8127 (m-40) REVERT: D 599 ASP cc_start: 0.7613 (t0) cc_final: 0.7396 (t0) REVERT: D 608 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7497 (p) REVERT: D 647 GLN cc_start: 0.7456 (pt0) cc_final: 0.7082 (pt0) REVERT: D 669 LEU cc_start: 0.8107 (mp) cc_final: 0.7872 (mt) REVERT: D 688 ASN cc_start: 0.7460 (m110) cc_final: 0.7215 (m110) REVERT: D 706 THR cc_start: 0.7816 (p) cc_final: 0.7612 (t) REVERT: D 741 VAL cc_start: 0.8104 (t) cc_final: 0.7826 (p) REVERT: D 786 GLN cc_start: 0.7310 (mt0) cc_final: 0.7011 (mt0) REVERT: F 4 THR cc_start: 0.8548 (m) cc_final: 0.8170 (p) REVERT: F 123 ASN cc_start: 0.7901 (t0) cc_final: 0.7523 (t0) REVERT: C 4 LEU cc_start: 0.8573 (mt) cc_final: 0.8342 (mp) REVERT: C 75 LEU cc_start: 0.8145 (mm) cc_final: 0.7843 (mt) REVERT: C 151 THR cc_start: 0.8639 (m) cc_final: 0.8281 (p) REVERT: H 167 ASP cc_start: 0.6960 (t0) cc_final: 0.6711 (t0) REVERT: H 191 GLN cc_start: 0.8183 (pt0) cc_final: 0.7959 (pt0) REVERT: H 193 LEU cc_start: 0.8236 (tp) cc_final: 0.7987 (tt) REVERT: H 269 GLN cc_start: 0.7438 (tt0) cc_final: 0.6870 (tt0) outliers start: 56 outliers final: 26 residues processed: 308 average time/residue: 0.1846 time to fit residues: 81.7961 Evaluate side-chains 293 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 696 TRP Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 239 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 129 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 9522 Z= 0.544 Angle : 0.754 12.175 13079 Z= 0.404 Chirality : 0.049 0.223 1569 Planarity : 0.005 0.065 1758 Dihedral : 4.809 20.442 1519 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.83 % Favored : 94.10 % Rotamer: Outliers : 10.64 % Allowed : 29.30 % Favored : 60.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.24 (0.22), residues: 1424 helix: -2.09 (0.72), residues: 44 sheet: 0.55 (0.20), residues: 624 loop : -0.61 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP D 204 HIS 0.021 0.004 HIS D 809 PHE 0.028 0.003 PHE D 378 TYR 0.033 0.003 TYR D 375 ARG 0.007 0.001 ARG H 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 308 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: D 257 HIS cc_start: 0.7493 (m-70) cc_final: 0.7220 (m-70) REVERT: D 323 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7227 (mm) REVERT: D 379 ASN cc_start: 0.7603 (t0) cc_final: 0.7280 (t0) REVERT: D 382 ILE cc_start: 0.8566 (mp) cc_final: 0.8262 (mm) REVERT: D 386 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6276 (mtp) REVERT: D 484 LEU cc_start: 0.8444 (tp) cc_final: 0.8176 (tt) REVERT: D 489 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.8011 (p) REVERT: D 503 SER cc_start: 0.8712 (m) cc_final: 0.8315 (p) REVERT: D 537 THR cc_start: 0.8038 (m) cc_final: 0.7688 (p) REVERT: D 557 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7921 (m-10) REVERT: D 588 ASN cc_start: 0.8193 (m-40) cc_final: 0.7800 (m-40) REVERT: D 599 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7704 (t0) REVERT: D 608 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7522 (p) REVERT: D 632 TYR cc_start: 0.7998 (m-10) cc_final: 0.7680 (m-10) REVERT: D 647 GLN cc_start: 0.7612 (pt0) cc_final: 0.7252 (pt0) REVERT: D 683 ASP cc_start: 0.7622 (t0) cc_final: 0.7356 (t0) REVERT: D 728 ASN cc_start: 0.7831 (t0) cc_final: 0.7555 (t0) REVERT: D 784 ASN cc_start: 0.8010 (m-40) cc_final: 0.7370 (t0) REVERT: D 786 GLN cc_start: 0.7208 (mt0) cc_final: 0.6802 (mt0) REVERT: F 4 THR cc_start: 0.8596 (m) cc_final: 0.8255 (p) REVERT: F 65 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8579 (p) REVERT: F 123 ASN cc_start: 0.8137 (t0) cc_final: 0.7702 (t0) REVERT: C 32 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7174 (pt) REVERT: C 75 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7879 (mt) REVERT: C 151 THR cc_start: 0.8677 (m) cc_final: 0.8176 (p) REVERT: H 167 ASP cc_start: 0.7287 (t0) cc_final: 0.7035 (t0) REVERT: H 191 GLN cc_start: 0.8197 (pt0) cc_final: 0.7924 (pt0) outliers start: 73 outliers final: 42 residues processed: 328 average time/residue: 0.1884 time to fit residues: 89.0695 Evaluate side-chains 340 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 289 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 696 TRP Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 271 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 86 optimal weight: 0.3980 chunk 129 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 GLN C 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9522 Z= 0.210 Angle : 0.631 13.668 13079 Z= 0.322 Chirality : 0.047 0.235 1569 Planarity : 0.004 0.052 1758 Dihedral : 4.054 17.716 1519 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 6.85 % Allowed : 35.13 % Favored : 58.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.12 (0.22), residues: 1424 helix: -1.77 (0.77), residues: 44 sheet: 0.62 (0.20), residues: 638 loop : -0.57 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 204 HIS 0.009 0.002 HIS D 659 PHE 0.026 0.002 PHE C 55 TYR 0.023 0.002 TYR H 186 ARG 0.004 0.001 ARG D 709 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 287 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: D 257 HIS cc_start: 0.7195 (m-70) cc_final: 0.6958 (m90) REVERT: D 379 ASN cc_start: 0.7690 (t0) cc_final: 0.7290 (t0) REVERT: D 382 ILE cc_start: 0.8534 (mp) cc_final: 0.8182 (mm) REVERT: D 394 VAL cc_start: 0.8490 (p) cc_final: 0.8097 (m) REVERT: D 442 PHE cc_start: 0.7301 (m-80) cc_final: 0.7047 (m-10) REVERT: D 489 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7955 (p) REVERT: D 503 SER cc_start: 0.8630 (m) cc_final: 0.8261 (p) REVERT: D 518 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7746 (tm-30) REVERT: D 532 LEU cc_start: 0.8829 (tp) cc_final: 0.8555 (tp) REVERT: D 537 THR cc_start: 0.7993 (m) cc_final: 0.7667 (p) REVERT: D 588 ASN cc_start: 0.8260 (m-40) cc_final: 0.7836 (m-40) REVERT: D 608 THR cc_start: 0.7937 (t) cc_final: 0.7451 (p) REVERT: D 647 GLN cc_start: 0.7501 (pt0) cc_final: 0.7164 (pt0) REVERT: D 652 VAL cc_start: 0.8607 (m) cc_final: 0.8378 (p) REVERT: D 683 ASP cc_start: 0.7437 (t0) cc_final: 0.7154 (t0) REVERT: D 756 THR cc_start: 0.8702 (m) cc_final: 0.8074 (p) REVERT: D 784 ASN cc_start: 0.7987 (m-40) cc_final: 0.7377 (t0) REVERT: D 786 GLN cc_start: 0.7079 (mt0) cc_final: 0.6826 (mt0) REVERT: F 4 THR cc_start: 0.8561 (m) cc_final: 0.8207 (p) REVERT: F 65 VAL cc_start: 0.9015 (t) cc_final: 0.8607 (p) REVERT: F 123 ASN cc_start: 0.7982 (t0) cc_final: 0.7547 (t0) REVERT: C 75 LEU cc_start: 0.8191 (mm) cc_final: 0.7887 (mt) REVERT: C 151 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8326 (p) REVERT: H 167 ASP cc_start: 0.7078 (t0) cc_final: 0.6855 (t0) outliers start: 47 outliers final: 32 residues processed: 307 average time/residue: 0.1980 time to fit residues: 86.5380 Evaluate side-chains 317 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 283 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 685 LYS Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 249 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 GLN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9522 Z= 0.319 Angle : 0.644 13.208 13079 Z= 0.334 Chirality : 0.046 0.192 1569 Planarity : 0.004 0.055 1758 Dihedral : 4.230 19.082 1519 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 7.58 % Allowed : 33.24 % Favored : 59.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.26 (0.22), residues: 1424 helix: -1.75 (0.78), residues: 44 sheet: 0.57 (0.20), residues: 632 loop : -0.71 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 204 HIS 0.008 0.002 HIS D 659 PHE 0.019 0.002 PHE D 350 TYR 0.026 0.002 TYR H 186 ARG 0.004 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 294 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 257 HIS cc_start: 0.7242 (m-70) cc_final: 0.7026 (m90) REVERT: D 259 ILE cc_start: 0.7944 (mm) cc_final: 0.7595 (mm) REVERT: D 295 ASN cc_start: 0.7932 (p0) cc_final: 0.7663 (p0) REVERT: D 323 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7164 (mm) REVERT: D 379 ASN cc_start: 0.7696 (t0) cc_final: 0.7253 (t0) REVERT: D 382 ILE cc_start: 0.8453 (mp) cc_final: 0.8113 (mm) REVERT: D 386 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6359 (mtp) REVERT: D 489 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7980 (p) REVERT: D 500 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8433 (tp) REVERT: D 503 SER cc_start: 0.8642 (m) cc_final: 0.8309 (p) REVERT: D 518 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7868 (tm-30) REVERT: D 532 LEU cc_start: 0.8854 (tp) cc_final: 0.8593 (tp) REVERT: D 537 THR cc_start: 0.8018 (m) cc_final: 0.7720 (p) REVERT: D 576 TYR cc_start: 0.7699 (t80) cc_final: 0.7389 (t80) REVERT: D 588 ASN cc_start: 0.8186 (m-40) cc_final: 0.7759 (m-40) REVERT: D 599 ASP cc_start: 0.8042 (t0) cc_final: 0.7692 (t0) REVERT: D 608 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7458 (p) REVERT: D 647 GLN cc_start: 0.7556 (pt0) cc_final: 0.7218 (pt0) REVERT: D 652 VAL cc_start: 0.8566 (m) cc_final: 0.8340 (p) REVERT: D 683 ASP cc_start: 0.7493 (t0) cc_final: 0.7244 (t0) REVERT: D 695 ASP cc_start: 0.6179 (p0) cc_final: 0.5953 (p0) REVERT: D 756 THR cc_start: 0.8710 (m) cc_final: 0.8102 (p) REVERT: D 784 ASN cc_start: 0.7985 (m-40) cc_final: 0.7400 (t0) REVERT: D 786 GLN cc_start: 0.7085 (mt0) cc_final: 0.6825 (mt0) REVERT: F 4 THR cc_start: 0.8573 (m) cc_final: 0.8192 (p) REVERT: F 65 VAL cc_start: 0.8981 (t) cc_final: 0.8613 (p) REVERT: F 123 ASN cc_start: 0.8052 (t0) cc_final: 0.7610 (t0) REVERT: C 75 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7961 (mm) REVERT: C 151 THR cc_start: 0.8729 (m) cc_final: 0.8348 (p) REVERT: H 167 ASP cc_start: 0.7074 (t0) cc_final: 0.6838 (t0) outliers start: 52 outliers final: 41 residues processed: 314 average time/residue: 0.2000 time to fit residues: 89.7334 Evaluate side-chains 335 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 288 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 269 GLN Chi-restraints excluded: chain H residue 271 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 114 optimal weight: 0.0870 chunk 63 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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: 0.7315 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9522 Z= 0.190 Angle : 0.611 12.850 13079 Z= 0.313 Chirality : 0.046 0.188 1569 Planarity : 0.004 0.054 1758 Dihedral : 3.916 18.150 1519 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 6.56 % Allowed : 35.86 % Favored : 57.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.15 (0.22), residues: 1424 helix: -1.57 (0.81), residues: 44 sheet: 0.62 (0.20), residues: 640 loop : -0.62 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 204 HIS 0.006 0.001 HIS D 659 PHE 0.019 0.002 PHE D 416 TYR 0.025 0.002 TYR H 186 ARG 0.003 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 286 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 210 ILE cc_start: 0.8714 (mm) cc_final: 0.8410 (mm) REVERT: D 257 HIS cc_start: 0.7104 (m-70) cc_final: 0.6816 (m90) REVERT: D 259 ILE cc_start: 0.7958 (mm) cc_final: 0.6417 (pt) REVERT: D 295 ASN cc_start: 0.7878 (p0) cc_final: 0.7636 (p0) REVERT: D 322 LEU cc_start: 0.8433 (tp) cc_final: 0.8171 (pt) REVERT: D 323 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7050 (tp) REVERT: D 344 GLN cc_start: 0.8033 (pm20) cc_final: 0.7751 (pt0) REVERT: D 379 ASN cc_start: 0.7722 (t0) cc_final: 0.7399 (t0) REVERT: D 489 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.8000 (p) REVERT: D 503 SER cc_start: 0.8625 (m) cc_final: 0.8286 (p) REVERT: D 518 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7815 (tm-30) REVERT: D 532 LEU cc_start: 0.8789 (tp) cc_final: 0.8529 (tp) REVERT: D 537 THR cc_start: 0.8022 (m) cc_final: 0.7692 (p) REVERT: D 588 ASN cc_start: 0.8217 (m-40) cc_final: 0.7771 (m-40) REVERT: D 599 ASP cc_start: 0.7915 (t0) cc_final: 0.7599 (t0) REVERT: D 608 THR cc_start: 0.7914 (t) cc_final: 0.7436 (p) REVERT: D 647 GLN cc_start: 0.7465 (pt0) cc_final: 0.7035 (pt0) REVERT: D 652 VAL cc_start: 0.8542 (m) cc_final: 0.8299 (p) REVERT: D 683 ASP cc_start: 0.7363 (t0) cc_final: 0.7105 (t0) REVERT: D 695 ASP cc_start: 0.6082 (p0) cc_final: 0.5799 (p0) REVERT: D 756 THR cc_start: 0.8684 (m) cc_final: 0.8095 (p) REVERT: D 784 ASN cc_start: 0.7963 (m-40) cc_final: 0.7437 (t0) REVERT: D 786 GLN cc_start: 0.7118 (mt0) cc_final: 0.6852 (mt0) REVERT: F 4 THR cc_start: 0.8550 (m) cc_final: 0.8173 (p) REVERT: F 65 VAL cc_start: 0.8923 (t) cc_final: 0.8483 (p) REVERT: F 123 ASN cc_start: 0.7945 (t0) cc_final: 0.7522 (t0) REVERT: C 75 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7801 (mt) REVERT: C 151 THR cc_start: 0.8673 (m) cc_final: 0.8366 (p) outliers start: 45 outliers final: 33 residues processed: 306 average time/residue: 0.1881 time to fit residues: 82.5359 Evaluate side-chains 320 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 284 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 269 GLN Chi-restraints excluded: chain H residue 271 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 115 optimal weight: 0.0670 chunk 76 optimal weight: 0.0270 chunk 136 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 84 optimal weight: 6.9990 overall best weight: 0.2776 ------------------------------------------------------------------------------- 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: 0.7275 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9522 Z= 0.155 Angle : 0.590 8.844 13079 Z= 0.301 Chirality : 0.046 0.174 1569 Planarity : 0.004 0.056 1758 Dihedral : 3.681 17.176 1519 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.98 % Allowed : 36.73 % Favored : 57.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.01 (0.22), residues: 1424 helix: -1.42 (0.83), residues: 44 sheet: 0.85 (0.21), residues: 611 loop : -0.62 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 183 HIS 0.004 0.001 HIS D 659 PHE 0.023 0.002 PHE C 55 TYR 0.025 0.001 TYR H 186 ARG 0.008 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 289 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 205 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8496 (pp) REVERT: D 210 ILE cc_start: 0.8721 (mm) cc_final: 0.8358 (mm) REVERT: D 257 HIS cc_start: 0.6966 (m-70) cc_final: 0.6702 (m90) REVERT: D 259 ILE cc_start: 0.7923 (mm) cc_final: 0.6401 (pt) REVERT: D 379 ASN cc_start: 0.7651 (t0) cc_final: 0.7314 (t0) REVERT: D 489 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7995 (p) REVERT: D 503 SER cc_start: 0.8578 (m) cc_final: 0.8247 (p) REVERT: D 518 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7774 (tm-30) REVERT: D 531 THR cc_start: 0.7442 (OUTLIER) cc_final: 0.7140 (p) REVERT: D 537 THR cc_start: 0.8001 (m) cc_final: 0.7683 (p) REVERT: D 588 ASN cc_start: 0.8234 (m-40) cc_final: 0.7920 (m-40) REVERT: D 599 ASP cc_start: 0.7885 (t0) cc_final: 0.7539 (t0) REVERT: D 608 THR cc_start: 0.7962 (t) cc_final: 0.7496 (p) REVERT: D 647 GLN cc_start: 0.7422 (pt0) cc_final: 0.7012 (pt0) REVERT: D 652 VAL cc_start: 0.8504 (m) cc_final: 0.8255 (p) REVERT: D 683 ASP cc_start: 0.7243 (t0) cc_final: 0.6957 (t0) REVERT: D 695 ASP cc_start: 0.6023 (p0) cc_final: 0.5754 (p0) REVERT: D 756 THR cc_start: 0.8701 (m) cc_final: 0.8104 (p) REVERT: D 784 ASN cc_start: 0.7940 (m-40) cc_final: 0.7372 (t0) REVERT: D 786 GLN cc_start: 0.7112 (mt0) cc_final: 0.6841 (mt0) REVERT: F 4 THR cc_start: 0.8525 (m) cc_final: 0.8145 (p) REVERT: F 65 VAL cc_start: 0.8866 (t) cc_final: 0.8411 (p) REVERT: F 123 ASN cc_start: 0.7875 (t0) cc_final: 0.7439 (t0) REVERT: C 75 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7755 (mt) REVERT: C 151 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8406 (p) outliers start: 41 outliers final: 28 residues processed: 312 average time/residue: 0.1963 time to fit residues: 87.9368 Evaluate side-chains 318 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 285 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 269 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 67 optimal weight: 0.0020 chunk 12 optimal weight: 0.0050 chunk 107 optimal weight: 0.0570 chunk 124 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 overall best weight: 0.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9522 Z= 0.163 Angle : 0.605 9.052 13079 Z= 0.307 Chirality : 0.046 0.175 1569 Planarity : 0.004 0.057 1758 Dihedral : 3.672 17.048 1519 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.83 % Allowed : 37.03 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.11 (0.23), residues: 1424 helix: -1.38 (0.83), residues: 44 sheet: 0.92 (0.21), residues: 612 loop : -0.53 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 183 HIS 0.004 0.001 HIS D 659 PHE 0.016 0.001 PHE D 350 TYR 0.023 0.001 TYR H 186 ARG 0.007 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: D 142 LEU cc_start: 0.8504 (tt) cc_final: 0.8032 (mp) REVERT: D 210 ILE cc_start: 0.8699 (mm) cc_final: 0.8370 (mm) REVERT: D 259 ILE cc_start: 0.7938 (mm) cc_final: 0.6410 (pt) REVERT: D 322 LEU cc_start: 0.8672 (tp) cc_final: 0.8209 (pt) REVERT: D 379 ASN cc_start: 0.7641 (t0) cc_final: 0.7256 (t0) REVERT: D 489 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8022 (p) REVERT: D 503 SER cc_start: 0.8592 (m) cc_final: 0.8239 (p) REVERT: D 518 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7735 (tm-30) REVERT: D 537 THR cc_start: 0.8022 (m) cc_final: 0.7683 (p) REVERT: D 588 ASN cc_start: 0.8214 (m-40) cc_final: 0.7906 (m-40) REVERT: D 600 ASN cc_start: 0.8162 (m-40) cc_final: 0.7465 (m-40) REVERT: D 608 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7501 (p) REVERT: D 647 GLN cc_start: 0.7472 (pt0) cc_final: 0.7032 (pt0) REVERT: D 652 VAL cc_start: 0.8498 (m) cc_final: 0.8269 (p) REVERT: D 683 ASP cc_start: 0.7223 (t0) cc_final: 0.6983 (t0) REVERT: D 695 ASP cc_start: 0.6089 (p0) cc_final: 0.5772 (p0) REVERT: D 746 LYS cc_start: 0.8028 (mmmm) cc_final: 0.7789 (mmmm) REVERT: D 756 THR cc_start: 0.8660 (m) cc_final: 0.8094 (p) REVERT: D 784 ASN cc_start: 0.7917 (m-40) cc_final: 0.7387 (t0) REVERT: D 786 GLN cc_start: 0.7106 (mt0) cc_final: 0.6835 (mt0) REVERT: F 4 THR cc_start: 0.8548 (m) cc_final: 0.8154 (p) REVERT: F 65 VAL cc_start: 0.8845 (t) cc_final: 0.8377 (p) REVERT: F 123 ASN cc_start: 0.7892 (t0) cc_final: 0.7441 (t0) REVERT: C 75 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7709 (mt) REVERT: C 151 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8424 (p) REVERT: H 236 ASN cc_start: 0.8511 (t0) cc_final: 0.8235 (t0) outliers start: 40 outliers final: 34 residues processed: 295 average time/residue: 0.1928 time to fit residues: 80.3904 Evaluate side-chains 315 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 277 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 269 GLN Chi-restraints excluded: chain H residue 271 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 GLN D 257 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9522 Z= 0.236 Angle : 0.655 13.043 13079 Z= 0.329 Chirality : 0.046 0.179 1569 Planarity : 0.004 0.058 1758 Dihedral : 3.889 16.918 1519 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.54 % Allowed : 37.46 % Favored : 57.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.01 (0.23), residues: 1424 helix: -1.46 (0.82), residues: 44 sheet: 0.86 (0.21), residues: 614 loop : -0.63 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 114 HIS 0.005 0.001 HIS D 504 PHE 0.018 0.002 PHE D 416 TYR 0.023 0.002 TYR H 186 ARG 0.008 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 281 time to evaluate : 0.987 Fit side-chains REVERT: D 142 LEU cc_start: 0.8529 (tt) cc_final: 0.8236 (tt) REVERT: D 210 ILE cc_start: 0.8737 (mm) cc_final: 0.8381 (mm) REVERT: D 259 ILE cc_start: 0.7989 (mm) cc_final: 0.6501 (pt) REVERT: D 344 GLN cc_start: 0.8058 (pm20) cc_final: 0.7806 (pt0) REVERT: D 379 ASN cc_start: 0.7615 (t0) cc_final: 0.7220 (t0) REVERT: D 382 ILE cc_start: 0.8538 (mp) cc_final: 0.8168 (mm) REVERT: D 489 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8007 (p) REVERT: D 503 SER cc_start: 0.8606 (m) cc_final: 0.8263 (p) REVERT: D 518 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7791 (tm-30) REVERT: D 537 THR cc_start: 0.8042 (m) cc_final: 0.7714 (p) REVERT: D 557 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7809 (m-10) REVERT: D 588 ASN cc_start: 0.8137 (m-40) cc_final: 0.7661 (m-40) REVERT: D 600 ASN cc_start: 0.8134 (m-40) cc_final: 0.7543 (m-40) REVERT: D 608 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7531 (p) REVERT: D 647 GLN cc_start: 0.7491 (pt0) cc_final: 0.7076 (pt0) REVERT: D 652 VAL cc_start: 0.8502 (m) cc_final: 0.8253 (p) REVERT: D 683 ASP cc_start: 0.7364 (t0) cc_final: 0.7134 (t0) REVERT: D 695 ASP cc_start: 0.6276 (p0) cc_final: 0.5922 (p0) REVERT: D 756 THR cc_start: 0.8686 (m) cc_final: 0.8141 (p) REVERT: D 784 ASN cc_start: 0.7946 (m-40) cc_final: 0.7453 (t0) REVERT: D 786 GLN cc_start: 0.7091 (mt0) cc_final: 0.6830 (mt0) REVERT: F 4 THR cc_start: 0.8525 (m) cc_final: 0.8157 (p) REVERT: F 65 VAL cc_start: 0.8859 (t) cc_final: 0.8381 (p) REVERT: F 123 ASN cc_start: 0.7984 (t0) cc_final: 0.7542 (t0) REVERT: C 151 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8377 (p) outliers start: 38 outliers final: 33 residues processed: 297 average time/residue: 0.1960 time to fit residues: 82.9675 Evaluate side-chains 314 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 277 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 269 GLN Chi-restraints excluded: chain H residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 93 optimal weight: 0.4980 chunk 141 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 112 optimal weight: 0.0980 chunk 11 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 69 optimal weight: 0.0060 chunk 89 optimal weight: 6.9990 chunk 120 optimal weight: 30.0000 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 257 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9522 Z= 0.164 Angle : 0.641 9.447 13079 Z= 0.320 Chirality : 0.046 0.171 1569 Planarity : 0.004 0.059 1758 Dihedral : 3.730 18.285 1519 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.66 % Allowed : 38.19 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.10 (0.23), residues: 1424 helix: -1.35 (0.83), residues: 44 sheet: 0.91 (0.21), residues: 611 loop : -0.54 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 508 HIS 0.005 0.001 HIS D 659 PHE 0.013 0.001 PHE D 416 TYR 0.023 0.001 TYR D 708 ARG 0.007 0.001 ARG C 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.033 Fit side-chains REVERT: D 142 LEU cc_start: 0.8547 (tt) cc_final: 0.8269 (tt) REVERT: D 210 ILE cc_start: 0.8677 (mm) cc_final: 0.8357 (mm) REVERT: D 259 ILE cc_start: 0.7957 (mm) cc_final: 0.6444 (pt) REVERT: D 312 ILE cc_start: 0.8693 (mp) cc_final: 0.8439 (mp) REVERT: D 344 GLN cc_start: 0.8028 (pm20) cc_final: 0.7807 (pt0) REVERT: D 379 ASN cc_start: 0.7698 (t0) cc_final: 0.7298 (t0) REVERT: D 489 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.7994 (p) REVERT: D 503 SER cc_start: 0.8585 (m) cc_final: 0.8246 (p) REVERT: D 518 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7779 (tm-30) REVERT: D 531 THR cc_start: 0.7568 (OUTLIER) cc_final: 0.7268 (p) REVERT: D 537 THR cc_start: 0.8028 (m) cc_final: 0.7689 (p) REVERT: D 588 ASN cc_start: 0.8154 (m-40) cc_final: 0.7669 (m-40) REVERT: D 600 ASN cc_start: 0.8142 (m-40) cc_final: 0.7557 (t0) REVERT: D 647 GLN cc_start: 0.7458 (pt0) cc_final: 0.7018 (pt0) REVERT: D 652 VAL cc_start: 0.8491 (m) cc_final: 0.8244 (p) REVERT: D 695 ASP cc_start: 0.6089 (p0) cc_final: 0.5881 (p0) REVERT: D 756 THR cc_start: 0.8673 (m) cc_final: 0.8338 (p) REVERT: D 784 ASN cc_start: 0.7909 (m-40) cc_final: 0.7427 (t0) REVERT: D 786 GLN cc_start: 0.7094 (mt0) cc_final: 0.6831 (mt0) REVERT: F 4 THR cc_start: 0.8526 (m) cc_final: 0.8163 (p) REVERT: F 65 VAL cc_start: 0.8784 (t) cc_final: 0.8309 (p) REVERT: F 123 ASN cc_start: 0.7882 (t0) cc_final: 0.7442 (t0) REVERT: C 151 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8420 (p) REVERT: H 236 ASN cc_start: 0.8513 (t0) cc_final: 0.8245 (t0) outliers start: 32 outliers final: 29 residues processed: 287 average time/residue: 0.1960 time to fit residues: 79.5490 Evaluate side-chains 304 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 269 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 112 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 115 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 257 HIS D 728 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.101953 restraints weight = 17317.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105401 restraints weight = 9681.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107707 restraints weight = 6247.761| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9522 Z= 0.196 Angle : 0.655 14.571 13079 Z= 0.325 Chirality : 0.046 0.172 1569 Planarity : 0.004 0.059 1758 Dihedral : 3.791 18.852 1519 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.69 % Allowed : 37.17 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.11 (0.23), residues: 1424 helix: -1.37 (0.82), residues: 44 sheet: 0.92 (0.21), residues: 611 loop : -0.54 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 114 HIS 0.004 0.001 HIS D 504 PHE 0.018 0.002 PHE C 55 TYR 0.023 0.002 TYR H 186 ARG 0.006 0.001 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2357.95 seconds wall clock time: 43 minutes 25.65 seconds (2605.65 seconds total)