Starting phenix.real_space_refine on Fri Aug 22 23:42:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9l_35275/08_2025/8i9l_35275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9l_35275/08_2025/8i9l_35275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i9l_35275/08_2025/8i9l_35275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9l_35275/08_2025/8i9l_35275.map" model { file = "/net/cci-nas-00/data/ceres_data/8i9l_35275/08_2025/8i9l_35275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9l_35275/08_2025/8i9l_35275.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 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 60 5.16 5 C 5488 2.51 5 N 1485 2.21 5 O 1584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8617 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2421 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 90 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1575 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 51 Chain: "G" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 398 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1698 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2056 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TRP:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'ARG:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 57 Time building chain proxies: 2.39, per 1000 atoms: 0.28 Number of scatterers: 8617 At special positions: 0 Unit cell: (89.3004, 119.067, 140.329, 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 60 16.00 O 1584 8.00 N 1485 7.00 C 5488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 49 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 56 " distance=2.03 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 57 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 507.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.4% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.597A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.917A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.554A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.769A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.991A pdb=" N VAL A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 4.028A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.772A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.602A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 50 Proline residue: C 39 - end of helix Processing helix chain 'C' and resid 55 through 84 removed outlier: 3.878A pdb=" N TRP C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 91 through 126 removed outlier: 3.528A pdb=" N CYS C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Proline residue: C 99 - end of helix removed outlier: 5.101A pdb=" N VAL C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 133 removed outlier: 3.726A pdb=" N ASN C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 159 Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 332 through 363 removed outlier: 4.792A pdb=" N LEU C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 374 through 390 Processing helix chain 'C' and resid 390 through 403 removed outlier: 3.999A pdb=" N LEU C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 402 " --> pdb=" O VAL C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 436 removed outlier: 3.834A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'C' and resid 439 through 450 Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.824A pdb=" N LYS D 7 " --> pdb=" O GLN D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 4.214A pdb=" N ALA D 48 " --> pdb=" O LEU D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 49 through 71 removed outlier: 3.684A pdb=" N ASN D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.579A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.012A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.102A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.056A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.619A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.694A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 275 removed outlier: 3.991A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 186 through 192 removed outlier: 3.866A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.898A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.368A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.593A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 149 removed outlier: 3.963A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL H 149 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 162 through 163 465 hydrogen bonds defined for protein. 1311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2803 1.34 - 1.46: 1766 1.46 - 1.58: 4157 1.58 - 1.70: 0 1.70 - 1.81: 77 Bond restraints: 8803 Sorted by residual: bond pdb=" N THR C 337 " pdb=" CA THR C 337 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.30e-02 5.92e+03 8.88e+00 bond pdb=" N ASN A 43 " pdb=" CA ASN A 43 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.72e+00 bond pdb=" N VAL C 103 " pdb=" CA VAL C 103 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.33e-02 5.65e+03 6.25e+00 bond pdb=" N ASP C 167 " pdb=" CA ASP C 167 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.17e-02 7.31e+03 6.19e+00 bond pdb=" N LEU D 75 " pdb=" CA LEU D 75 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.48e-02 4.57e+03 5.64e+00 ... (remaining 8798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 11816 2.06 - 4.12: 145 4.12 - 6.17: 31 6.17 - 8.23: 5 8.23 - 10.29: 1 Bond angle restraints: 11998 Sorted by residual: angle pdb=" N LEU D 73 " pdb=" CA LEU D 73 " pdb=" C LEU D 73 " ideal model delta sigma weight residual 108.67 98.38 10.29 1.55e+00 4.16e-01 4.41e+01 angle pdb=" N ILE C 163 " pdb=" CA ILE C 163 " pdb=" C ILE C 163 " ideal model delta sigma weight residual 107.75 99.79 7.96 1.46e+00 4.69e-01 2.97e+01 angle pdb=" C PHE D 42 " pdb=" CA PHE D 42 " pdb=" CB PHE D 42 " ideal model delta sigma weight residual 115.79 109.69 6.10 1.19e+00 7.06e-01 2.63e+01 angle pdb=" N LEU D 75 " pdb=" CA LEU D 75 " pdb=" C LEU D 75 " ideal model delta sigma weight residual 112.47 117.52 -5.05 1.24e+00 6.50e-01 1.66e+01 angle pdb=" N LEU A 13 " pdb=" CA LEU A 13 " pdb=" C LEU A 13 " ideal model delta sigma weight residual 111.28 107.18 4.10 1.09e+00 8.42e-01 1.42e+01 ... (remaining 11993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 4624 16.29 - 32.59: 425 32.59 - 48.88: 77 48.88 - 65.18: 8 65.18 - 81.47: 7 Dihedral angle restraints: 5141 sinusoidal: 1731 harmonic: 3410 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 49 " pdb=" CB CYS D 49 " ideal model delta sinusoidal sigma weight residual -86.00 -52.60 -33.40 1 1.00e+01 1.00e-02 1.59e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 56 " pdb=" CB CYS D 56 " ideal model delta sinusoidal sigma weight residual -86.00 -115.09 29.09 1 1.00e+01 1.00e-02 1.21e+01 dihedral pdb=" CA PRO C 99 " pdb=" C PRO C 99 " pdb=" N SER C 100 " pdb=" CA SER C 100 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1189 0.056 - 0.112: 186 0.112 - 0.168: 19 0.168 - 0.223: 2 0.223 - 0.279: 2 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CA LEU D 73 " pdb=" N LEU D 73 " pdb=" C LEU D 73 " pdb=" CB LEU D 73 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1395 not shown) Planarity restraints: 1535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 162 " -0.023 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C GLU C 162 " 0.084 2.00e-02 2.50e+03 pdb=" O GLU C 162 " -0.033 2.00e-02 2.50e+03 pdb=" N ILE C 163 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 72 " 0.023 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" C HIS D 72 " -0.080 2.00e-02 2.50e+03 pdb=" O HIS D 72 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU D 73 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 74 " -0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C GLY D 74 " 0.065 2.00e-02 2.50e+03 pdb=" O GLY D 74 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU D 75 " -0.022 2.00e-02 2.50e+03 ... (remaining 1532 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1503 2.77 - 3.30: 8306 3.30 - 3.83: 14508 3.83 - 4.37: 16466 4.37 - 4.90: 29548 Nonbonded interactions: 70331 Sorted by model distance: nonbonded pdb=" OG1 THR B 165 " pdb=" O PHE B 180 " model vdw 2.235 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.241 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.291 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.295 3.040 nonbonded pdb=" O PHE H 32 " pdb=" NH2 ARG H 72 " model vdw 2.306 3.120 ... (remaining 70326 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8809 Z= 0.157 Angle : 0.582 10.291 12010 Z= 0.345 Chirality : 0.042 0.279 1398 Planarity : 0.004 0.057 1535 Dihedral : 12.918 81.470 2921 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.96 % Allowed : 0.84 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.26), residues: 1161 helix: 1.79 (0.27), residues: 419 sheet: -0.40 (0.31), residues: 276 loop : -0.82 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 160 TYR 0.016 0.001 TYR A 231 PHE 0.016 0.001 PHE C 430 TRP 0.008 0.001 TRP H 111 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8803) covalent geometry : angle 0.58158 (11998) SS BOND : bond 0.00160 ( 6) SS BOND : angle 1.06300 ( 12) hydrogen bonds : bond 0.18506 ( 460) hydrogen bonds : angle 7.34254 ( 1311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6632 (mtm110) REVERT: D 72 HIS cc_start: 0.7071 (m90) cc_final: 0.6757 (m90) REVERT: D 73 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7408 (tm) outliers start: 8 outliers final: 3 residues processed: 151 average time/residue: 0.0875 time to fit residues: 17.6137 Evaluate side-chains 134 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 77 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN H 113 GLN C 41 ASN D 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.141179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.115484 restraints weight = 14033.991| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.00 r_work: 0.3497 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8809 Z= 0.144 Angle : 0.556 6.835 12010 Z= 0.294 Chirality : 0.043 0.185 1398 Planarity : 0.004 0.042 1535 Dihedral : 4.976 68.653 1270 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.20 % Allowed : 8.13 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.26), residues: 1161 helix: 1.77 (0.27), residues: 422 sheet: -0.41 (0.31), residues: 273 loop : -0.66 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 46 TYR 0.014 0.001 TYR D 59 PHE 0.024 0.001 PHE C 151 TRP 0.011 0.001 TRP B 297 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8803) covalent geometry : angle 0.55472 (11998) SS BOND : bond 0.00253 ( 6) SS BOND : angle 1.10319 ( 12) hydrogen bonds : bond 0.04063 ( 460) hydrogen bonds : angle 5.33088 ( 1311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: B 298 ASP cc_start: 0.7864 (t70) cc_final: 0.7568 (t70) REVERT: A 10 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6843 (mtt180) REVERT: H 178 LEU cc_start: 0.8083 (tp) cc_final: 0.7844 (tp) REVERT: C 88 TRP cc_start: 0.7096 (t-100) cc_final: 0.6812 (t-100) REVERT: C 92 ARG cc_start: 0.6807 (ttt180) cc_final: 0.6588 (ttt180) REVERT: C 340 ARG cc_start: 0.7407 (ttm170) cc_final: 0.6560 (ttm110) REVERT: D 72 HIS cc_start: 0.7641 (m90) cc_final: 0.7437 (m-70) REVERT: D 73 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7619 (tm) outliers start: 10 outliers final: 3 residues processed: 144 average time/residue: 0.0831 time to fit residues: 15.8442 Evaluate side-chains 138 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 77 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 90 optimal weight: 0.0030 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN C 427 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.144441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.117280 restraints weight = 13659.995| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.09 r_work: 0.3451 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8809 Z= 0.195 Angle : 0.572 6.903 12010 Z= 0.303 Chirality : 0.044 0.178 1398 Planarity : 0.004 0.040 1535 Dihedral : 5.005 73.045 1262 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.20 % Allowed : 11.96 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.26), residues: 1161 helix: 1.69 (0.27), residues: 423 sheet: -0.48 (0.30), residues: 281 loop : -0.85 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 46 TYR 0.015 0.002 TYR D 59 PHE 0.023 0.002 PHE C 151 TRP 0.012 0.002 TRP B 99 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 8803) covalent geometry : angle 0.57154 (11998) SS BOND : bond 0.00228 ( 6) SS BOND : angle 0.98125 ( 12) hydrogen bonds : bond 0.03978 ( 460) hydrogen bonds : angle 5.07618 ( 1311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.7284 (t0) cc_final: 0.6823 (t0) REVERT: B 298 ASP cc_start: 0.7953 (t70) cc_final: 0.7666 (t70) REVERT: H 178 LEU cc_start: 0.8076 (tp) cc_final: 0.7799 (tp) REVERT: C 88 TRP cc_start: 0.7236 (t-100) cc_final: 0.6995 (t-100) REVERT: C 340 ARG cc_start: 0.7486 (ttm170) cc_final: 0.6535 (ttm110) REVERT: D 72 HIS cc_start: 0.7643 (m90) cc_final: 0.7435 (m-70) REVERT: D 73 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8085 (tm) outliers start: 10 outliers final: 7 residues processed: 139 average time/residue: 0.0752 time to fit residues: 14.2228 Evaluate side-chains 138 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 51 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.142937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.115484 restraints weight = 14085.397| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.18 r_work: 0.3454 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8809 Z= 0.150 Angle : 0.543 7.024 12010 Z= 0.285 Chirality : 0.042 0.172 1398 Planarity : 0.004 0.036 1535 Dihedral : 4.676 73.011 1258 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.44 % Allowed : 13.16 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.25), residues: 1161 helix: 1.67 (0.26), residues: 422 sheet: -0.40 (0.32), residues: 268 loop : -0.88 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 46 TYR 0.013 0.001 TYR D 59 PHE 0.024 0.001 PHE C 151 TRP 0.012 0.001 TRP B 99 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8803) covalent geometry : angle 0.54282 (11998) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.85940 ( 12) hydrogen bonds : bond 0.03548 ( 460) hydrogen bonds : angle 4.92264 ( 1311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: B 298 ASP cc_start: 0.7966 (t70) cc_final: 0.7669 (t70) REVERT: A 195 LEU cc_start: 0.7682 (tt) cc_final: 0.7482 (tp) REVERT: A 244 MET cc_start: 0.4932 (tpt) cc_final: 0.4677 (tpp) REVERT: C 88 TRP cc_start: 0.7237 (t-100) cc_final: 0.7007 (t-100) REVERT: C 340 ARG cc_start: 0.7454 (ttm170) cc_final: 0.6482 (ttm110) outliers start: 12 outliers final: 10 residues processed: 151 average time/residue: 0.0792 time to fit residues: 16.0169 Evaluate side-chains 144 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 0.0470 chunk 58 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 overall best weight: 0.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.138801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.112922 restraints weight = 14266.392| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.05 r_work: 0.3463 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8809 Z= 0.129 Angle : 0.524 7.757 12010 Z= 0.274 Chirality : 0.042 0.158 1398 Planarity : 0.004 0.037 1535 Dihedral : 4.614 73.221 1258 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.79 % Allowed : 14.11 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.26), residues: 1161 helix: 1.72 (0.26), residues: 421 sheet: -0.35 (0.32), residues: 269 loop : -0.84 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 160 TYR 0.013 0.001 TYR C 435 PHE 0.020 0.001 PHE C 151 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8803) covalent geometry : angle 0.52404 (11998) SS BOND : bond 0.00173 ( 6) SS BOND : angle 0.75818 ( 12) hydrogen bonds : bond 0.03326 ( 460) hydrogen bonds : angle 4.76773 ( 1311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: B 298 ASP cc_start: 0.7921 (t70) cc_final: 0.7620 (t70) REVERT: B 301 LYS cc_start: 0.8194 (mmpt) cc_final: 0.7910 (mmmt) REVERT: C 88 TRP cc_start: 0.7225 (t-100) cc_final: 0.6975 (t-100) REVERT: C 337 THR cc_start: 0.5445 (t) cc_final: 0.5244 (t) REVERT: C 340 ARG cc_start: 0.7404 (ttm170) cc_final: 0.6454 (ttm110) REVERT: C 437 LEU cc_start: 0.6922 (mp) cc_final: 0.6387 (mp) REVERT: C 443 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7390 (ttm170) outliers start: 15 outliers final: 11 residues processed: 148 average time/residue: 0.0741 time to fit residues: 15.1303 Evaluate side-chains 144 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.141484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114361 restraints weight = 13994.701| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.12 r_work: 0.3439 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8809 Z= 0.182 Angle : 0.563 8.817 12010 Z= 0.295 Chirality : 0.043 0.192 1398 Planarity : 0.004 0.038 1535 Dihedral : 4.763 74.146 1258 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.15 % Allowed : 16.27 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.25), residues: 1161 helix: 1.68 (0.27), residues: 420 sheet: -0.47 (0.31), residues: 273 loop : -0.91 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 160 TYR 0.015 0.002 TYR C 435 PHE 0.018 0.002 PHE C 151 TRP 0.011 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 8803) covalent geometry : angle 0.56300 (11998) SS BOND : bond 0.00202 ( 6) SS BOND : angle 0.88041 ( 12) hydrogen bonds : bond 0.03603 ( 460) hydrogen bonds : angle 4.86145 ( 1311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: B 298 ASP cc_start: 0.7930 (t70) cc_final: 0.7659 (t70) REVERT: B 301 LYS cc_start: 0.8338 (mmpt) cc_final: 0.8030 (mmtt) REVERT: A 10 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6799 (mtt180) REVERT: C 88 TRP cc_start: 0.7329 (t-100) cc_final: 0.7095 (t-100) REVERT: C 337 THR cc_start: 0.5754 (t) cc_final: 0.5550 (t) REVERT: C 340 ARG cc_start: 0.7463 (ttm170) cc_final: 0.6501 (ttm110) REVERT: C 437 LEU cc_start: 0.6981 (mp) cc_final: 0.6420 (mp) REVERT: C 443 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7487 (ttm170) outliers start: 18 outliers final: 11 residues processed: 152 average time/residue: 0.0830 time to fit residues: 16.9068 Evaluate side-chains 148 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 77 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.141742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114508 restraints weight = 14042.627| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.12 r_work: 0.3424 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8809 Z= 0.174 Angle : 0.564 8.803 12010 Z= 0.295 Chirality : 0.044 0.188 1398 Planarity : 0.004 0.038 1535 Dihedral : 4.758 73.374 1258 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.15 % Allowed : 16.75 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.25), residues: 1161 helix: 1.63 (0.26), residues: 420 sheet: -0.51 (0.32), residues: 268 loop : -0.90 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 160 TYR 0.015 0.002 TYR C 435 PHE 0.029 0.002 PHE C 151 TRP 0.012 0.002 TRP B 99 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8803) covalent geometry : angle 0.56406 (11998) SS BOND : bond 0.00188 ( 6) SS BOND : angle 0.84266 ( 12) hydrogen bonds : bond 0.03527 ( 460) hydrogen bonds : angle 4.84714 ( 1311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: B 273 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7533 (mp) REVERT: A 10 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6731 (mtt180) REVERT: A 299 ASP cc_start: 0.7325 (t0) cc_final: 0.7063 (t0) REVERT: C 88 TRP cc_start: 0.7296 (t-100) cc_final: 0.7051 (t-100) REVERT: C 337 THR cc_start: 0.5758 (t) cc_final: 0.5548 (t) REVERT: C 340 ARG cc_start: 0.7425 (ttm170) cc_final: 0.6475 (ttm110) REVERT: C 437 LEU cc_start: 0.7005 (mp) cc_final: 0.6466 (mp) REVERT: C 443 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7332 (ttm170) outliers start: 18 outliers final: 13 residues processed: 148 average time/residue: 0.0757 time to fit residues: 15.2560 Evaluate side-chains 150 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 43 optimal weight: 0.0870 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 0.0770 chunk 62 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.0050 chunk 66 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.3730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.138561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112886 restraints weight = 14065.051| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.02 r_work: 0.3475 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8809 Z= 0.131 Angle : 0.542 9.325 12010 Z= 0.282 Chirality : 0.042 0.167 1398 Planarity : 0.004 0.038 1535 Dihedral : 4.659 71.956 1258 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.03 % Allowed : 16.75 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.25), residues: 1161 helix: 1.64 (0.26), residues: 420 sheet: -0.56 (0.32), residues: 267 loop : -0.81 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 160 TYR 0.014 0.001 TYR C 435 PHE 0.024 0.001 PHE C 151 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8803) covalent geometry : angle 0.54221 (11998) SS BOND : bond 0.00167 ( 6) SS BOND : angle 0.73610 ( 12) hydrogen bonds : bond 0.03311 ( 460) hydrogen bonds : angle 4.74037 ( 1311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: B 298 ASP cc_start: 0.7946 (t70) cc_final: 0.7602 (t0) REVERT: A 10 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6672 (mtt180) REVERT: A 244 MET cc_start: 0.4815 (tpt) cc_final: 0.4483 (tpp) REVERT: A 299 ASP cc_start: 0.7245 (t0) cc_final: 0.6990 (t0) REVERT: C 88 TRP cc_start: 0.7284 (t-100) cc_final: 0.7058 (t-100) REVERT: C 340 ARG cc_start: 0.7418 (ttm170) cc_final: 0.6476 (ttm110) REVERT: C 437 LEU cc_start: 0.6948 (mp) cc_final: 0.6415 (mp) REVERT: C 443 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7407 (ttm170) outliers start: 17 outliers final: 12 residues processed: 151 average time/residue: 0.0830 time to fit residues: 16.9632 Evaluate side-chains 148 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.1980 chunk 109 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 48 optimal weight: 0.0970 chunk 103 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 0.0870 chunk 55 optimal weight: 3.9990 overall best weight: 0.1494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.140863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.115263 restraints weight = 14095.732| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.04 r_work: 0.3522 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8809 Z= 0.103 Angle : 0.518 10.012 12010 Z= 0.271 Chirality : 0.042 0.140 1398 Planarity : 0.003 0.036 1535 Dihedral : 4.422 69.477 1258 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.08 % Allowed : 17.94 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.26), residues: 1161 helix: 1.74 (0.27), residues: 421 sheet: -0.52 (0.32), residues: 272 loop : -0.65 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 160 TYR 0.014 0.001 TYR D 59 PHE 0.023 0.001 PHE C 151 TRP 0.014 0.001 TRP H 111 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 8803) covalent geometry : angle 0.51826 (11998) SS BOND : bond 0.00188 ( 6) SS BOND : angle 0.58528 ( 12) hydrogen bonds : bond 0.03048 ( 460) hydrogen bonds : angle 4.51842 ( 1311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: B 189 SER cc_start: 0.7731 (p) cc_final: 0.7489 (p) REVERT: B 298 ASP cc_start: 0.7941 (t70) cc_final: 0.7593 (t0) REVERT: A 244 MET cc_start: 0.4887 (tpt) cc_final: 0.4582 (tpp) REVERT: H 178 LEU cc_start: 0.8095 (tp) cc_final: 0.7796 (tp) REVERT: C 88 TRP cc_start: 0.7192 (t-100) cc_final: 0.6940 (t-100) REVERT: C 340 ARG cc_start: 0.7346 (ttm170) cc_final: 0.6408 (ttm110) REVERT: C 367 ARG cc_start: 0.6515 (ttt-90) cc_final: 0.6151 (ttt-90) REVERT: C 443 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7540 (mtm180) outliers start: 9 outliers final: 7 residues processed: 148 average time/residue: 0.0814 time to fit residues: 16.1633 Evaluate side-chains 145 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 35 optimal weight: 0.0670 chunk 58 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 0.0040 chunk 46 optimal weight: 0.0970 chunk 82 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.2928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.140764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.115221 restraints weight = 14046.552| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.98 r_work: 0.3491 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8809 Z= 0.119 Angle : 0.549 10.509 12010 Z= 0.281 Chirality : 0.042 0.142 1398 Planarity : 0.004 0.039 1535 Dihedral : 4.411 68.166 1258 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.96 % Allowed : 18.42 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.26), residues: 1161 helix: 1.77 (0.27), residues: 421 sheet: -0.52 (0.31), residues: 277 loop : -0.63 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 160 TYR 0.018 0.001 TYR H 60 PHE 0.022 0.001 PHE C 151 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8803) covalent geometry : angle 0.54877 (11998) SS BOND : bond 0.00181 ( 6) SS BOND : angle 0.65538 ( 12) hydrogen bonds : bond 0.03137 ( 460) hydrogen bonds : angle 4.50523 ( 1311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: B 298 ASP cc_start: 0.7917 (t70) cc_final: 0.7570 (t0) REVERT: A 217 GLU cc_start: 0.6469 (mm-30) cc_final: 0.6030 (mm-30) REVERT: A 244 MET cc_start: 0.4793 (tpt) cc_final: 0.4480 (tpp) REVERT: H 178 LEU cc_start: 0.8100 (tp) cc_final: 0.7795 (tp) REVERT: C 88 TRP cc_start: 0.7141 (t-100) cc_final: 0.6855 (t-100) REVERT: C 340 ARG cc_start: 0.7319 (ttm170) cc_final: 0.6472 (ttm110) REVERT: C 443 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7327 (ttm170) outliers start: 8 outliers final: 6 residues processed: 146 average time/residue: 0.1083 time to fit residues: 21.2194 Evaluate side-chains 143 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 115 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.138536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112467 restraints weight = 14092.103| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.03 r_work: 0.3453 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8809 Z= 0.156 Angle : 0.570 10.409 12010 Z= 0.294 Chirality : 0.043 0.152 1398 Planarity : 0.004 0.040 1535 Dihedral : 4.547 68.076 1258 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.20 % Allowed : 18.54 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.26), residues: 1161 helix: 1.73 (0.26), residues: 421 sheet: -0.59 (0.31), residues: 278 loop : -0.65 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 160 TYR 0.014 0.002 TYR C 435 PHE 0.025 0.002 PHE C 151 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8803) covalent geometry : angle 0.57003 (11998) SS BOND : bond 0.00185 ( 6) SS BOND : angle 0.79715 ( 12) hydrogen bonds : bond 0.03376 ( 460) hydrogen bonds : angle 4.65812 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2348.92 seconds wall clock time: 40 minutes 49.56 seconds (2449.56 seconds total)