Starting phenix.real_space_refine on Tue Apr 29 11:00:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9l_35275/04_2025/8i9l_35275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9l_35275/04_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_35275/04_2025/8i9l_35275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9l_35275/04_2025/8i9l_35275.map" model { file = "/net/cci-nas-00/data/ceres_data/8i9l_35275/04_2025/8i9l_35275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9l_35275/04_2025/8i9l_35275.cif" } resolution = 3.18 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= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 10} 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: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} 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, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLN:plan1': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} 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: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 57 Time building chain proxies: 5.52, per 1000 atoms: 0.64 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: 1.97 Conformation dependent library (CDL) restraints added in 998.6 milliseconds 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: 0.97 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: 2.36 Time building geometry restraints manager: 2.36 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: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.920 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.310 ------------------------------------------------------------------------------- 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 : 8.98 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 (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: 0.32 (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 TRP 0.008 0.001 TRP H 111 HIS 0.003 0.001 HIS C 418 PHE 0.016 0.001 PHE C 430 TYR 0.016 0.001 TYR A 231 ARG 0.008 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.18506 ( 460) hydrogen bonds : angle 7.34254 ( 1311) SS BOND : bond 0.00160 ( 6) SS BOND : angle 1.06300 ( 12) covalent geometry : bond 0.00258 ( 8803) covalent geometry : angle 0.58158 (11998) *********************** 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 : 0.835 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: 0.2466 time to fit residues: 49.1790 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 : 1.014 ------------------------------------------------------------------------------- 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 97 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN A 256 ASN H 113 GLN C 41 ASN D 66 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.139020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111486 restraints weight = 13814.552| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.17 r_work: 0.3422 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8809 Z= 0.268 Angle : 0.637 6.963 12010 Z= 0.338 Chirality : 0.047 0.205 1398 Planarity : 0.005 0.050 1535 Dihedral : 5.337 72.450 1270 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.67 % Allowed : 9.45 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.19 (0.26), residues: 1161 helix: 1.62 (0.26), residues: 427 sheet: -0.50 (0.31), residues: 279 loop : -0.83 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 60 HIS 0.006 0.002 HIS B 142 PHE 0.025 0.002 PHE C 151 TYR 0.016 0.002 TYR H 103 ARG 0.005 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.04902 ( 460) hydrogen bonds : angle 5.53894 ( 1311) SS BOND : bond 0.00300 ( 6) SS BOND : angle 1.31154 ( 12) covalent geometry : bond 0.00626 ( 8803) covalent geometry : angle 0.63584 (11998) *********************** 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 147 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.7356 (t0) cc_final: 0.6942 (t0) REVERT: A 10 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.6926 (mtt180) REVERT: A 244 MET cc_start: 0.5593 (tpp) cc_final: 0.5084 (tpp) REVERT: C 88 TRP cc_start: 0.7232 (t-100) cc_final: 0.6998 (t-100) REVERT: C 340 ARG cc_start: 0.7684 (ttm170) cc_final: 0.6734 (ttm110) REVERT: D 72 HIS cc_start: 0.7585 (m90) cc_final: 0.7292 (m-70) REVERT: D 73 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7588 (tm) outliers start: 14 outliers final: 9 residues processed: 140 average time/residue: 0.2378 time to fit residues: 44.5393 Evaluate side-chains 140 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 10 ARG Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 220 THR 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 C residue 393 TYR 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 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.135146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109224 restraints weight = 14278.561| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.00 r_work: 0.3450 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8809 Z= 0.189 Angle : 0.573 7.214 12010 Z= 0.301 Chirality : 0.044 0.178 1398 Planarity : 0.004 0.046 1535 Dihedral : 5.119 76.919 1264 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.32 % Allowed : 13.04 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.08 (0.25), residues: 1161 helix: 1.59 (0.26), residues: 422 sheet: -0.55 (0.31), residues: 269 loop : -0.94 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.005 0.001 HIS B 142 PHE 0.018 0.002 PHE C 430 TYR 0.014 0.002 TYR D 59 ARG 0.005 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 460) hydrogen bonds : angle 5.12193 ( 1311) SS BOND : bond 0.00205 ( 6) SS BOND : angle 0.98216 ( 12) covalent geometry : bond 0.00438 ( 8803) covalent geometry : angle 0.57199 (11998) *********************** 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 147 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: B 273 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7510 (mp) REVERT: A 244 MET cc_start: 0.5555 (tpp) cc_final: 0.5022 (tpp) REVERT: C 88 TRP cc_start: 0.7260 (t-100) cc_final: 0.7046 (t-100) REVERT: C 340 ARG cc_start: 0.7494 (ttm170) cc_final: 0.6534 (ttm110) REVERT: D 72 HIS cc_start: 0.7588 (m90) cc_final: 0.7294 (m-70) REVERT: D 73 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8115 (tm) outliers start: 11 outliers final: 7 residues processed: 143 average time/residue: 0.2316 time to fit residues: 44.6242 Evaluate side-chains 136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 26 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.140232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.112797 restraints weight = 13993.166| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.16 r_work: 0.3411 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8809 Z= 0.217 Angle : 0.595 8.076 12010 Z= 0.313 Chirality : 0.045 0.200 1398 Planarity : 0.004 0.043 1535 Dihedral : 5.015 78.794 1258 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.91 % Allowed : 15.07 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.05 (0.25), residues: 1161 helix: 1.51 (0.26), residues: 421 sheet: -0.71 (0.31), residues: 269 loop : -0.99 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS B 142 PHE 0.028 0.002 PHE C 151 TYR 0.013 0.002 TYR H 103 ARG 0.007 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 460) hydrogen bonds : angle 5.08694 ( 1311) SS BOND : bond 0.00237 ( 6) SS BOND : angle 1.05225 ( 12) covalent geometry : bond 0.00506 ( 8803) covalent geometry : angle 0.59433 (11998) *********************** 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 151 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6819 (mtt180) REVERT: A 244 MET cc_start: 0.5747 (tpp) cc_final: 0.5222 (tpp) REVERT: H 77 ASN cc_start: 0.8021 (t0) cc_final: 0.7595 (t0) REVERT: C 88 TRP cc_start: 0.7347 (t-100) cc_final: 0.7146 (t-100) REVERT: C 337 THR cc_start: 0.5673 (t) cc_final: 0.5467 (t) REVERT: C 340 ARG cc_start: 0.7560 (ttm170) cc_final: 0.6620 (ttm110) REVERT: D 72 HIS cc_start: 0.7656 (m90) cc_final: 0.7392 (m-70) outliers start: 16 outliers final: 11 residues processed: 146 average time/residue: 0.2337 time to fit residues: 45.8849 Evaluate side-chains 141 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 109 ASP 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 D residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.140723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.113480 restraints weight = 13937.139| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.12 r_work: 0.3426 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 0.050 8809 Z= 0.190 Angle : 0.577 7.723 12010 Z= 0.303 Chirality : 0.044 0.195 1398 Planarity : 0.004 0.041 1535 Dihedral : 5.011 79.576 1258 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.15 % Allowed : 16.15 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.06 (0.25), residues: 1161 helix: 1.53 (0.26), residues: 420 sheet: -0.79 (0.31), residues: 269 loop : -0.96 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.021 0.002 PHE C 151 TYR 0.014 0.002 TYR H 103 ARG 0.006 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 460) hydrogen bonds : angle 5.00940 ( 1311) SS BOND : bond 0.00203 ( 6) SS BOND : angle 0.94533 ( 12) covalent geometry : bond 0.00444 ( 8803) covalent geometry : angle 0.57615 (11998) *********************** 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 152 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.7298 (t0) cc_final: 0.6978 (t0) REVERT: A 10 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6766 (mtt180) REVERT: A 244 MET cc_start: 0.5725 (tpp) cc_final: 0.5196 (tpp) REVERT: C 88 TRP cc_start: 0.7361 (t-100) cc_final: 0.7160 (t-100) REVERT: C 340 ARG cc_start: 0.7494 (ttm170) cc_final: 0.6538 (ttm110) REVERT: C 443 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7425 (ttm170) outliers start: 18 outliers final: 13 residues processed: 147 average time/residue: 0.2245 time to fit residues: 44.6549 Evaluate side-chains 146 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 109 ASP Chi-restraints excluded: chain H residue 115 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.140716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.113411 restraints weight = 13871.262| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.15 r_work: 0.3420 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8809 Z= 0.191 Angle : 0.577 8.231 12010 Z= 0.303 Chirality : 0.044 0.189 1398 Planarity : 0.004 0.038 1535 Dihedral : 5.033 81.154 1258 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.63 % Allowed : 17.58 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.05 (0.25), residues: 1161 helix: 1.54 (0.26), residues: 420 sheet: -0.82 (0.31), residues: 269 loop : -0.92 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.019 0.002 PHE C 151 TYR 0.014 0.002 TYR H 103 ARG 0.006 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 460) hydrogen bonds : angle 4.98044 ( 1311) SS BOND : bond 0.00199 ( 6) SS BOND : angle 0.92045 ( 12) covalent geometry : bond 0.00444 ( 8803) covalent geometry : angle 0.57607 (11998) *********************** 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 155 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.7358 (t0) cc_final: 0.7028 (t0) REVERT: A 10 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6830 (mtt180) REVERT: A 244 MET cc_start: 0.5692 (tpp) cc_final: 0.5194 (tpp) REVERT: C 88 TRP cc_start: 0.7347 (t-100) cc_final: 0.7130 (t-100) REVERT: C 340 ARG cc_start: 0.7509 (ttm170) cc_final: 0.6546 (ttm110) REVERT: C 443 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7454 (ttm170) outliers start: 22 outliers final: 18 residues processed: 148 average time/residue: 0.2254 time to fit residues: 44.7187 Evaluate side-chains 149 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 115 THR Chi-restraints excluded: chain H residue 117 LEU 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 388 VAL Chi-restraints excluded: chain C residue 407 THR 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 55 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 0.0970 chunk 73 optimal weight: 4.9990 chunk 95 optimal weight: 0.3980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.141128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113845 restraints weight = 13949.139| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.14 r_work: 0.3432 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8809 Z= 0.168 Angle : 0.566 8.864 12010 Z= 0.298 Chirality : 0.043 0.180 1398 Planarity : 0.004 0.038 1535 Dihedral : 5.001 82.280 1258 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.63 % Allowed : 18.18 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.03 (0.25), residues: 1161 helix: 1.56 (0.26), residues: 420 sheet: -0.84 (0.31), residues: 269 loop : -0.89 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.018 0.001 PHE C 151 TYR 0.013 0.002 TYR B 59 ARG 0.007 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 460) hydrogen bonds : angle 4.91500 ( 1311) SS BOND : bond 0.00192 ( 6) SS BOND : angle 0.87400 ( 12) covalent geometry : bond 0.00388 ( 8803) covalent geometry : angle 0.56601 (11998) *********************** 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 157 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.7304 (t0) cc_final: 0.6960 (t0) REVERT: A 10 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6751 (mtt180) REVERT: A 244 MET cc_start: 0.5634 (tpp) cc_final: 0.5174 (tpp) REVERT: H 178 LEU cc_start: 0.8126 (tp) cc_final: 0.7800 (tp) REVERT: C 88 TRP cc_start: 0.7336 (t-100) cc_final: 0.7119 (t-100) REVERT: C 340 ARG cc_start: 0.7482 (ttm170) cc_final: 0.6519 (ttm110) REVERT: C 443 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7476 (ttm170) outliers start: 22 outliers final: 16 residues processed: 150 average time/residue: 0.2245 time to fit residues: 45.7880 Evaluate side-chains 153 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 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 115 THR Chi-restraints excluded: chain H residue 117 LEU 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 388 VAL Chi-restraints excluded: chain C residue 407 THR 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 84 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 25 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 47 optimal weight: 0.0770 chunk 99 optimal weight: 0.2980 chunk 95 optimal weight: 0.0670 chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.2374 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.147784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.120912 restraints weight = 13849.473| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.09 r_work: 0.3486 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8809 Z= 0.110 Angle : 0.531 9.501 12010 Z= 0.278 Chirality : 0.042 0.137 1398 Planarity : 0.004 0.040 1535 Dihedral : 4.769 82.008 1258 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.56 % Allowed : 19.38 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.26), residues: 1161 helix: 1.62 (0.27), residues: 421 sheet: -0.73 (0.31), residues: 274 loop : -0.80 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 111 HIS 0.004 0.001 HIS D 72 PHE 0.027 0.001 PHE C 151 TYR 0.013 0.001 TYR D 59 ARG 0.008 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 460) hydrogen bonds : angle 4.63625 ( 1311) SS BOND : bond 0.00197 ( 6) SS BOND : angle 0.67393 ( 12) covalent geometry : bond 0.00234 ( 8803) covalent geometry : angle 0.53105 (11998) *********************** 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 149 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: B 298 ASP cc_start: 0.8032 (t70) cc_final: 0.7665 (t70) REVERT: A 244 MET cc_start: 0.5530 (tpp) cc_final: 0.5072 (tpp) REVERT: H 178 LEU cc_start: 0.8122 (tp) cc_final: 0.7814 (tp) REVERT: C 88 TRP cc_start: 0.7235 (t-100) cc_final: 0.7009 (t-100) REVERT: C 340 ARG cc_start: 0.7420 (ttm170) cc_final: 0.6560 (ttm110) outliers start: 13 outliers final: 10 residues processed: 142 average time/residue: 0.2155 time to fit residues: 41.6459 Evaluate side-chains 142 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 155 ILE 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 32 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.142184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114929 restraints weight = 14003.942| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.13 r_work: 0.3441 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8809 Z= 0.172 Angle : 0.569 9.959 12010 Z= 0.297 Chirality : 0.043 0.161 1398 Planarity : 0.004 0.040 1535 Dihedral : 4.890 83.198 1258 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.67 % Allowed : 19.26 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.26), residues: 1161 helix: 1.68 (0.27), residues: 420 sheet: -0.70 (0.31), residues: 279 loop : -0.86 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.027 0.002 PHE C 151 TYR 0.015 0.002 TYR D 59 ARG 0.008 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 460) hydrogen bonds : angle 4.78392 ( 1311) SS BOND : bond 0.00205 ( 6) SS BOND : angle 0.87727 ( 12) covalent geometry : bond 0.00397 ( 8803) covalent geometry : angle 0.56818 (11998) *********************** 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 147 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6730 (mtt180) REVERT: A 244 MET cc_start: 0.5585 (tpp) cc_final: 0.5162 (tpp) REVERT: H 178 LEU cc_start: 0.8117 (tp) cc_final: 0.7795 (tp) REVERT: C 88 TRP cc_start: 0.7289 (t-100) cc_final: 0.7058 (t-100) REVERT: C 340 ARG cc_start: 0.7457 (ttm170) cc_final: 0.6515 (ttm110) outliers start: 14 outliers final: 8 residues processed: 143 average time/residue: 0.2264 time to fit residues: 43.5637 Evaluate side-chains 140 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 155 ILE 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 98 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.140230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112841 restraints weight = 13924.041| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.14 r_work: 0.3416 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8809 Z= 0.209 Angle : 0.604 10.151 12010 Z= 0.313 Chirality : 0.045 0.187 1398 Planarity : 0.004 0.039 1535 Dihedral : 5.065 85.685 1258 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.67 % Allowed : 19.62 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.03 (0.26), residues: 1161 helix: 1.62 (0.27), residues: 420 sheet: -0.89 (0.31), residues: 272 loop : -0.81 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.004 0.001 HIS B 142 PHE 0.027 0.002 PHE C 151 TYR 0.015 0.002 TYR D 59 ARG 0.009 0.001 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 460) hydrogen bonds : angle 4.90446 ( 1311) SS BOND : bond 0.00205 ( 6) SS BOND : angle 0.95956 ( 12) covalent geometry : bond 0.00489 ( 8803) covalent geometry : angle 0.60359 (11998) ********************** 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 147 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6751 (mtt180) REVERT: A 244 MET cc_start: 0.5630 (tpp) cc_final: 0.5161 (tpp) REVERT: C 88 TRP cc_start: 0.7349 (t-100) cc_final: 0.7090 (t-100) REVERT: C 340 ARG cc_start: 0.7467 (ttm170) cc_final: 0.6537 (ttm110) outliers start: 14 outliers final: 11 residues processed: 145 average time/residue: 0.2258 time to fit residues: 44.1806 Evaluate side-chains 142 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 LEU 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 388 VAL 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 24 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 29 optimal weight: 0.0000 chunk 57 optimal weight: 0.7980 chunk 71 optimal weight: 0.0060 chunk 11 optimal weight: 0.0770 chunk 64 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.2958 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.142753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115565 restraints weight = 14068.925| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.16 r_work: 0.3459 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8809 Z= 0.125 Angle : 0.555 10.296 12010 Z= 0.291 Chirality : 0.043 0.171 1398 Planarity : 0.004 0.040 1535 Dihedral : 4.891 86.533 1258 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.32 % Allowed : 19.86 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.26), residues: 1161 helix: 1.67 (0.27), residues: 420 sheet: -0.79 (0.32), residues: 272 loop : -0.77 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.025 0.001 PHE C 151 TYR 0.014 0.001 TYR D 59 ARG 0.008 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 460) hydrogen bonds : angle 4.72713 ( 1311) SS BOND : bond 0.00177 ( 6) SS BOND : angle 0.74794 ( 12) covalent geometry : bond 0.00274 ( 8803) covalent geometry : angle 0.55495 (11998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5687.56 seconds wall clock time: 97 minutes 49.75 seconds (5869.75 seconds total)