Starting phenix.real_space_refine on Thu Feb 13 02:43:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9l_35275/02_2025/8i9l_35275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9l_35275/02_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_35275/02_2025/8i9l_35275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9l_35275/02_2025/8i9l_35275.map" model { file = "/net/cci-nas-00/data/ceres_data/8i9l_35275/02_2025/8i9l_35275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9l_35275/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.68, per 1000 atoms: 0.66 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.54 Time building geometry restraints manager: 2.64 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: 2.270 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.670 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- 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 8803 Z= 0.167 Angle : 0.582 10.291 11998 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 *********************** 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 : 0.976 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: 0.2709 time to fit residues: 54.1717 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 : 0.996 ------------------------------------------------------------------------------- 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: 0.1980 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: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.138293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112496 restraints weight = 13895.515| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.98 r_work: 0.3473 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8803 Z= 0.305 Angle : 0.590 6.679 11998 Z= 0.312 Chirality : 0.045 0.193 1398 Planarity : 0.004 0.046 1535 Dihedral : 5.158 70.705 1270 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.79 % Allowed : 8.25 % Favored : 89.95 % 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: 0.30 (0.26), residues: 1161 helix: 1.68 (0.27), residues: 427 sheet: -0.44 (0.31), residues: 280 loop : -0.74 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 60 HIS 0.007 0.001 HIS B 142 PHE 0.025 0.002 PHE C 151 TYR 0.014 0.002 TYR D 59 ARG 0.005 0.001 ARG B 46 *********************** 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: 15 poor density : 135 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.7177 (t0) cc_final: 0.6724 (t0) REVERT: A 10 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6840 (mtt180) REVERT: H 178 LEU cc_start: 0.8079 (tp) cc_final: 0.7812 (tp) REVERT: C 88 TRP cc_start: 0.7187 (t-100) cc_final: 0.6942 (t-100) REVERT: C 340 ARG cc_start: 0.7607 (ttm170) cc_final: 0.6679 (ttm110) REVERT: D 72 HIS cc_start: 0.7575 (m90) cc_final: 0.7358 (m-70) REVERT: D 73 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7540 (tm) outliers start: 15 outliers final: 9 residues processed: 142 average time/residue: 0.2416 time to fit residues: 45.6573 Evaluate side-chains 143 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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: 1.9990 chunk 69 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 0.1980 chunk 29 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.136586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.110661 restraints weight = 14214.986| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.01 r_work: 0.3474 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8803 Z= 0.240 Angle : 0.551 7.080 11998 Z= 0.290 Chirality : 0.043 0.175 1398 Planarity : 0.004 0.041 1535 Dihedral : 4.950 74.082 1264 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.08 % Allowed : 11.72 % Favored : 87.20 % 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: 0.25 (0.26), residues: 1161 helix: 1.69 (0.26), residues: 423 sheet: -0.41 (0.31), residues: 269 loop : -0.85 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.005 0.001 HIS B 142 PHE 0.023 0.001 PHE C 151 TYR 0.015 0.002 TYR D 59 ARG 0.006 0.000 ARG B 46 *********************** 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 148 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: B 298 ASP cc_start: 0.7921 (t70) cc_final: 0.7610 (t70) REVERT: H 178 LEU cc_start: 0.8059 (tp) cc_final: 0.7790 (tp) REVERT: C 88 TRP cc_start: 0.7216 (t-100) cc_final: 0.6978 (t-100) REVERT: C 340 ARG cc_start: 0.7474 (ttm170) cc_final: 0.6494 (ttm110) REVERT: D 72 HIS cc_start: 0.7634 (m90) cc_final: 0.7428 (m-70) REVERT: D 73 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8025 (tm) outliers start: 9 outliers final: 5 residues processed: 142 average time/residue: 0.2318 time to fit residues: 44.2066 Evaluate side-chains 135 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 THR 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 393 TYR 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: 0.9980 chunk 115 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.142691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.115286 restraints weight = 13920.213| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.16 r_work: 0.3441 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8803 Z= 0.228 Angle : 0.546 7.558 11998 Z= 0.285 Chirality : 0.043 0.173 1398 Planarity : 0.004 0.035 1535 Dihedral : 4.699 74.853 1260 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % 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 (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: 0.23 (0.26), residues: 1161 helix: 1.67 (0.26), residues: 423 sheet: -0.40 (0.32), residues: 268 loop : -0.87 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.018 0.001 PHE C 151 TYR 0.013 0.001 TYR C 435 ARG 0.005 0.000 ARG H 180 *********************** 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 150 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: B 298 ASP cc_start: 0.8000 (t70) cc_final: 0.7668 (t70) REVERT: A 299 ASP cc_start: 0.7311 (t0) cc_final: 0.7036 (t0) REVERT: H 178 LEU cc_start: 0.8039 (tp) cc_final: 0.7764 (tp) REVERT: C 88 TRP cc_start: 0.7233 (t-100) cc_final: 0.7006 (t-100) REVERT: C 337 THR cc_start: 0.5565 (t) cc_final: 0.5363 (t) REVERT: C 340 ARG cc_start: 0.7452 (ttm170) cc_final: 0.6497 (ttm110) outliers start: 12 outliers final: 10 residues processed: 147 average time/residue: 0.2389 time to fit residues: 46.7894 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 : 0.978 ------------------------------------------------------------------------------- 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 57 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS C 427 ASN D 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.140589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113320 restraints weight = 13937.051| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.11 r_work: 0.3429 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8803 Z= 0.329 Angle : 0.580 7.148 11998 Z= 0.304 Chirality : 0.044 0.200 1398 Planarity : 0.004 0.036 1535 Dihedral : 4.896 77.018 1258 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.27 % Allowed : 15.07 % Favored : 82.66 % 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 (0.25), residues: 1161 helix: 1.64 (0.26), residues: 421 sheet: -0.54 (0.31), residues: 273 loop : -0.96 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.005 0.001 HIS B 142 PHE 0.027 0.002 PHE C 151 TYR 0.014 0.002 TYR C 435 ARG 0.006 0.001 ARG H 160 *********************** 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 157 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6842 (mtt180) REVERT: H 77 ASN cc_start: 0.8056 (t0) cc_final: 0.7628 (t0) REVERT: C 88 TRP cc_start: 0.7344 (t-100) cc_final: 0.7115 (t-100) REVERT: C 337 THR cc_start: 0.5750 (t) cc_final: 0.5533 (t) REVERT: C 340 ARG cc_start: 0.7481 (ttm170) cc_final: 0.6519 (ttm110) REVERT: C 443 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7411 (ttm170) REVERT: D 72 HIS cc_start: 0.7768 (m170) cc_final: 0.7483 (m-70) outliers start: 19 outliers final: 13 residues processed: 150 average time/residue: 0.2397 time to fit residues: 48.3186 Evaluate side-chains 147 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.141041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.113834 restraints weight = 13883.972| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.11 r_work: 0.3429 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8803 Z= 0.299 Angle : 0.578 7.751 11998 Z= 0.302 Chirality : 0.044 0.198 1398 Planarity : 0.004 0.037 1535 Dihedral : 4.920 76.598 1258 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.27 % Allowed : 16.03 % 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: 0.05 (0.25), residues: 1161 helix: 1.59 (0.26), residues: 420 sheet: -0.63 (0.31), residues: 268 loop : -0.94 (0.28), residues: 473 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 0.021 0.002 PHE C 151 TYR 0.014 0.002 TYR C 435 ARG 0.007 0.000 ARG H 160 *********************** 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: 19 poor density : 139 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.7299 (t0) cc_final: 0.6999 (t0) REVERT: A 10 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.6808 (mtt180) REVERT: C 88 TRP cc_start: 0.7327 (t-100) cc_final: 0.7114 (t-100) REVERT: C 337 THR cc_start: 0.5792 (t) cc_final: 0.5558 (t) REVERT: C 340 ARG cc_start: 0.7487 (ttm170) cc_final: 0.6532 (ttm110) REVERT: C 443 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7431 (ttm170) outliers start: 19 outliers final: 13 residues processed: 151 average time/residue: 0.2284 time to fit residues: 46.5230 Evaluate side-chains 149 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 0.0040 chunk 73 optimal weight: 4.9990 chunk 95 optimal weight: 0.0870 overall best weight: 0.3970 ------------------------------------------------------------------------------- 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 = 0.142557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.115378 restraints weight = 13890.484| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.16 r_work: 0.3454 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8803 Z= 0.202 Angle : 0.541 8.687 11998 Z= 0.283 Chirality : 0.043 0.159 1398 Planarity : 0.004 0.038 1535 Dihedral : 4.739 74.885 1258 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.79 % Allowed : 17.22 % 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 (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: 1.64 (0.27), residues: 420 sheet: -0.63 (0.31), residues: 273 loop : -0.87 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.001 PHE C 151 TYR 0.014 0.001 TYR C 435 ARG 0.007 0.000 ARG H 160 *********************** 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 153 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6736 (mtt180) REVERT: A 244 MET cc_start: 0.4960 (tpt) cc_final: 0.4645 (tpp) REVERT: C 88 TRP cc_start: 0.7308 (t-100) cc_final: 0.7089 (t-100) REVERT: C 337 THR cc_start: 0.5775 (t) cc_final: 0.5545 (t) REVERT: C 340 ARG cc_start: 0.7451 (ttm170) cc_final: 0.6497 (ttm110) REVERT: C 443 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7388 (ttm170) REVERT: D 72 HIS cc_start: 0.7818 (m90) cc_final: 0.7610 (m90) outliers start: 15 outliers final: 10 residues processed: 147 average time/residue: 0.2405 time to fit residues: 47.1919 Evaluate side-chains 145 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 93 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 99 optimal weight: 0.4980 chunk 95 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.137784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.111933 restraints weight = 14280.279| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.04 r_work: 0.3464 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8803 Z= 0.207 Angle : 0.548 9.351 11998 Z= 0.284 Chirality : 0.043 0.162 1398 Planarity : 0.004 0.039 1535 Dihedral : 4.699 74.403 1258 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.39 % Allowed : 16.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1161 helix: 1.67 (0.27), residues: 420 sheet: -0.58 (0.32), residues: 273 loop : -0.87 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.018 0.001 PHE C 151 TYR 0.014 0.001 TYR D 59 ARG 0.007 0.000 ARG H 160 *********************** 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 156 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: B 298 ASP cc_start: 0.7977 (t70) cc_final: 0.7591 (t70) REVERT: A 10 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6699 (mtt180) REVERT: A 244 MET cc_start: 0.4755 (tpt) cc_final: 0.4552 (tpp) REVERT: C 88 TRP cc_start: 0.7258 (t-100) cc_final: 0.7028 (t-100) REVERT: C 337 THR cc_start: 0.5744 (t) cc_final: 0.5511 (t) REVERT: C 340 ARG cc_start: 0.7411 (ttm170) cc_final: 0.6463 (ttm110) REVERT: C 443 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7428 (ttm170) outliers start: 20 outliers final: 12 residues processed: 149 average time/residue: 0.2247 time to fit residues: 45.5139 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 : 0.874 ------------------------------------------------------------------------------- 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 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 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 32 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 0.0870 chunk 36 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.141989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.114693 restraints weight = 14013.215| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.13 r_work: 0.3426 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8803 Z= 0.247 Angle : 0.557 9.851 11998 Z= 0.291 Chirality : 0.043 0.185 1398 Planarity : 0.004 0.039 1535 Dihedral : 4.758 74.469 1258 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.79 % Allowed : 18.30 % Favored : 79.90 % 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: 0.13 (0.26), residues: 1161 helix: 1.68 (0.27), residues: 420 sheet: -0.61 (0.31), residues: 279 loop : -0.90 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.027 0.001 PHE C 151 TYR 0.015 0.002 TYR D 59 ARG 0.008 0.000 ARG H 160 *********************** 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 148 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: B 273 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7521 (mp) REVERT: A 10 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6686 (mtt180) REVERT: C 88 TRP cc_start: 0.7269 (t-100) cc_final: 0.7027 (t-100) REVERT: C 337 THR cc_start: 0.5818 (t) cc_final: 0.5587 (t) REVERT: C 340 ARG cc_start: 0.7419 (ttm170) cc_final: 0.6481 (ttm110) REVERT: C 443 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7397 (ttm170) outliers start: 15 outliers final: 12 residues processed: 143 average time/residue: 0.2336 time to fit residues: 45.2748 Evaluate side-chains 144 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU 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 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 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 98 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 0.0980 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 = 0.142148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114874 restraints weight = 13904.552| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.12 r_work: 0.3434 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8803 Z= 0.269 Angle : 0.578 10.285 11998 Z= 0.299 Chirality : 0.043 0.162 1398 Planarity : 0.004 0.040 1535 Dihedral : 4.787 73.822 1258 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.03 % Allowed : 18.42 % Favored : 79.55 % 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: 1.66 (0.27), residues: 420 sheet: -0.64 (0.31), residues: 279 loop : -0.89 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.004 0.001 HIS B 142 PHE 0.028 0.002 PHE C 151 TYR 0.015 0.002 TYR D 59 ARG 0.008 0.000 ARG H 160 ********************** 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 148 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: B 273 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7528 (mp) REVERT: A 10 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6745 (mtt180) REVERT: C 88 TRP cc_start: 0.7238 (t-100) cc_final: 0.6974 (t-100) REVERT: C 337 THR cc_start: 0.5861 (t) cc_final: 0.5626 (t) REVERT: C 340 ARG cc_start: 0.7379 (ttm170) cc_final: 0.6438 (ttm110) REVERT: C 443 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7293 (ttm170) outliers start: 17 outliers final: 12 residues processed: 142 average time/residue: 0.2227 time to fit residues: 42.8019 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 : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU 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 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 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 24 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 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 = 0.3961 r_free = 0.3961 target = 0.141441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114115 restraints weight = 14091.253| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.14 r_work: 0.3435 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8803 Z= 0.270 Angle : 0.575 10.415 11998 Z= 0.301 Chirality : 0.044 0.161 1398 Planarity : 0.004 0.040 1535 Dihedral : 4.799 73.008 1258 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.27 % Allowed : 18.18 % Favored : 79.55 % 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: 1.64 (0.27), residues: 420 sheet: -0.64 (0.32), residues: 267 loop : -0.85 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.004 0.001 HIS B 142 PHE 0.027 0.002 PHE C 151 TYR 0.018 0.002 TYR H 60 ARG 0.009 0.000 ARG H 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5363.41 seconds wall clock time: 95 minutes 38.73 seconds (5738.73 seconds total)