Starting phenix.real_space_refine on Mon May 12 01:35:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9l_35275/05_2025/8i9l_35275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9l_35275/05_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_35275/05_2025/8i9l_35275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9l_35275/05_2025/8i9l_35275.map" model { file = "/net/cci-nas-00/data/ceres_data/8i9l_35275/05_2025/8i9l_35275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9l_35275/05_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-5687/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: 5.54, 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: 2.30 Conformation dependent library (CDL) restraints added in 1.2 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: 0.96 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: 2.43 Time building geometry restraints manager: 2.68 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.430 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: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.590 ------------------------------------------------------------------------------- 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 : 0.996 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: 0.2525 time to fit residues: 50.1210 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 : 1.012 ------------------------------------------------------------------------------- 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 = 0.139025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111488 restraints weight = 13812.929| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.17 r_work: 0.3423 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1387 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 6.962 12010 Z= 0.338 Chirality : 0.047 0.205 1398 Planarity : 0.005 0.050 1535 Dihedral : 5.337 72.454 1270 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.67 % Allowed : 9.57 % Favored : 88.76 % 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 0.04903 ( 460) hydrogen bonds : angle 5.53877 ( 1311) SS BOND : bond 0.00300 ( 6) SS BOND : angle 1.31170 ( 12) covalent geometry : bond 0.00626 ( 8803) covalent geometry : angle 0.63589 (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 : 0.913 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.7337 (t0) cc_final: 0.6919 (t0) REVERT: A 10 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6920 (mtt180) REVERT: A 244 MET cc_start: 0.5603 (tpp) cc_final: 0.5096 (tpp) REVERT: C 88 TRP cc_start: 0.7236 (t-100) cc_final: 0.6998 (t-100) REVERT: C 340 ARG cc_start: 0.7668 (ttm170) cc_final: 0.6717 (ttm110) REVERT: D 72 HIS cc_start: 0.7570 (m90) cc_final: 0.7281 (m-70) REVERT: D 73 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7589 (tm) outliers start: 14 outliers final: 9 residues processed: 140 average time/residue: 0.2353 time to fit residues: 43.8414 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 : 0.923 ------------------------------------------------------------------------------- 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: 0.5980 chunk 4 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 112 optimal weight: 0.0170 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.136247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.110256 restraints weight = 14191.804| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.04 r_work: 0.3468 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8809 Z= 0.150 Angle : 0.549 6.821 12010 Z= 0.289 Chirality : 0.043 0.173 1398 Planarity : 0.004 0.043 1535 Dihedral : 5.000 75.332 1264 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.84 % Allowed : 12.44 % Favored : 86.72 % 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: 0.18 (0.25), residues: 1161 helix: 1.64 (0.26), residues: 423 sheet: -0.48 (0.31), residues: 269 loop : -0.88 (0.29), residues: 469 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 0.018 0.001 PHE C 151 TYR 0.014 0.002 TYR D 59 ARG 0.005 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 460) hydrogen bonds : angle 5.06265 ( 1311) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.92251 ( 12) covalent geometry : bond 0.00340 ( 8803) covalent geometry : angle 0.54899 (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 146 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.5637 (tpp) cc_final: 0.5052 (tpp) REVERT: H 178 LEU cc_start: 0.8048 (tp) cc_final: 0.7776 (tp) REVERT: C 88 TRP cc_start: 0.7237 (t-100) cc_final: 0.7020 (t-100) REVERT: C 92 ARG cc_start: 0.6837 (ttt180) cc_final: 0.6616 (ttt180) REVERT: C 340 ARG cc_start: 0.7495 (ttm170) cc_final: 0.6521 (ttm110) REVERT: D 72 HIS cc_start: 0.7638 (m90) cc_final: 0.7377 (m-70) REVERT: D 73 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7801 (tm) outliers start: 7 outliers final: 4 residues processed: 142 average time/residue: 0.2402 time to fit residues: 45.0870 Evaluate side-chains 135 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 26 optimal weight: 0.9980 chunk 115 optimal weight: 0.0570 chunk 12 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.141353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113988 restraints weight = 13978.473| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.13 r_work: 0.3433 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8809 Z= 0.187 Angle : 0.576 7.788 12010 Z= 0.301 Chirality : 0.044 0.183 1398 Planarity : 0.004 0.039 1535 Dihedral : 4.887 77.629 1258 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.67 % Allowed : 14.00 % Favored : 84.33 % 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: 0.09 (0.25), residues: 1161 helix: 1.61 (0.26), residues: 421 sheet: -0.54 (0.31), residues: 273 loop : -0.95 (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 0.026 0.002 PHE C 151 TYR 0.014 0.002 TYR C 435 ARG 0.007 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 460) hydrogen bonds : angle 4.98598 ( 1311) SS BOND : bond 0.00208 ( 6) SS BOND : angle 0.94540 ( 12) covalent geometry : bond 0.00430 ( 8803) covalent geometry : angle 0.57583 (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: 14 poor density : 137 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.7377 (t0) cc_final: 0.6953 (t0) REVERT: B 273 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7524 (mp) REVERT: A 10 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6750 (mtt180) REVERT: A 244 MET cc_start: 0.5650 (tpp) cc_final: 0.5114 (tpp) REVERT: H 77 ASN cc_start: 0.8036 (t0) cc_final: 0.7629 (t0) REVERT: C 88 TRP cc_start: 0.7292 (t-100) cc_final: 0.7087 (t-100) REVERT: C 337 THR cc_start: 0.5623 (t) cc_final: 0.5421 (t) REVERT: C 340 ARG cc_start: 0.7525 (ttm170) cc_final: 0.6544 (ttm110) REVERT: D 72 HIS cc_start: 0.7622 (m90) cc_final: 0.7414 (m-70) outliers start: 14 outliers final: 9 residues processed: 147 average time/residue: 0.2630 time to fit residues: 52.3420 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 : 1.116 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 77 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.140929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113494 restraints weight = 13914.789| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.16 r_work: 0.3425 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8809 Z= 0.193 Angle : 0.576 7.159 12010 Z= 0.302 Chirality : 0.044 0.193 1398 Planarity : 0.004 0.038 1535 Dihedral : 4.938 78.656 1258 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.27 % Allowed : 15.91 % Favored : 81.82 % 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: -0.01 (0.25), residues: 1161 helix: 1.57 (0.26), residues: 421 sheet: -0.72 (0.31), residues: 269 loop : -0.96 (0.28), residues: 471 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 0.020 0.002 PHE C 151 TYR 0.015 0.002 TYR H 103 ARG 0.006 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 460) hydrogen bonds : angle 4.95230 ( 1311) SS BOND : bond 0.00204 ( 6) SS BOND : angle 0.93553 ( 12) covalent geometry : bond 0.00451 ( 8803) covalent geometry : angle 0.57578 (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 154 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6824 (mtt180) REVERT: A 244 MET cc_start: 0.5760 (tpp) cc_final: 0.5253 (tpp) REVERT: H 172 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7337 (m) REVERT: C 88 TRP cc_start: 0.7313 (t-100) cc_final: 0.7106 (t-100) REVERT: C 340 ARG cc_start: 0.7503 (ttm170) cc_final: 0.6536 (ttm110) REVERT: C 443 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7393 (ttm170) outliers start: 19 outliers final: 13 residues processed: 148 average time/residue: 0.2296 time to fit residues: 45.7091 Evaluate side-chains 149 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 109 ASP Chi-restraints excluded: chain H residue 172 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: 0.4980 chunk 54 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 41 optimal weight: 0.0770 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: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.140125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112571 restraints weight = 13892.616| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.20 r_work: 0.3439 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8809 Z= 0.159 Angle : 0.559 7.932 12010 Z= 0.292 Chirality : 0.043 0.173 1398 Planarity : 0.004 0.037 1535 Dihedral : 4.882 78.364 1258 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.39 % Allowed : 16.87 % Favored : 80.74 % 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: 1.59 (0.26), residues: 420 sheet: -0.73 (0.31), residues: 269 loop : -0.91 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.018 0.001 PHE C 151 TYR 0.014 0.002 TYR C 435 ARG 0.007 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 460) hydrogen bonds : angle 4.86683 ( 1311) SS BOND : bond 0.00187 ( 6) SS BOND : angle 0.84483 ( 12) covalent geometry : bond 0.00364 ( 8803) covalent geometry : angle 0.55848 (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 160 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.6808 (mtt180) REVERT: A 244 MET cc_start: 0.5686 (tpp) cc_final: 0.5212 (tpp) REVERT: H 178 LEU cc_start: 0.8134 (tp) cc_final: 0.7815 (tp) REVERT: C 88 TRP cc_start: 0.7353 (t-100) cc_final: 0.7134 (t-100) REVERT: C 340 ARG cc_start: 0.7448 (ttm170) cc_final: 0.6455 (ttm110) REVERT: C 443 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7396 (ttm170) outliers start: 20 outliers final: 14 residues processed: 153 average time/residue: 0.2355 time to fit residues: 48.1951 Evaluate side-chains 149 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR 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 H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 334 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: 0.8980 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 87 optimal weight: 0.0370 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.142536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.115309 restraints weight = 13902.098| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.16 r_work: 0.3454 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8809 Z= 0.136 Angle : 0.545 8.776 12010 Z= 0.285 Chirality : 0.043 0.157 1398 Planarity : 0.004 0.039 1535 Dihedral : 4.800 78.427 1258 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.27 % Allowed : 17.22 % Favored : 80.50 % 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: 0.09 (0.26), residues: 1161 helix: 1.63 (0.27), residues: 420 sheet: -0.72 (0.31), residues: 274 loop : -0.83 (0.29), residues: 467 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 0.017 0.001 PHE C 151 TYR 0.014 0.001 TYR C 435 ARG 0.007 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 460) hydrogen bonds : angle 4.73818 ( 1311) SS BOND : bond 0.00184 ( 6) SS BOND : angle 0.75429 ( 12) covalent geometry : bond 0.00307 ( 8803) covalent geometry : angle 0.54451 (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 158 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 298 ASP cc_start: 0.7982 (t70) cc_final: 0.7683 (t70) REVERT: A 10 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6727 (mtt180) REVERT: A 244 MET cc_start: 0.5598 (tpp) cc_final: 0.5124 (tpp) REVERT: H 117 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6440 (tp) REVERT: H 178 LEU cc_start: 0.8120 (tp) cc_final: 0.7798 (tp) REVERT: C 88 TRP cc_start: 0.7323 (t-100) cc_final: 0.7109 (t-100) REVERT: C 337 THR cc_start: 0.5756 (t) cc_final: 0.5546 (t) REVERT: C 340 ARG cc_start: 0.7483 (ttm170) cc_final: 0.6526 (ttm110) REVERT: C 443 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7456 (ttm170) outliers start: 19 outliers final: 13 residues processed: 151 average time/residue: 0.2360 time to fit residues: 47.4120 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 : 0.897 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 107 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 95 optimal weight: 0.0050 chunk 65 optimal weight: 0.0070 chunk 58 optimal weight: 0.3980 overall best weight: 0.3412 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.138828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112920 restraints weight = 14236.898| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.03 r_work: 0.3477 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8809 Z= 0.125 Angle : 0.540 9.548 12010 Z= 0.281 Chirality : 0.042 0.139 1398 Planarity : 0.004 0.040 1535 Dihedral : 4.700 78.399 1258 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.51 % Allowed : 17.94 % 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: 0.16 (0.26), residues: 1161 helix: 1.69 (0.27), residues: 420 sheet: -0.66 (0.32), residues: 274 loop : -0.81 (0.29), residues: 467 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 0.027 0.001 PHE C 151 TYR 0.015 0.001 TYR D 59 ARG 0.008 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 460) hydrogen bonds : angle 4.65862 ( 1311) SS BOND : bond 0.00183 ( 6) SS BOND : angle 0.73577 ( 12) covalent geometry : bond 0.00276 ( 8803) covalent geometry : angle 0.53927 (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 157 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 298 ASP cc_start: 0.7958 (t70) cc_final: 0.7644 (t70) REVERT: A 10 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6666 (mtt180) REVERT: A 244 MET cc_start: 0.5427 (tpp) cc_final: 0.4963 (tpp) REVERT: H 178 LEU cc_start: 0.8120 (tp) cc_final: 0.7816 (tp) REVERT: C 88 TRP cc_start: 0.7271 (t-100) cc_final: 0.7046 (t-100) REVERT: C 340 ARG cc_start: 0.7435 (ttm170) cc_final: 0.6498 (ttm110) REVERT: C 443 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7526 (ttm170) outliers start: 21 outliers final: 14 residues processed: 151 average time/residue: 0.2249 time to fit residues: 45.7110 Evaluate side-chains 147 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL 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 341 ASP 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 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: 0.4980 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 36 optimal weight: 0.0060 chunk 95 optimal weight: 0.2980 chunk 83 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 15 optimal weight: 0.0980 overall best weight: 0.1914 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.138221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.112446 restraints weight = 14259.451| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.04 r_work: 0.3503 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8809 Z= 0.104 Angle : 0.520 9.834 12010 Z= 0.272 Chirality : 0.042 0.142 1398 Planarity : 0.003 0.040 1535 Dihedral : 4.568 77.250 1258 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.67 % Allowed : 19.02 % Favored : 79.31 % 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: 0.27 (0.26), residues: 1161 helix: 1.76 (0.27), residues: 421 sheet: -0.66 (0.32), residues: 266 loop : -0.69 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 111 HIS 0.003 0.000 HIS H 35 PHE 0.013 0.001 PHE C 430 TYR 0.015 0.001 TYR D 59 ARG 0.008 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 460) hydrogen bonds : angle 4.52904 ( 1311) SS BOND : bond 0.00184 ( 6) SS BOND : angle 0.64003 ( 12) covalent geometry : bond 0.00219 ( 8803) covalent geometry : angle 0.52024 (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 154 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 298 ASP cc_start: 0.7895 (t70) cc_final: 0.7593 (t70) REVERT: A 10 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6602 (mtt180) REVERT: A 244 MET cc_start: 0.5563 (tpp) cc_final: 0.5106 (tpp) REVERT: H 178 LEU cc_start: 0.8107 (tp) cc_final: 0.7802 (tp) REVERT: C 88 TRP cc_start: 0.7201 (t-100) cc_final: 0.6955 (t-100) REVERT: C 151 PHE cc_start: 0.7825 (t80) cc_final: 0.7619 (t80) REVERT: C 340 ARG cc_start: 0.7379 (ttm170) cc_final: 0.6423 (ttm110) REVERT: C 443 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7600 (mtm180) outliers start: 14 outliers final: 10 residues processed: 150 average time/residue: 0.2417 time to fit residues: 48.6091 Evaluate side-chains 149 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 100 VAL 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 H residue 109 ASP Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 76 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 85 optimal weight: 0.0270 chunk 61 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.137338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.111482 restraints weight = 14191.707| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.03 r_work: 0.3489 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8809 Z= 0.128 Angle : 0.547 10.592 12010 Z= 0.282 Chirality : 0.042 0.135 1398 Planarity : 0.004 0.040 1535 Dihedral : 4.584 76.975 1258 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.67 % Allowed : 18.90 % Favored : 79.43 % 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: 0.29 (0.26), residues: 1161 helix: 1.77 (0.27), residues: 421 sheet: -0.68 (0.32), residues: 267 loop : -0.65 (0.30), residues: 473 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 0.014 0.001 PHE C 430 TYR 0.014 0.001 TYR H 60 ARG 0.008 0.000 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 460) hydrogen bonds : angle 4.55952 ( 1311) SS BOND : bond 0.00184 ( 6) SS BOND : angle 0.72180 ( 12) covalent geometry : bond 0.00287 ( 8803) covalent geometry : angle 0.54676 (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 153 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 298 ASP cc_start: 0.7931 (t70) cc_final: 0.7626 (t70) REVERT: A 10 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6632 (mtt180) REVERT: A 244 MET cc_start: 0.5611 (tpp) cc_final: 0.5113 (tpp) REVERT: H 178 LEU cc_start: 0.8115 (tp) cc_final: 0.7818 (tp) REVERT: C 88 TRP cc_start: 0.7223 (t-100) cc_final: 0.6974 (t-100) REVERT: C 340 ARG cc_start: 0.7432 (ttm170) cc_final: 0.6470 (ttm110) REVERT: C 443 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7635 (mtm180) outliers start: 14 outliers final: 12 residues processed: 148 average time/residue: 0.2210 time to fit residues: 44.0776 Evaluate side-chains 153 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL 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 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: 1.9990 chunk 110 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 86 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.142076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114478 restraints weight = 14124.775| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.16 r_work: 0.3435 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8809 Z= 0.187 Angle : 0.585 10.451 12010 Z= 0.304 Chirality : 0.044 0.164 1398 Planarity : 0.004 0.040 1535 Dihedral : 4.817 77.730 1258 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.67 % Allowed : 19.02 % Favored : 79.31 % 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: 0.21 (0.26), residues: 1161 helix: 1.72 (0.27), residues: 420 sheet: -0.75 (0.31), residues: 278 loop : -0.69 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.022 0.002 PHE C 151 TYR 0.015 0.002 TYR H 60 ARG 0.008 0.001 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 460) hydrogen bonds : angle 4.77236 ( 1311) SS BOND : bond 0.00188 ( 6) SS BOND : angle 0.90291 ( 12) covalent geometry : bond 0.00435 ( 8803) covalent geometry : angle 0.58433 (11998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5610.79 seconds wall clock time: 98 minutes 11.26 seconds (5891.26 seconds total)