Starting phenix.real_space_refine on Tue Apr 29 00:07:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vvh_43559/04_2025/8vvh_43559.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vvh_43559/04_2025/8vvh_43559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vvh_43559/04_2025/8vvh_43559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vvh_43559/04_2025/8vvh_43559.map" model { file = "/net/cci-nas-00/data/ceres_data/8vvh_43559/04_2025/8vvh_43559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vvh_43559/04_2025/8vvh_43559.cif" } resolution = 3.95 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= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1632 atoms to isotropic. 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 27 5.16 5 C 4368 2.51 5 N 1180 2.21 5 O 1302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6877 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2684 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 17, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 134 Chain: "B" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2624 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 13, 'TRANS': 340} Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 10, 'TYR:plan': 3, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 140 Chain: "H" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 833 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 108} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 726 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 108, 726 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 728 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS L 8 " occ=0.82 ... (18 atoms not shown) pdb=" NE2BHIS L 8 " occ=0.18 Time building chain proxies: 5.39, per 1000 atoms: 0.78 Number of scatterers: 6877 At special positions: 0 Unit cell: (109.568, 123.264, 83.888, 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 27 16.00 O 1302 8.00 N 1180 7.00 C 4368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1754 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 12 sheets defined 28.3% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.507A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.627A pdb=" N SER A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 3.695A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.561A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.925A pdb=" N GLN A 147 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.924A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.471A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 4.068A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.700A pdb=" N SER A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 4.059A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.587A pdb=" N ALA B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 3.761A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 223 removed outlier: 4.015A pdb=" N ILE B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.857A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.908A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 312 Processing helix chain 'B' and resid 333 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 6.357A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.854A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 168 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.095A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 72 removed outlier: 6.328A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ALA B 100 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY B 128 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASP B 101 " --> pdb=" O GLY B 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.308A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 228 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 280 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 362 " --> pdb=" O TRP B 379 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.951A pdb=" N PHE B 344 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.718A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 51 through 52 Processing sheet with id=AA9, first strand: chain 'H' and resid 39 through 40 Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB2, first strand: chain 'L' and resid 46 through 50 removed outlier: 6.631A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER L 93 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL L 100 " --> pdb=" O SER L 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 46 through 50 removed outlier: 6.631A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 2.11 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: 2263 1.34 - 1.46: 1659 1.46 - 1.58: 3053 1.58 - 1.71: 0 1.71 - 1.83: 45 Bond restraints: 7020 Sorted by residual: bond pdb=" CA ILE L 29 " pdb=" CB ILE L 29 " ideal model delta sigma weight residual 1.527 1.547 -0.020 1.31e-02 5.83e+03 2.43e+00 bond pdb=" CA VAL B 258 " pdb=" CB VAL B 258 " ideal model delta sigma weight residual 1.547 1.536 0.011 1.10e-02 8.26e+03 1.02e+00 bond pdb=" CB GLU L 51 " pdb=" CG GLU L 51 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.36e-01 bond pdb=" CB ASP B 138 " pdb=" CG ASP B 138 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.89e-01 bond pdb=" CD GLU L 51 " pdb=" OE1 GLU L 51 " ideal model delta sigma weight residual 1.249 1.234 0.015 1.90e-02 2.77e+03 6.45e-01 ... (remaining 7015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 9347 1.66 - 3.32: 197 3.32 - 4.98: 31 4.98 - 6.64: 10 6.64 - 8.30: 6 Bond angle restraints: 9591 Sorted by residual: angle pdb=" N VAL B 376 " pdb=" CA VAL B 376 " pdb=" C VAL B 376 " ideal model delta sigma weight residual 113.71 110.66 3.05 9.50e-01 1.11e+00 1.03e+01 angle pdb=" N GLY H 56 " pdb=" CA GLY H 56 " pdb=" C GLY H 56 " ideal model delta sigma weight residual 113.18 120.59 -7.41 2.37e+00 1.78e-01 9.78e+00 angle pdb=" CA ILE L 29 " pdb=" CB ILE L 29 " pdb=" CG1 ILE L 29 " ideal model delta sigma weight residual 110.40 115.64 -5.24 1.70e+00 3.46e-01 9.51e+00 angle pdb=" C GLU A 213 " pdb=" N LEU A 214 " pdb=" CA LEU A 214 " ideal model delta sigma weight residual 121.54 116.32 5.22 1.91e+00 2.74e-01 7.48e+00 angle pdb=" C THR H 23 " pdb=" N VAL H 24 " pdb=" CA VAL H 24 " ideal model delta sigma weight residual 121.97 126.79 -4.82 1.80e+00 3.09e-01 7.16e+00 ... (remaining 9586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 3545 17.51 - 35.02: 459 35.02 - 52.53: 126 52.53 - 70.04: 18 70.04 - 87.55: 7 Dihedral angle restraints: 4155 sinusoidal: 1429 harmonic: 2726 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -133.41 47.41 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CA GLU A 215 " pdb=" C GLU A 215 " pdb=" N ALA A 216 " pdb=" CA ALA A 216 " ideal model delta harmonic sigma weight residual 180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 91 " pdb=" CB CYS L 91 " ideal model delta sinusoidal sigma weight residual 93.00 58.31 34.69 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 4152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 825 0.042 - 0.084: 216 0.084 - 0.126: 79 0.126 - 0.169: 7 0.169 - 0.211: 3 Chirality restraints: 1130 Sorted by residual: chirality pdb=" CB ILE B 35 " pdb=" CA ILE B 35 " pdb=" CG1 ILE B 35 " pdb=" CG2 ILE B 35 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA GLU L 51 " pdb=" N GLU L 51 " pdb=" C GLU L 51 " pdb=" CB GLU L 51 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CB ILE B 190 " pdb=" CA ILE B 190 " pdb=" CG1 ILE B 190 " pdb=" CG2 ILE B 190 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.08e-01 ... (remaining 1127 not shown) Planarity restraints: 1230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 289 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO B 290 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 290 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 290 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 318 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO A 319 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 319 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 319 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 50 " -0.008 2.00e-02 2.50e+03 1.05e-02 2.21e+00 pdb=" CG TYR L 50 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR L 50 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR L 50 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR L 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR L 50 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR L 50 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 50 " 0.001 2.00e-02 2.50e+03 ... (remaining 1227 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 961 2.76 - 3.29: 6587 3.29 - 3.83: 10529 3.83 - 4.36: 10885 4.36 - 4.90: 19889 Nonbonded interactions: 48851 Sorted by model distance: nonbonded pdb=" NH1 ARG L 24 " pdb=" O SER L 26 " model vdw 2.220 3.120 nonbonded pdb=" OG SER B 149 " pdb=" OE1 GLN B 152 " model vdw 2.240 3.040 nonbonded pdb=" O MET B 89 " pdb=" OG SER B 319 " model vdw 2.253 3.040 nonbonded pdb=" ND2 ASN L 32 " pdb=" O TYR L 94 " model vdw 2.283 3.120 nonbonded pdb=" NH2 ARG L 40 " pdb=" O GLU L 84 " model vdw 2.291 3.120 ... (remaining 48846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.18 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.630 Find NCS groups from input model: 0.100 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7024 Z= 0.115 Angle : 0.614 8.302 9599 Z= 0.313 Chirality : 0.044 0.211 1130 Planarity : 0.004 0.054 1230 Dihedral : 17.029 87.552 2389 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.09 % Favored : 92.70 % Rotamer: Outliers : 0.88 % Allowed : 35.98 % Favored : 63.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.64 (0.27), residues: 934 helix: 1.11 (0.33), residues: 249 sheet: -1.06 (0.36), residues: 222 loop : -2.44 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS H 54 PHE 0.008 0.001 PHE A 197 TYR 0.026 0.001 TYR L 50 ARG 0.004 0.000 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.16224 ( 244) hydrogen bonds : angle 5.97565 ( 702) SS BOND : bond 0.00310 ( 4) SS BOND : angle 1.02882 ( 8) covalent geometry : bond 0.00237 ( 7020) covalent geometry : angle 0.61386 ( 9591) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 0.798 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 147 average time/residue: 0.1661 time to fit residues: 33.7704 Evaluate side-chains 143 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain L residue 51 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.4980 chunk 69 optimal weight: 0.0060 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 72 optimal weight: 0.3980 chunk 27 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 overall best weight: 0.2374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.175037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.145358 restraints weight = 31543.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.148593 restraints weight = 21909.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.148291 restraints weight = 9197.394| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7024 Z= 0.104 Angle : 0.577 13.483 9599 Z= 0.291 Chirality : 0.043 0.156 1130 Planarity : 0.004 0.054 1230 Dihedral : 4.194 35.515 1009 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.23 % Favored : 93.56 % Rotamer: Outliers : 5.73 % Allowed : 30.84 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.50 (0.27), residues: 934 helix: 1.05 (0.33), residues: 255 sheet: -0.76 (0.37), residues: 211 loop : -2.38 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 34 HIS 0.001 0.000 HIS A 293 PHE 0.014 0.001 PHE A 152 TYR 0.017 0.001 TYR L 50 ARG 0.008 0.000 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 244) hydrogen bonds : angle 4.71966 ( 702) SS BOND : bond 0.00199 ( 4) SS BOND : angle 0.64729 ( 8) covalent geometry : bond 0.00215 ( 7020) covalent geometry : angle 0.57656 ( 9591) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.739 Fit side-chains REVERT: A 132 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8520 (t) REVERT: A 322 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8191 (tttt) REVERT: H 44 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8165 (mptt) outliers start: 39 outliers final: 18 residues processed: 178 average time/residue: 0.1644 time to fit residues: 39.8902 Evaluate side-chains 162 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 60 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN L 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.168393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.133218 restraints weight = 19786.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.137052 restraints weight = 24036.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.138176 restraints weight = 10822.884| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7024 Z= 0.192 Angle : 0.647 14.121 9599 Z= 0.330 Chirality : 0.045 0.171 1130 Planarity : 0.004 0.056 1230 Dihedral : 4.171 22.603 1002 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.92 % Favored : 90.87 % Rotamer: Outliers : 8.52 % Allowed : 27.46 % Favored : 64.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.71 (0.27), residues: 934 helix: 0.98 (0.32), residues: 253 sheet: -1.00 (0.36), residues: 226 loop : -2.53 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 35 HIS 0.003 0.001 HIS H 54 PHE 0.019 0.002 PHE B 169 TYR 0.017 0.001 TYR L 50 ARG 0.004 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 244) hydrogen bonds : angle 4.84173 ( 702) SS BOND : bond 0.00268 ( 4) SS BOND : angle 1.52180 ( 8) covalent geometry : bond 0.00451 ( 7020) covalent geometry : angle 0.64619 ( 9591) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 140 time to evaluate : 0.746 Fit side-chains REVERT: A 322 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8564 (ttmm) outliers start: 58 outliers final: 43 residues processed: 179 average time/residue: 0.1548 time to fit residues: 38.2020 Evaluate side-chains 183 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 1 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 22 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.171588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141243 restraints weight = 34459.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143500 restraints weight = 22633.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140127 restraints weight = 10111.999| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7024 Z= 0.118 Angle : 0.601 14.381 9599 Z= 0.303 Chirality : 0.043 0.160 1130 Planarity : 0.004 0.055 1230 Dihedral : 4.030 21.843 1002 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.98 % Favored : 92.91 % Rotamer: Outliers : 8.08 % Allowed : 28.49 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.56 (0.27), residues: 934 helix: 1.10 (0.32), residues: 254 sheet: -0.87 (0.37), residues: 221 loop : -2.45 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 48 HIS 0.001 0.000 HIS H 54 PHE 0.025 0.001 PHE A 152 TYR 0.016 0.001 TYR L 50 ARG 0.003 0.000 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 244) hydrogen bonds : angle 4.59020 ( 702) SS BOND : bond 0.00292 ( 4) SS BOND : angle 0.88992 ( 8) covalent geometry : bond 0.00263 ( 7020) covalent geometry : angle 0.60119 ( 9591) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 0.750 Fit side-chains REVERT: A 275 LYS cc_start: 0.8263 (mmpt) cc_final: 0.8039 (mptt) REVERT: A 322 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8510 (ttmm) REVERT: B 371 ARG cc_start: 0.8029 (mmm-85) cc_final: 0.7769 (mmt90) REVERT: L 24 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7478 (ttm-80) outliers start: 55 outliers final: 37 residues processed: 186 average time/residue: 0.1719 time to fit residues: 43.4027 Evaluate side-chains 177 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 1 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 chunk 71 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.171851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141883 restraints weight = 28556.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142234 restraints weight = 21125.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.139604 restraints weight = 10489.359| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7024 Z= 0.118 Angle : 0.612 15.215 9599 Z= 0.304 Chirality : 0.044 0.175 1130 Planarity : 0.004 0.054 1230 Dihedral : 3.972 21.346 1002 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.73 % Favored : 92.16 % Rotamer: Outliers : 7.34 % Allowed : 30.10 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.53 (0.27), residues: 934 helix: 1.08 (0.32), residues: 256 sheet: -0.88 (0.37), residues: 222 loop : -2.40 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 48 HIS 0.002 0.000 HIS H 54 PHE 0.009 0.001 PHE A 340 TYR 0.015 0.001 TYR L 50 ARG 0.003 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 244) hydrogen bonds : angle 4.53476 ( 702) SS BOND : bond 0.00322 ( 4) SS BOND : angle 1.42276 ( 8) covalent geometry : bond 0.00268 ( 7020) covalent geometry : angle 0.61052 ( 9591) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 0.774 Fit side-chains REVERT: A 132 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8674 (t) REVERT: A 322 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8521 (ttmm) REVERT: B 371 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.7698 (mmt90) REVERT: L 24 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7921 (ttm-80) outliers start: 50 outliers final: 37 residues processed: 175 average time/residue: 0.1673 time to fit residues: 40.3404 Evaluate side-chains 177 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 1 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 0.0050 chunk 74 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 0.0870 chunk 67 optimal weight: 0.0770 chunk 52 optimal weight: 2.9990 overall best weight: 0.1930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.175291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.144525 restraints weight = 37850.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.146931 restraints weight = 23925.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145141 restraints weight = 10045.323| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7024 Z= 0.099 Angle : 0.601 15.199 9599 Z= 0.294 Chirality : 0.043 0.187 1130 Planarity : 0.004 0.053 1230 Dihedral : 3.776 19.913 1002 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.23 % Favored : 93.66 % Rotamer: Outliers : 6.02 % Allowed : 32.16 % Favored : 61.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.36 (0.27), residues: 934 helix: 1.19 (0.33), residues: 257 sheet: -0.57 (0.38), residues: 215 loop : -2.40 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 48 HIS 0.001 0.000 HIS B 127 PHE 0.017 0.001 PHE B 241 TYR 0.011 0.001 TYR L 50 ARG 0.003 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.02939 ( 244) hydrogen bonds : angle 4.37367 ( 702) SS BOND : bond 0.00348 ( 4) SS BOND : angle 0.91143 ( 8) covalent geometry : bond 0.00211 ( 7020) covalent geometry : angle 0.60078 ( 9591) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.782 Fit side-chains REVERT: A 132 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8655 (t) REVERT: A 322 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8519 (ttmm) REVERT: A 392 TYR cc_start: 0.6182 (OUTLIER) cc_final: 0.5627 (t80) REVERT: B 157 MET cc_start: 0.7422 (tpp) cc_final: 0.6976 (tpp) REVERT: B 230 LEU cc_start: 0.8477 (tp) cc_final: 0.7999 (tp) REVERT: B 273 PHE cc_start: 0.7165 (m-10) cc_final: 0.6952 (m-80) REVERT: B 371 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7606 (mmt90) REVERT: H 44 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8164 (mptt) REVERT: H 60 TYR cc_start: 0.9248 (m-80) cc_final: 0.8902 (m-80) REVERT: L 24 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7840 (ttm-80) outliers start: 41 outliers final: 29 residues processed: 172 average time/residue: 0.1745 time to fit residues: 40.6052 Evaluate side-chains 170 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 76 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 75 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.0370 chunk 36 optimal weight: 5.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143608 restraints weight = 35916.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146630 restraints weight = 26817.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.147721 restraints weight = 10468.658| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7024 Z= 0.120 Angle : 0.618 14.555 9599 Z= 0.303 Chirality : 0.043 0.170 1130 Planarity : 0.004 0.054 1230 Dihedral : 3.826 20.671 1002 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.84 % Favored : 92.05 % Rotamer: Outliers : 7.20 % Allowed : 31.86 % Favored : 60.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.39 (0.27), residues: 934 helix: 1.17 (0.33), residues: 257 sheet: -0.62 (0.38), residues: 217 loop : -2.41 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 35 HIS 0.002 0.000 HIS H 54 PHE 0.018 0.001 PHE B 241 TYR 0.017 0.001 TYR B 356 ARG 0.003 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 244) hydrogen bonds : angle 4.36281 ( 702) SS BOND : bond 0.00326 ( 4) SS BOND : angle 0.90034 ( 8) covalent geometry : bond 0.00276 ( 7020) covalent geometry : angle 0.61807 ( 9591) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 0.801 Fit side-chains REVERT: A 132 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8647 (t) REVERT: A 322 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8606 (ttmm) REVERT: H 44 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8172 (mptt) REVERT: L 24 ARG cc_start: 0.8103 (ttm-80) cc_final: 0.7839 (ttm-80) outliers start: 49 outliers final: 35 residues processed: 173 average time/residue: 0.1803 time to fit residues: 42.7572 Evaluate side-chains 177 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 1 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.171271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141240 restraints weight = 32279.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143420 restraints weight = 22743.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.140789 restraints weight = 10450.611| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 0.045 7024 Z= 0.139 Angle : 0.641 13.946 9599 Z= 0.317 Chirality : 0.044 0.173 1130 Planarity : 0.004 0.054 1230 Dihedral : 4.026 21.269 1002 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.16 % Favored : 91.73 % Rotamer: Outliers : 7.20 % Allowed : 31.13 % Favored : 61.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.50 (0.27), residues: 934 helix: 1.08 (0.32), residues: 256 sheet: -0.76 (0.37), residues: 220 loop : -2.42 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 34 HIS 0.002 0.000 HIS H 54 PHE 0.019 0.001 PHE B 241 TYR 0.015 0.001 TYR B 356 ARG 0.004 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 244) hydrogen bonds : angle 4.47655 ( 702) SS BOND : bond 0.00542 ( 4) SS BOND : angle 1.38908 ( 8) covalent geometry : bond 0.00323 ( 7020) covalent geometry : angle 0.64020 ( 9591) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 0.859 Fit side-chains REVERT: A 132 SER cc_start: 0.8988 (OUTLIER) cc_final: 0.8728 (t) REVERT: A 320 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8808 (tt) REVERT: B 157 MET cc_start: 0.7416 (tpp) cc_final: 0.7185 (tpp) REVERT: B 239 TYR cc_start: 0.7147 (t80) cc_final: 0.6857 (t80) REVERT: H 44 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8162 (mptt) REVERT: L 24 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7891 (ttm-80) outliers start: 49 outliers final: 35 residues processed: 168 average time/residue: 0.1922 time to fit residues: 45.5283 Evaluate side-chains 171 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 1 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 51 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 53 optimal weight: 0.0030 chunk 30 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.171607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.143052 restraints weight = 38438.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.145133 restraints weight = 22478.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.142548 restraints weight = 10267.231| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7024 Z= 0.111 Angle : 0.619 13.425 9599 Z= 0.306 Chirality : 0.043 0.184 1130 Planarity : 0.004 0.054 1230 Dihedral : 3.898 20.702 1002 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.98 % Favored : 92.91 % Rotamer: Outliers : 6.02 % Allowed : 32.31 % Favored : 61.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.41 (0.27), residues: 934 helix: 1.14 (0.33), residues: 257 sheet: -0.68 (0.37), residues: 220 loop : -2.38 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 285 HIS 0.001 0.000 HIS A 67 PHE 0.018 0.001 PHE B 241 TYR 0.015 0.001 TYR L 50 ARG 0.006 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 244) hydrogen bonds : angle 4.38502 ( 702) SS BOND : bond 0.00495 ( 4) SS BOND : angle 1.35619 ( 8) covalent geometry : bond 0.00253 ( 7020) covalent geometry : angle 0.61822 ( 9591) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.770 Fit side-chains REVERT: A 132 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8745 (t) REVERT: A 320 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8782 (tt) REVERT: A 392 TYR cc_start: 0.6167 (OUTLIER) cc_final: 0.5611 (t80) REVERT: B 157 MET cc_start: 0.7309 (tpp) cc_final: 0.7058 (tpp) REVERT: B 158 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7665 (mt) REVERT: H 44 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8150 (mptt) REVERT: L 24 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7836 (ttm-80) REVERT: L 33 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7626 (p90) outliers start: 41 outliers final: 31 residues processed: 160 average time/residue: 0.1587 time to fit residues: 35.4734 Evaluate side-chains 171 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 1 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.169707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141017 restraints weight = 38783.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144152 restraints weight = 26564.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145202 restraints weight = 10397.018| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7024 Z= 0.157 Angle : 0.655 13.231 9599 Z= 0.327 Chirality : 0.044 0.180 1130 Planarity : 0.004 0.055 1230 Dihedral : 4.091 21.629 1002 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.34 % Favored : 90.55 % Rotamer: Outliers : 6.46 % Allowed : 32.01 % Favored : 61.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.52 (0.27), residues: 934 helix: 1.12 (0.33), residues: 255 sheet: -0.78 (0.37), residues: 222 loop : -2.47 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 34 HIS 0.003 0.001 HIS H 54 PHE 0.014 0.001 PHE B 169 TYR 0.016 0.001 TYR B 239 ARG 0.004 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 244) hydrogen bonds : angle 4.52683 ( 702) SS BOND : bond 0.00516 ( 4) SS BOND : angle 1.33285 ( 8) covalent geometry : bond 0.00370 ( 7020) covalent geometry : angle 0.65458 ( 9591) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 0.831 Fit side-chains REVERT: A 320 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8807 (tt) REVERT: H 44 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8132 (mptt) REVERT: L 24 ARG cc_start: 0.8195 (ttm-80) cc_final: 0.7981 (ttm-80) REVERT: L 33 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7723 (p90) outliers start: 44 outliers final: 39 residues processed: 161 average time/residue: 0.1610 time to fit residues: 36.0782 Evaluate side-chains 173 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 1 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 45 optimal weight: 0.0050 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.172317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.143018 restraints weight = 32739.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.145957 restraints weight = 25497.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.144834 restraints weight = 10475.227| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7024 Z= 0.116 Angle : 0.633 13.192 9599 Z= 0.312 Chirality : 0.044 0.187 1130 Planarity : 0.004 0.054 1230 Dihedral : 3.996 21.021 1002 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.09 % Favored : 92.80 % Rotamer: Outliers : 6.31 % Allowed : 31.86 % Favored : 61.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.43 (0.27), residues: 934 helix: 1.13 (0.33), residues: 255 sheet: -0.67 (0.38), residues: 220 loop : -2.40 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 285 HIS 0.001 0.000 HIS A 162 PHE 0.024 0.001 PHE B 241 TYR 0.018 0.001 TYR B 239 ARG 0.005 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 244) hydrogen bonds : angle 4.44787 ( 702) SS BOND : bond 0.00441 ( 4) SS BOND : angle 1.21850 ( 8) covalent geometry : bond 0.00266 ( 7020) covalent geometry : angle 0.63204 ( 9591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2824.17 seconds wall clock time: 50 minutes 22.02 seconds (3022.02 seconds total)