Starting phenix.real_space_refine on Wed Sep 17 07:11:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1c_61971/09_2025/9k1c_61971.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1c_61971/09_2025/9k1c_61971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k1c_61971/09_2025/9k1c_61971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1c_61971/09_2025/9k1c_61971.map" model { file = "/net/cci-nas-00/data/ceres_data/9k1c_61971/09_2025/9k1c_61971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1c_61971/09_2025/9k1c_61971.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.117 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4220 2.51 5 N 1140 2.21 5 O 1205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6611 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 1982 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 20, 'TRANS': 258} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'GLU:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1745 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2513 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 347 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'HXA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.82, per 1000 atoms: 0.28 Number of scatterers: 6611 At special positions: 0 Unit cell: (77.112, 98.532, 131.733, 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 46 16.00 O 1205 8.00 N 1140 7.00 C 4220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 79 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 376.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1614 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 44.3% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'R' and resid 4 through 37 Proline residue: R 21 - end of helix removed outlier: 3.528A pdb=" N LEU R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 66 removed outlier: 3.537A pdb=" N TYR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Proline residue: R 60 - end of helix Processing helix chain 'R' and resid 75 through 77 No H-bonds generated for 'chain 'R' and resid 75 through 77' Processing helix chain 'R' and resid 78 through 110 Proline residue: R 89 - end of helix removed outlier: 3.803A pdb=" N GLY R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 117 Processing helix chain 'R' and resid 119 through 146 removed outlier: 3.682A pdb=" N SER R 123 " --> pdb=" O ARG R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 212 removed outlier: 5.139A pdb=" N LEU R 193 " --> pdb=" O LEU R 189 " (cutoff:3.500A) Proline residue: R 194 - end of helix Processing helix chain 'R' and resid 215 through 250 Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 256 through 276 removed outlier: 3.551A pdb=" N SER R 268 " --> pdb=" O THR R 264 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL R 269 " --> pdb=" O GLY R 265 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.100A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.849A pdb=" N GLY A 45 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 4.408A pdb=" N LYS A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.176A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.179A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.644A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.933A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.634A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.109A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.731A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.629A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.675A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.660A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 336 hydrogen bonds defined for protein. 984 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: 0.89 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2155 1.35 - 1.46: 1621 1.46 - 1.58: 2918 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 6754 Sorted by residual: bond pdb=" C20 HXA R 401 " pdb=" C21 HXA R 401 " ideal model delta sigma weight residual 1.497 1.566 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C17 HXA R 401 " pdb=" C18 HXA R 401 " ideal model delta sigma weight residual 1.501 1.559 -0.058 2.00e-02 2.50e+03 8.43e+00 bond pdb=" C18 HXA R 401 " pdb=" C19 HXA R 401 " ideal model delta sigma weight residual 1.503 1.559 -0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" C15 HXA R 401 " pdb=" C16 HXA R 401 " ideal model delta sigma weight residual 1.502 1.546 -0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" C3 HXA R 401 " pdb=" C4 HXA R 401 " ideal model delta sigma weight residual 1.496 1.534 -0.038 2.00e-02 2.50e+03 3.66e+00 ... (remaining 6749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.90: 9154 5.90 - 11.80: 3 11.80 - 17.70: 5 17.70 - 23.60: 0 23.60 - 29.49: 7 Bond angle restraints: 9169 Sorted by residual: angle pdb=" C18 HXA R 401 " pdb=" C19 HXA R 401 " pdb=" C20 HXA R 401 " ideal model delta sigma weight residual 127.19 97.70 29.49 3.00e+00 1.11e-01 9.67e+01 angle pdb=" C12 HXA R 401 " pdb=" C13 HXA R 401 " pdb=" C14 HXA R 401 " ideal model delta sigma weight residual 127.67 153.55 -25.88 3.00e+00 1.11e-01 7.44e+01 angle pdb=" C11 HXA R 401 " pdb=" C12 HXA R 401 " pdb=" C13 HXA R 401 " ideal model delta sigma weight residual 110.71 136.06 -25.35 3.00e+00 1.11e-01 7.14e+01 angle pdb=" C6 HXA R 401 " pdb=" C7 HXA R 401 " pdb=" C8 HXA R 401 " ideal model delta sigma weight residual 127.48 152.77 -25.29 3.00e+00 1.11e-01 7.11e+01 angle pdb=" C11 HXA R 401 " pdb=" C10 HXA R 401 " pdb=" C9 HXA R 401 " ideal model delta sigma weight residual 127.25 152.14 -24.89 3.00e+00 1.11e-01 6.89e+01 ... (remaining 9164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 3568 17.01 - 34.02: 329 34.02 - 51.03: 69 51.03 - 68.04: 7 68.04 - 85.05: 7 Dihedral angle restraints: 3980 sinusoidal: 1476 harmonic: 2504 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 178.05 -85.05 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS R 79 " pdb=" SG CYS R 79 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 153.08 -60.08 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CB GLU A 308 " pdb=" CG GLU A 308 " pdb=" CD GLU A 308 " pdb=" OE1 GLU A 308 " ideal model delta sinusoidal sigma weight residual 0.00 -83.37 83.37 1 3.00e+01 1.11e-03 9.43e+00 ... (remaining 3977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 677 0.025 - 0.051: 221 0.051 - 0.076: 75 0.076 - 0.102: 47 0.102 - 0.127: 26 Chirality restraints: 1046 Sorted by residual: chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA ASP A 309 " pdb=" N ASP A 309 " pdb=" C ASP A 309 " pdb=" CB ASP A 309 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.54e-01 ... (remaining 1043 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 238 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO R 239 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO R 239 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 239 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C THR B 87 " 0.024 2.00e-02 2.50e+03 pdb=" O THR B 87 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN B 88 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO B 236 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.017 5.00e-02 4.00e+02 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 730 2.75 - 3.29: 6215 3.29 - 3.83: 11069 3.83 - 4.36: 12172 4.36 - 4.90: 22132 Nonbonded interactions: 52318 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.213 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.262 3.040 nonbonded pdb=" O ASP R 175 " pdb=" OG SER R 178 " model vdw 2.274 3.040 nonbonded pdb=" OG SER B 147 " pdb=" OG SER B 160 " model vdw 2.285 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.308 3.040 ... (remaining 52313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.990 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 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 0.069 6756 Z= 0.127 Angle : 0.917 29.494 9173 Z= 0.357 Chirality : 0.036 0.127 1046 Planarity : 0.003 0.036 1173 Dihedral : 13.741 83.366 2360 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.31), residues: 859 helix: 3.30 (0.28), residues: 368 sheet: 1.33 (0.45), residues: 150 loop : -0.33 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.008 0.000 TYR B 111 PHE 0.007 0.001 PHE R 184 TRP 0.013 0.001 TRP R 131 HIS 0.001 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6754) covalent geometry : angle 0.91744 ( 9169) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.66359 ( 4) hydrogen bonds : bond 0.15529 ( 336) hydrogen bonds : angle 5.18712 ( 984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.254 Fit side-chains REVERT: A 231 ASP cc_start: 0.8213 (t70) cc_final: 0.7948 (t0) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0911 time to fit residues: 11.4924 Evaluate side-chains 77 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.184111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139339 restraints weight = 6902.768| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.83 r_work: 0.3350 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6756 Z= 0.121 Angle : 0.503 8.315 9173 Z= 0.249 Chirality : 0.039 0.148 1046 Planarity : 0.003 0.033 1173 Dihedral : 5.450 58.663 948 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.74 % Allowed : 8.71 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.30), residues: 859 helix: 3.15 (0.28), residues: 371 sheet: 0.85 (0.41), residues: 162 loop : -0.32 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 62 TYR 0.010 0.001 TYR R 250 PHE 0.010 0.001 PHE R 82 TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6754) covalent geometry : angle 0.50253 ( 9169) SS BOND : bond 0.00445 ( 2) SS BOND : angle 0.97276 ( 4) hydrogen bonds : bond 0.03127 ( 336) hydrogen bonds : angle 3.95390 ( 984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.257 Fit side-chains REVERT: B 156 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8051 (mt0) REVERT: B 215 GLU cc_start: 0.7484 (pt0) cc_final: 0.7050 (pt0) outliers start: 5 outliers final: 4 residues processed: 75 average time/residue: 0.0928 time to fit residues: 9.4073 Evaluate side-chains 69 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 269 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 0.0170 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.178388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133026 restraints weight = 6838.828| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.87 r_work: 0.3370 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6756 Z= 0.132 Angle : 0.502 9.000 9173 Z= 0.249 Chirality : 0.039 0.135 1046 Planarity : 0.004 0.037 1173 Dihedral : 5.388 53.289 948 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.92 % Allowed : 11.37 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.30), residues: 859 helix: 3.11 (0.28), residues: 369 sheet: 0.54 (0.41), residues: 162 loop : -0.49 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 62 TYR 0.008 0.001 TYR R 202 PHE 0.010 0.001 PHE A 189 TRP 0.012 0.001 TRP R 131 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6754) covalent geometry : angle 0.50179 ( 9169) SS BOND : bond 0.00574 ( 2) SS BOND : angle 1.16342 ( 4) hydrogen bonds : bond 0.03266 ( 336) hydrogen bonds : angle 3.84117 ( 984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.246 Fit side-chains REVERT: B 156 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8272 (mt0) REVERT: B 215 GLU cc_start: 0.7438 (pt0) cc_final: 0.7011 (pt0) REVERT: B 226 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8061 (mp0) REVERT: B 327 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8207 (p) outliers start: 13 outliers final: 9 residues processed: 89 average time/residue: 0.1036 time to fit residues: 12.1122 Evaluate side-chains 90 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 50.0000 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.174749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129715 restraints weight = 6838.371| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.94 r_work: 0.3180 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6756 Z= 0.164 Angle : 0.526 9.121 9173 Z= 0.262 Chirality : 0.040 0.134 1046 Planarity : 0.004 0.034 1173 Dihedral : 5.596 55.935 948 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.92 % Allowed : 13.88 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.30), residues: 859 helix: 2.96 (0.28), residues: 369 sheet: 0.45 (0.42), residues: 166 loop : -0.67 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 62 TYR 0.010 0.001 TYR R 202 PHE 0.013 0.001 PHE A 189 TRP 0.008 0.001 TRP B 63 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 6754) covalent geometry : angle 0.52517 ( 9169) SS BOND : bond 0.00600 ( 2) SS BOND : angle 1.34590 ( 4) hydrogen bonds : bond 0.03322 ( 336) hydrogen bonds : angle 3.90225 ( 984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: B 212 ASP cc_start: 0.7855 (m-30) cc_final: 0.7638 (m-30) REVERT: B 215 GLU cc_start: 0.7642 (pt0) cc_final: 0.7255 (pt0) REVERT: B 269 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6560 (pt) outliers start: 13 outliers final: 8 residues processed: 95 average time/residue: 0.1008 time to fit residues: 12.5887 Evaluate side-chains 91 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.174378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.129599 restraints weight = 6933.914| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.91 r_work: 0.3182 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6756 Z= 0.142 Angle : 0.509 8.472 9173 Z= 0.255 Chirality : 0.039 0.131 1046 Planarity : 0.003 0.035 1173 Dihedral : 5.520 54.282 948 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.36 % Allowed : 14.48 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.30), residues: 859 helix: 2.96 (0.28), residues: 368 sheet: 0.42 (0.43), residues: 167 loop : -0.74 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 46 TYR 0.008 0.001 TYR R 202 PHE 0.013 0.001 PHE A 189 TRP 0.007 0.001 TRP B 169 HIS 0.002 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6754) covalent geometry : angle 0.50858 ( 9169) SS BOND : bond 0.00552 ( 2) SS BOND : angle 1.23367 ( 4) hydrogen bonds : bond 0.03188 ( 336) hydrogen bonds : angle 3.83272 ( 984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: B 212 ASP cc_start: 0.7969 (m-30) cc_final: 0.7681 (m-30) REVERT: B 215 GLU cc_start: 0.7717 (pt0) cc_final: 0.7426 (pt0) REVERT: B 234 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8973 (m-80) REVERT: B 269 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6540 (pt) REVERT: B 304 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7464 (mtm180) outliers start: 16 outliers final: 8 residues processed: 94 average time/residue: 0.1018 time to fit residues: 12.4351 Evaluate side-chains 92 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 0.4980 chunk 83 optimal weight: 0.0470 chunk 16 optimal weight: 30.0000 chunk 81 optimal weight: 0.4980 chunk 72 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.176083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131675 restraints weight = 6878.337| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.90 r_work: 0.3212 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6756 Z= 0.104 Angle : 0.484 7.773 9173 Z= 0.240 Chirality : 0.038 0.131 1046 Planarity : 0.003 0.036 1173 Dihedral : 5.382 53.793 948 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.77 % Allowed : 14.92 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.30), residues: 859 helix: 3.02 (0.28), residues: 368 sheet: 0.56 (0.43), residues: 166 loop : -0.73 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.008 0.001 TYR R 202 PHE 0.012 0.001 PHE A 189 TRP 0.008 0.001 TRP B 169 HIS 0.002 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6754) covalent geometry : angle 0.48364 ( 9169) SS BOND : bond 0.00422 ( 2) SS BOND : angle 0.92531 ( 4) hydrogen bonds : bond 0.02919 ( 336) hydrogen bonds : angle 3.68354 ( 984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.264 Fit side-chains REVERT: B 125 ASN cc_start: 0.8531 (t0) cc_final: 0.8321 (t0) REVERT: B 215 GLU cc_start: 0.7713 (pt0) cc_final: 0.7428 (pt0) REVERT: B 234 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8984 (m-80) REVERT: B 269 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6564 (pt) outliers start: 12 outliers final: 6 residues processed: 95 average time/residue: 0.0886 time to fit residues: 11.2314 Evaluate side-chains 91 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.174574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129999 restraints weight = 6852.725| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.88 r_work: 0.3183 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6756 Z= 0.132 Angle : 0.515 10.417 9173 Z= 0.253 Chirality : 0.039 0.130 1046 Planarity : 0.003 0.036 1173 Dihedral : 5.425 53.448 948 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.22 % Allowed : 15.21 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.30), residues: 859 helix: 2.98 (0.28), residues: 368 sheet: 0.53 (0.44), residues: 166 loop : -0.78 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.008 0.001 TYR R 202 PHE 0.013 0.001 PHE A 189 TRP 0.007 0.001 TRP B 169 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6754) covalent geometry : angle 0.51459 ( 9169) SS BOND : bond 0.00507 ( 2) SS BOND : angle 1.07183 ( 4) hydrogen bonds : bond 0.03056 ( 336) hydrogen bonds : angle 3.70444 ( 984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.267 Fit side-chains REVERT: B 125 ASN cc_start: 0.8561 (t0) cc_final: 0.8322 (t0) REVERT: B 215 GLU cc_start: 0.7721 (pt0) cc_final: 0.7338 (pt0) REVERT: B 217 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7259 (pmm) REVERT: B 234 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8955 (m-80) REVERT: B 269 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6525 (pt) outliers start: 15 outliers final: 12 residues processed: 98 average time/residue: 0.0929 time to fit residues: 12.1298 Evaluate side-chains 98 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.173413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128130 restraints weight = 6876.536| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.95 r_work: 0.3165 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6756 Z= 0.142 Angle : 0.534 9.967 9173 Z= 0.261 Chirality : 0.039 0.130 1046 Planarity : 0.003 0.037 1173 Dihedral : 5.516 53.442 948 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.66 % Allowed : 14.92 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.30), residues: 859 helix: 2.92 (0.28), residues: 368 sheet: 0.46 (0.44), residues: 159 loop : -0.85 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.008 0.001 TYR R 202 PHE 0.014 0.001 PHE A 189 TRP 0.009 0.001 TRP R 131 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6754) covalent geometry : angle 0.53328 ( 9169) SS BOND : bond 0.00563 ( 2) SS BOND : angle 1.19506 ( 4) hydrogen bonds : bond 0.03186 ( 336) hydrogen bonds : angle 3.74422 ( 984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.251 Fit side-chains REVERT: B 125 ASN cc_start: 0.8597 (t0) cc_final: 0.8376 (t0) REVERT: B 215 GLU cc_start: 0.7963 (pt0) cc_final: 0.7650 (pt0) REVERT: B 217 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7456 (pmm) REVERT: B 234 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.8970 (m-80) REVERT: B 269 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6556 (pt) outliers start: 18 outliers final: 13 residues processed: 102 average time/residue: 0.0944 time to fit residues: 12.4940 Evaluate side-chains 104 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 74 optimal weight: 0.0970 chunk 79 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.172725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.128342 restraints weight = 6893.438| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.04 r_work: 0.3149 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6756 Z= 0.146 Angle : 0.551 9.979 9173 Z= 0.270 Chirality : 0.040 0.133 1046 Planarity : 0.003 0.037 1173 Dihedral : 5.628 56.639 948 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.51 % Allowed : 15.07 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.30), residues: 859 helix: 2.88 (0.28), residues: 368 sheet: 0.48 (0.45), residues: 157 loop : -0.85 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.008 0.001 TYR R 202 PHE 0.014 0.001 PHE A 189 TRP 0.006 0.001 TRP R 131 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6754) covalent geometry : angle 0.55082 ( 9169) SS BOND : bond 0.00587 ( 2) SS BOND : angle 1.23476 ( 4) hydrogen bonds : bond 0.03223 ( 336) hydrogen bonds : angle 3.78360 ( 984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.254 Fit side-chains REVERT: B 125 ASN cc_start: 0.8632 (t0) cc_final: 0.8399 (t0) REVERT: B 215 GLU cc_start: 0.8029 (pt0) cc_final: 0.7689 (pt0) REVERT: B 217 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7405 (pmm) REVERT: B 234 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8971 (m-80) REVERT: B 269 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.6565 (pt) outliers start: 17 outliers final: 14 residues processed: 100 average time/residue: 0.0962 time to fit residues: 12.6136 Evaluate side-chains 103 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 33 optimal weight: 0.0010 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.172929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128466 restraints weight = 6873.591| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.98 r_work: 0.3159 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6756 Z= 0.136 Angle : 0.550 10.119 9173 Z= 0.267 Chirality : 0.040 0.132 1046 Planarity : 0.003 0.037 1173 Dihedral : 5.591 55.956 948 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.51 % Allowed : 15.21 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.30), residues: 859 helix: 2.89 (0.28), residues: 368 sheet: 0.51 (0.45), residues: 157 loop : -0.87 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.008 0.001 TYR R 202 PHE 0.014 0.001 PHE A 189 TRP 0.007 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6754) covalent geometry : angle 0.54949 ( 9169) SS BOND : bond 0.00532 ( 2) SS BOND : angle 1.15943 ( 4) hydrogen bonds : bond 0.03146 ( 336) hydrogen bonds : angle 3.76710 ( 984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.259 Fit side-chains REVERT: B 125 ASN cc_start: 0.8582 (t0) cc_final: 0.8364 (t0) REVERT: B 215 GLU cc_start: 0.8050 (pt0) cc_final: 0.7695 (pt0) REVERT: B 217 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7364 (pmm) REVERT: B 226 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8314 (mt-10) REVERT: B 234 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8978 (m-80) REVERT: B 269 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6555 (pt) outliers start: 17 outliers final: 14 residues processed: 102 average time/residue: 0.0962 time to fit residues: 12.7821 Evaluate side-chains 107 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 80 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.173540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129280 restraints weight = 6876.589| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.91 r_work: 0.3179 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6756 Z= 0.124 Angle : 0.549 14.028 9173 Z= 0.263 Chirality : 0.039 0.132 1046 Planarity : 0.003 0.038 1173 Dihedral : 5.423 57.997 948 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.51 % Allowed : 15.66 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.30), residues: 859 helix: 2.90 (0.28), residues: 368 sheet: 0.55 (0.46), residues: 157 loop : -0.84 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.007 0.001 TYR R 202 PHE 0.013 0.001 PHE A 189 TRP 0.007 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6754) covalent geometry : angle 0.54890 ( 9169) SS BOND : bond 0.00493 ( 2) SS BOND : angle 1.06827 ( 4) hydrogen bonds : bond 0.03044 ( 336) hydrogen bonds : angle 3.72122 ( 984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.13 seconds wall clock time: 37 minutes 2.45 seconds (2222.45 seconds total)