Starting phenix.real_space_refine on Wed Sep 17 06:26:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j05_61049/09_2025/9j05_61049.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j05_61049/09_2025/9j05_61049.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 { model { file = "/net/cci-nas-00/data/ceres_data/9j05_61049/09_2025/9j05_61049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j05_61049/09_2025/9j05_61049.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j05_61049/09_2025/9j05_61049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j05_61049/09_2025/9j05_61049.map" } 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= -0.002 sd= 0.071 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 22 5.16 5 C 3772 2.51 5 N 993 2.21 5 O 1124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 5911 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2754 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 11, 'TRANS': 369} Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 5, 'PHE:plan': 9, 'TRP:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "B" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1653 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1504 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 186} Chain breaks: 1 Time building chain proxies: 1.39, per 1000 atoms: 0.24 Number of scatterers: 5911 At special positions: 0 Unit cell: (64.896, 101.504, 128.96, 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 22 16.00 O 1124 8.00 N 993 7.00 C 3772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 138 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 109 " distance=2.09 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 218 " 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: 0.43 Conformation dependent library (CDL) restraints added in 193.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1508 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 45.8% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 4.059A pdb=" N ILE A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) Proline residue: A 26 - end of helix Processing helix chain 'A' and resid 28 through 45 removed outlier: 3.911A pdb=" N LEU A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 49 removed outlier: 3.739A pdb=" N TYR A 49 " --> pdb=" O ILE A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 57 through 82 removed outlier: 3.762A pdb=" N LYS A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) Proline residue: A 75 - end of helix removed outlier: 3.742A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 96 Processing helix chain 'A' and resid 96 through 124 removed outlier: 3.778A pdb=" N VAL A 110 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 151 removed outlier: 3.832A pdb=" N TRP A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 151 " --> pdb=" O MET A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 183 through 237 removed outlier: 3.605A pdb=" N PHE A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 200 " --> pdb=" O TRP A 196 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR A 207 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N THR A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 262 removed outlier: 3.614A pdb=" N VAL A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 264 No H-bonds generated for 'chain 'A' and resid 263 through 264' Processing helix chain 'A' and resid 265 through 269 removed outlier: 3.500A pdb=" N MET A 268 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 269' Processing helix chain 'A' and resid 270 through 291 removed outlier: 3.727A pdb=" N PHE A 275 " --> pdb=" O PHE A 271 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE A 277 " --> pdb=" O HIS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 327 removed outlier: 4.243A pdb=" N ALA A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 353 removed outlier: 3.602A pdb=" N PHE A 337 " --> pdb=" O PHE A 333 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Proline residue: A 339 - end of helix removed outlier: 3.699A pdb=" N ILE A 345 " --> pdb=" O HIS A 341 " (cutoff:3.500A) Proline residue: A 346 - end of helix Processing helix chain 'A' and resid 357 through 377 Processing helix chain 'A' and resid 377 through 390 Proline residue: A 383 - end of helix removed outlier: 3.570A pdb=" N CYS A 390 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.555A pdb=" N THR B 133 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'C' and resid 100 through 104 removed outlier: 4.149A pdb=" N PHE C 104 " --> pdb=" O PRO C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.926A pdb=" N HIS C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 49 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.607A pdb=" N MET B 76 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER B 92 " --> pdb=" O MET B 76 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP B 78 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'B' and resid 171 through 175 removed outlier: 3.787A pdb=" N LYS B 194 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR B 227 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 175 removed outlier: 3.787A pdb=" N LYS B 194 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR B 227 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 205 removed outlier: 4.383A pdb=" N TYR B 245 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA8, first strand: chain 'C' and resid 40 through 45 Processing sheet with id=AA9, first strand: chain 'C' and resid 138 through 142 removed outlier: 5.315A pdb=" N SER C 155 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU C 205 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL C 157 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU C 203 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU C 159 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER C 201 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASN C 161 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU C 199 " --> pdb=" O ASN C 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 177 through 178 349 hydrogen bonds defined for protein. 969 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: 0.96 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1004 1.32 - 1.45: 1643 1.45 - 1.57: 3368 1.57 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 6045 Sorted by residual: bond pdb=" CA SER C 117 " pdb=" CB SER C 117 " ideal model delta sigma weight residual 1.530 1.451 0.079 1.69e-02 3.50e+03 2.17e+01 bond pdb=" CA ALA C 118 " pdb=" CB ALA C 118 " ideal model delta sigma weight residual 1.533 1.464 0.069 1.66e-02 3.63e+03 1.74e+01 bond pdb=" N THR C 133 " pdb=" CA THR C 133 " ideal model delta sigma weight residual 1.457 1.507 -0.050 1.29e-02 6.01e+03 1.48e+01 bond pdb=" C SER C 117 " pdb=" N ALA C 118 " ideal model delta sigma weight residual 1.331 1.378 -0.047 1.24e-02 6.50e+03 1.43e+01 bond pdb=" N ALA C 118 " pdb=" CA ALA C 118 " ideal model delta sigma weight residual 1.455 1.500 -0.044 1.23e-02 6.61e+03 1.30e+01 ... (remaining 6040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 8123 3.27 - 6.54: 92 6.54 - 9.81: 14 9.81 - 13.08: 7 13.08 - 16.35: 1 Bond angle restraints: 8237 Sorted by residual: angle pdb=" N GLY C 116 " pdb=" CA GLY C 116 " pdb=" C GLY C 116 " ideal model delta sigma weight residual 115.46 99.11 16.35 1.63e+00 3.76e-01 1.01e+02 angle pdb=" N TRP C 113 " pdb=" CA TRP C 113 " pdb=" C TRP C 113 " ideal model delta sigma weight residual 111.02 100.62 10.40 1.25e+00 6.40e-01 6.92e+01 angle pdb=" N LEU C 119 " pdb=" CA LEU C 119 " pdb=" CB LEU C 119 " ideal model delta sigma weight residual 110.49 123.09 -12.60 1.69e+00 3.50e-01 5.55e+01 angle pdb=" C GLN C 110 " pdb=" CA GLN C 110 " pdb=" CB GLN C 110 " ideal model delta sigma weight residual 111.41 98.79 12.62 1.70e+00 3.46e-01 5.51e+01 angle pdb=" N VAL B 172 " pdb=" CA VAL B 172 " pdb=" CB VAL B 172 " ideal model delta sigma weight residual 111.39 103.07 8.32 1.16e+00 7.43e-01 5.15e+01 ... (remaining 8232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 3181 17.57 - 35.14: 308 35.14 - 52.71: 81 52.71 - 70.28: 21 70.28 - 87.85: 5 Dihedral angle restraints: 3596 sinusoidal: 1261 harmonic: 2335 Sorted by residual: dihedral pdb=" C GLN C 110 " pdb=" N GLN C 110 " pdb=" CA GLN C 110 " pdb=" CB GLN C 110 " ideal model delta harmonic sigma weight residual -122.60 -105.82 -16.78 0 2.50e+00 1.60e-01 4.50e+01 dihedral pdb=" CA TRP C 115 " pdb=" C TRP C 115 " pdb=" N GLY C 116 " pdb=" CA GLY C 116 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" N LEU C 119 " pdb=" C LEU C 119 " pdb=" CA LEU C 119 " pdb=" CB LEU C 119 " ideal model delta harmonic sigma weight residual 122.80 131.88 -9.08 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 3593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 828 0.066 - 0.132: 107 0.132 - 0.198: 12 0.198 - 0.264: 4 0.264 - 0.330: 2 Chirality restraints: 953 Sorted by residual: chirality pdb=" CA GLN C 110 " pdb=" N GLN C 110 " pdb=" C GLN C 110 " pdb=" CB GLN C 110 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA PRO C 112 " pdb=" N PRO C 112 " pdb=" C PRO C 112 " pdb=" CB PRO C 112 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA VAL A 294 " pdb=" N VAL A 294 " pdb=" C VAL A 294 " pdb=" CB VAL A 294 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 950 not shown) Planarity restraints: 1043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 288 " 0.023 2.00e-02 2.50e+03 4.49e-02 2.01e+01 pdb=" C LEU A 288 " -0.078 2.00e-02 2.50e+03 pdb=" O LEU A 288 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA A 289 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 203 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C ILE A 203 " -0.069 2.00e-02 2.50e+03 pdb=" O ILE A 203 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL A 204 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 118 " 0.017 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ALA C 118 " -0.063 2.00e-02 2.50e+03 pdb=" O ALA C 118 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU C 119 " 0.022 2.00e-02 2.50e+03 ... (remaining 1040 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 158 2.68 - 3.24: 5804 3.24 - 3.79: 9407 3.79 - 4.35: 12395 4.35 - 4.90: 20604 Nonbonded interactions: 48368 Sorted by model distance: nonbonded pdb=" OE1 GLN A 281 " pdb=" OG SER C 117 " model vdw 2.130 3.040 nonbonded pdb=" OD1 ASP A 284 " pdb=" OG SER B 97 " model vdw 2.178 3.040 nonbonded pdb=" OG SER C 84 " pdb=" OG1 THR C 95 " model vdw 2.212 3.040 nonbonded pdb=" O THR A 226 " pdb=" ND2 ASN A 230 " model vdw 2.274 3.120 nonbonded pdb=" OE1 GLN A 351 " pdb=" NZ LYS A 361 " model vdw 2.284 3.120 ... (remaining 48363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.020 Find NCS groups from input model: 0.020 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 : 0.005 0.079 6049 Z= 0.328 Angle : 0.919 16.350 8245 Z= 0.570 Chirality : 0.049 0.330 953 Planarity : 0.006 0.058 1043 Dihedral : 15.835 87.847 2076 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.76 % Allowed : 5.82 % Favored : 93.43 % Rotamer: Outliers : 3.46 % Allowed : 20.10 % Favored : 76.44 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 8.82 % 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: -0.50 (0.30), residues: 791 helix: 0.16 (0.30), residues: 300 sheet: 0.36 (0.34), residues: 197 loop : -1.22 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 45 TYR 0.014 0.001 TYR A 311 PHE 0.017 0.001 PHE A 111 TRP 0.019 0.002 TRP C 113 HIS 0.005 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 6045) covalent geometry : angle 0.91667 ( 8237) SS BOND : bond 0.03056 ( 4) SS BOND : angle 2.40803 ( 8) hydrogen bonds : bond 0.15358 ( 330) hydrogen bonds : angle 7.16346 ( 969) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6979 (tt) REVERT: A 269 LYS cc_start: 0.6157 (pptt) cc_final: 0.5877 (ptpp) REVERT: A 361 LYS cc_start: 0.6259 (mmmm) cc_final: 0.5925 (tppt) REVERT: C 114 SER cc_start: 0.6012 (OUTLIER) cc_final: 0.5658 (m) outliers start: 21 outliers final: 14 residues processed: 94 average time/residue: 0.0665 time to fit residues: 8.7431 Evaluate side-chains 86 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 109 CYS Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0470 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.5680 ------------------------------------------------------------------------------- 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 = 0.4768 r_free = 0.4768 target = 0.252280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.215318 restraints weight = 6300.182| |-----------------------------------------------------------------------------| r_work (start): 0.4495 rms_B_bonded: 1.85 r_work: 0.4062 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6049 Z= 0.153 Angle : 0.624 10.859 8245 Z= 0.334 Chirality : 0.041 0.156 953 Planarity : 0.005 0.058 1043 Dihedral : 6.764 61.849 873 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.76 % Allowed : 4.55 % Favored : 94.69 % Rotamer: Outliers : 4.94 % Allowed : 17.13 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -0.07 (0.31), residues: 791 helix: 0.67 (0.30), residues: 312 sheet: 0.39 (0.37), residues: 179 loop : -1.01 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 45 TYR 0.009 0.001 TYR C 164 PHE 0.025 0.002 PHE A 205 TRP 0.016 0.001 TRP C 113 HIS 0.003 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6045) covalent geometry : angle 0.62338 ( 8237) SS BOND : bond 0.00288 ( 4) SS BOND : angle 0.94674 ( 8) hydrogen bonds : bond 0.03909 ( 330) hydrogen bonds : angle 4.91780 ( 969) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6984 (mt) REVERT: A 197 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6596 (mp) REVERT: A 231 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7390 (tt) REVERT: A 269 LYS cc_start: 0.6253 (pptt) cc_final: 0.5899 (ptpp) REVERT: A 286 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7568 (tt) outliers start: 30 outliers final: 16 residues processed: 94 average time/residue: 0.0650 time to fit residues: 8.8221 Evaluate side-chains 91 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 219 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 0.0870 chunk 58 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 46 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 ASN C 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.251920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.218515 restraints weight = 6226.543| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 1.53 r_work: 0.4124 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6049 Z= 0.142 Angle : 0.581 10.096 8245 Z= 0.309 Chirality : 0.041 0.137 953 Planarity : 0.005 0.059 1043 Dihedral : 6.283 53.815 862 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.44 % Favored : 94.06 % Rotamer: Outliers : 4.45 % Allowed : 18.45 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: 0.07 (0.31), residues: 791 helix: 0.83 (0.30), residues: 311 sheet: 0.39 (0.36), residues: 194 loop : -1.00 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 45 TYR 0.016 0.001 TYR A 366 PHE 0.020 0.001 PHE A 205 TRP 0.013 0.001 TRP B 89 HIS 0.002 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6045) covalent geometry : angle 0.58111 ( 8237) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.83523 ( 8) hydrogen bonds : bond 0.03491 ( 330) hydrogen bonds : angle 4.64607 ( 969) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6690 (mp) REVERT: A 277 ILE cc_start: 0.6300 (OUTLIER) cc_final: 0.5967 (mp) REVERT: A 286 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7666 (tt) REVERT: C 115 TRP cc_start: 0.6676 (m100) cc_final: 0.6455 (m100) outliers start: 27 outliers final: 16 residues processed: 97 average time/residue: 0.0564 time to fit residues: 8.2173 Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 219 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4771 r_free = 0.4771 target = 0.254007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.221377 restraints weight = 6321.790| |-----------------------------------------------------------------------------| r_work (start): 0.4500 rms_B_bonded: 1.88 r_work: 0.4047 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6049 Z= 0.160 Angle : 0.589 10.585 8245 Z= 0.311 Chirality : 0.041 0.145 953 Planarity : 0.005 0.058 1043 Dihedral : 5.465 48.538 856 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.68 % Favored : 94.82 % Rotamer: Outliers : 4.78 % Allowed : 18.45 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.01 (0.31), residues: 791 helix: 0.79 (0.30), residues: 312 sheet: 0.20 (0.36), residues: 184 loop : -0.92 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 45 TYR 0.014 0.001 TYR A 366 PHE 0.017 0.001 PHE A 205 TRP 0.014 0.002 TRP B 89 HIS 0.002 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6045) covalent geometry : angle 0.58856 ( 8237) SS BOND : bond 0.00257 ( 4) SS BOND : angle 0.82281 ( 8) hydrogen bonds : bond 0.03423 ( 330) hydrogen bonds : angle 4.65409 ( 969) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7108 (OUTLIER) cc_final: 0.6699 (mp) REVERT: A 231 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7368 (tt) REVERT: A 267 GLU cc_start: 0.5804 (mp0) cc_final: 0.5553 (mp0) outliers start: 29 outliers final: 23 residues processed: 99 average time/residue: 0.0639 time to fit residues: 9.0676 Evaluate side-chains 97 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 7 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 63 optimal weight: 0.0770 chunk 27 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.0980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN C 161 ASN C 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.256346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.222742 restraints weight = 6423.498| |-----------------------------------------------------------------------------| r_work (start): 0.4514 rms_B_bonded: 1.84 r_work: 0.4073 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6049 Z= 0.128 Angle : 0.556 9.495 8245 Z= 0.295 Chirality : 0.040 0.136 953 Planarity : 0.005 0.060 1043 Dihedral : 4.811 34.291 853 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.06 % Favored : 94.44 % Rotamer: Outliers : 5.11 % Allowed : 17.79 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.19 (0.31), residues: 791 helix: 1.00 (0.30), residues: 311 sheet: 0.38 (0.37), residues: 179 loop : -0.90 (0.39), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 181 TYR 0.021 0.001 TYR A 366 PHE 0.017 0.001 PHE A 111 TRP 0.013 0.001 TRP C 115 HIS 0.002 0.000 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6045) covalent geometry : angle 0.55585 ( 8237) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.69965 ( 8) hydrogen bonds : bond 0.03151 ( 330) hydrogen bonds : angle 4.47238 ( 969) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6701 (mp) REVERT: A 231 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7397 (tt) REVERT: A 324 ARG cc_start: 0.6540 (mmt180) cc_final: 0.5970 (ptp-170) REVERT: A 365 ARG cc_start: 0.6871 (mmm160) cc_final: 0.6348 (tpp80) outliers start: 31 outliers final: 24 residues processed: 102 average time/residue: 0.0738 time to fit residues: 10.2469 Evaluate side-chains 104 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 0.0770 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 75 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.4756 r_free = 0.4756 target = 0.250938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.213884 restraints weight = 6241.269| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 1.88 r_work: 0.4027 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6049 Z= 0.139 Angle : 0.570 9.656 8245 Z= 0.302 Chirality : 0.041 0.139 953 Planarity : 0.005 0.066 1043 Dihedral : 4.836 34.813 853 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.42 % Favored : 95.07 % Rotamer: Outliers : 4.61 % Allowed : 18.95 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.22 (0.31), residues: 791 helix: 1.05 (0.30), residues: 312 sheet: 0.36 (0.37), residues: 179 loop : -0.87 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 251 TYR 0.020 0.001 TYR A 366 PHE 0.016 0.001 PHE A 111 TRP 0.019 0.002 TRP C 115 HIS 0.002 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6045) covalent geometry : angle 0.56996 ( 8237) SS BOND : bond 0.00216 ( 4) SS BOND : angle 0.72101 ( 8) hydrogen bonds : bond 0.03251 ( 330) hydrogen bonds : angle 4.47750 ( 969) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6698 (mp) REVERT: A 231 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7394 (tt) REVERT: A 324 ARG cc_start: 0.6405 (mmt180) cc_final: 0.5839 (ptp-170) REVERT: A 365 ARG cc_start: 0.6927 (mmm160) cc_final: 0.6566 (tpp80) outliers start: 28 outliers final: 24 residues processed: 99 average time/residue: 0.0698 time to fit residues: 9.7161 Evaluate side-chains 104 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 28 optimal weight: 0.2980 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 14 optimal weight: 0.0980 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 0.0670 chunk 2 optimal weight: 2.9990 overall best weight: 0.2318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.255524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.220294 restraints weight = 6259.375| |-----------------------------------------------------------------------------| r_work (start): 0.4533 rms_B_bonded: 1.70 r_work: 0.4073 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6049 Z= 0.109 Angle : 0.540 8.355 8245 Z= 0.286 Chirality : 0.040 0.147 953 Planarity : 0.005 0.060 1043 Dihedral : 4.544 34.999 851 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.17 % Favored : 95.45 % Rotamer: Outliers : 4.12 % Allowed : 19.77 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.38 (0.31), residues: 791 helix: 1.15 (0.30), residues: 313 sheet: 0.55 (0.36), residues: 189 loop : -0.90 (0.41), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 251 TYR 0.023 0.001 TYR A 366 PHE 0.012 0.001 PHE C 163 TRP 0.020 0.001 TRP C 115 HIS 0.002 0.000 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 6045) covalent geometry : angle 0.53956 ( 8237) SS BOND : bond 0.00158 ( 4) SS BOND : angle 0.60052 ( 8) hydrogen bonds : bond 0.03010 ( 330) hydrogen bonds : angle 4.31420 ( 969) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 190 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6465 (tp) REVERT: A 197 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6802 (mp) REVERT: A 231 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7513 (tt) REVERT: A 302 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: A 324 ARG cc_start: 0.6640 (mmt180) cc_final: 0.6121 (ptp-170) REVERT: B 67 SER cc_start: 0.8455 (t) cc_final: 0.8079 (m) REVERT: B 221 LEU cc_start: 0.8236 (tp) cc_final: 0.7936 (tp) outliers start: 25 outliers final: 19 residues processed: 101 average time/residue: 0.0644 time to fit residues: 9.0356 Evaluate side-chains 102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 0.0970 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.252400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.218398 restraints weight = 6256.917| |-----------------------------------------------------------------------------| r_work (start): 0.4518 rms_B_bonded: 1.50 r_work: 0.4120 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6049 Z= 0.140 Angle : 0.547 7.329 8245 Z= 0.288 Chirality : 0.041 0.150 953 Planarity : 0.005 0.059 1043 Dihedral : 4.651 36.915 851 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.17 % Favored : 95.58 % Rotamer: Outliers : 4.12 % Allowed : 20.43 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.34 (0.31), residues: 791 helix: 1.10 (0.30), residues: 314 sheet: 0.51 (0.36), residues: 189 loop : -0.89 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 45 TYR 0.020 0.001 TYR A 366 PHE 0.013 0.001 PHE A 111 TRP 0.018 0.001 TRP C 115 HIS 0.002 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6045) covalent geometry : angle 0.54706 ( 8237) SS BOND : bond 0.00212 ( 4) SS BOND : angle 0.72135 ( 8) hydrogen bonds : bond 0.03144 ( 330) hydrogen bonds : angle 4.39456 ( 969) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 190 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6342 (tp) REVERT: A 197 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6781 (mp) REVERT: A 231 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7427 (tt) REVERT: A 277 ILE cc_start: 0.6718 (OUTLIER) cc_final: 0.5757 (tt) REVERT: A 324 ARG cc_start: 0.6517 (mmt180) cc_final: 0.6066 (ptp-170) REVERT: B 221 LEU cc_start: 0.8266 (tp) cc_final: 0.8038 (tp) outliers start: 25 outliers final: 16 residues processed: 98 average time/residue: 0.0834 time to fit residues: 11.1066 Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4758 r_free = 0.4758 target = 0.251525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.217656 restraints weight = 6371.851| |-----------------------------------------------------------------------------| r_work (start): 0.4472 rms_B_bonded: 2.02 r_work: 0.3986 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6049 Z= 0.211 Angle : 0.604 7.962 8245 Z= 0.321 Chirality : 0.043 0.191 953 Planarity : 0.005 0.059 1043 Dihedral : 4.958 36.955 851 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.80 % Favored : 94.94 % Rotamer: Outliers : 4.61 % Allowed : 20.76 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.13 (0.31), residues: 791 helix: 0.95 (0.30), residues: 315 sheet: 0.23 (0.37), residues: 179 loop : -0.87 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 45 TYR 0.012 0.002 TYR A 120 PHE 0.016 0.002 PHE A 111 TRP 0.021 0.002 TRP C 113 HIS 0.003 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 6045) covalent geometry : angle 0.60315 ( 8237) SS BOND : bond 0.00340 ( 4) SS BOND : angle 1.00320 ( 8) hydrogen bonds : bond 0.03530 ( 330) hydrogen bonds : angle 4.69649 ( 969) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 190 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6422 (tp) REVERT: A 197 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6731 (mp) REVERT: A 231 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7295 (tt) REVERT: A 302 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7093 (mt-10) REVERT: A 324 ARG cc_start: 0.6450 (mmt180) cc_final: 0.5932 (ptp-170) REVERT: B 221 LEU cc_start: 0.8362 (tp) cc_final: 0.8158 (tp) outliers start: 28 outliers final: 21 residues processed: 100 average time/residue: 0.0749 time to fit residues: 10.3137 Evaluate side-chains 102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 38 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.0010 chunk 48 optimal weight: 0.0270 overall best weight: 0.1442 ------------------------------------------------------------------------------- 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 = 0.4793 r_free = 0.4793 target = 0.255675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.220232 restraints weight = 6311.908| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 1.62 r_work: 0.4122 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6049 Z= 0.109 Angle : 0.539 7.437 8245 Z= 0.287 Chirality : 0.040 0.173 953 Planarity : 0.005 0.059 1043 Dihedral : 4.553 35.263 851 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.17 % Favored : 95.58 % Rotamer: Outliers : 3.29 % Allowed : 21.58 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.42 (0.31), residues: 791 helix: 1.09 (0.30), residues: 316 sheet: 0.54 (0.37), residues: 188 loop : -0.73 (0.41), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 45 TYR 0.011 0.001 TYR A 366 PHE 0.013 0.001 PHE A 195 TRP 0.026 0.002 TRP C 113 HIS 0.001 0.000 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 6045) covalent geometry : angle 0.53840 ( 8237) SS BOND : bond 0.00194 ( 4) SS BOND : angle 0.64471 ( 8) hydrogen bonds : bond 0.02979 ( 330) hydrogen bonds : angle 4.29303 ( 969) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 190 ILE cc_start: 0.6753 (OUTLIER) cc_final: 0.6295 (tp) REVERT: A 197 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6757 (mp) REVERT: A 231 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7392 (tt) REVERT: A 277 ILE cc_start: 0.6639 (OUTLIER) cc_final: 0.5708 (tt) REVERT: A 302 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6916 (mt-10) REVERT: A 322 SER cc_start: 0.6784 (m) cc_final: 0.6445 (p) REVERT: A 324 ARG cc_start: 0.6412 (mmt180) cc_final: 0.5891 (ptp-170) REVERT: A 365 ARG cc_start: 0.7420 (tpp80) cc_final: 0.5986 (ttm110) REVERT: A 369 GLU cc_start: 0.7038 (mp0) cc_final: 0.6492 (mp0) REVERT: B 67 SER cc_start: 0.8375 (t) cc_final: 0.8024 (m) REVERT: B 221 LEU cc_start: 0.8219 (tp) cc_final: 0.7980 (tp) outliers start: 20 outliers final: 14 residues processed: 92 average time/residue: 0.0743 time to fit residues: 9.4502 Evaluate side-chains 92 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 50 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 0.0060 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN C 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.251958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.214792 restraints weight = 6222.765| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 1.94 r_work: 0.4022 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6049 Z= 0.142 Angle : 0.554 7.486 8245 Z= 0.293 Chirality : 0.041 0.166 953 Planarity : 0.005 0.059 1043 Dihedral : 4.654 35.595 851 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.17 % Favored : 95.70 % Rotamer: Outliers : 3.29 % Allowed : 21.75 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.37 (0.31), residues: 791 helix: 1.13 (0.30), residues: 315 sheet: 0.43 (0.38), residues: 179 loop : -0.75 (0.40), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 365 TYR 0.009 0.001 TYR B 101 PHE 0.012 0.001 PHE A 111 TRP 0.012 0.001 TRP C 115 HIS 0.002 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6045) covalent geometry : angle 0.55370 ( 8237) SS BOND : bond 0.00231 ( 4) SS BOND : angle 0.74622 ( 8) hydrogen bonds : bond 0.03134 ( 330) hydrogen bonds : angle 4.38605 ( 969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1681.83 seconds wall clock time: 29 minutes 40.16 seconds (1780.16 seconds total)