Starting phenix.real_space_refine on Tue Nov 18 11:52:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5z1w_6877/11_2025/5z1w_6877_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5z1w_6877/11_2025/5z1w_6877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5z1w_6877/11_2025/5z1w_6877_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5z1w_6877/11_2025/5z1w_6877_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5z1w_6877/11_2025/5z1w_6877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5z1w_6877/11_2025/5z1w_6877.map" } resolution = 3.38 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= 0.001 sd= 0.016 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 52 5.16 5 C 9124 2.51 5 N 2192 2.21 5 O 2456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13824 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3414 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 11, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 94 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 3.11, per 1000 atoms: 0.22 Number of scatterers: 13824 At special positions: 0 Unit cell: (108.24, 108.24, 97.68, 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 52 16.00 O 2456 8.00 N 2192 7.00 C 9124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 223 " distance=2.02 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 223 " distance=2.02 Simple disulfide: pdb=" SG CYS C 210 " - pdb=" SG CYS C 223 " distance=2.02 Simple disulfide: pdb=" SG CYS D 210 " - pdb=" SG CYS D 223 " distance=2.02 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 Links applied NAG-ASN " NAG A 800 " - " ASN A 177 " " NAG A 801 " - " ASN A 207 " " NAG A 802 " - " ASN A 241 " " NAG B 800 " - " ASN B 177 " " NAG B 801 " - " ASN B 207 " " NAG B 802 " - " ASN B 241 " " NAG C 800 " - " ASN C 177 " " NAG C 801 " - " ASN C 207 " " NAG C 802 " - " ASN C 241 " " NAG D 800 " - " ASN D 177 " " NAG D 801 " - " ASN D 207 " " NAG D 802 " - " ASN D 241 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 670.7 milliseconds 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 53.2% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.573A pdb=" N VAL A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.520A pdb=" N TYR A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.575A pdb=" N ASP A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.859A pdb=" N SER A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 372 removed outlier: 3.778A pdb=" N PHE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 372 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 421 removed outlier: 3.718A pdb=" N GLY A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N HIS A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 452 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 480 through 480 No H-bonds generated for 'chain 'A' and resid 480 through 480' Processing helix chain 'A' and resid 481 through 499 removed outlier: 3.636A pdb=" N VAL A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.834A pdb=" N ILE A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 562 removed outlier: 3.644A pdb=" N VAL A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.520A pdb=" N TYR B 129 " --> pdb=" O SER B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 163 through 168 removed outlier: 3.575A pdb=" N ASP B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.860A pdb=" N SER B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 372 removed outlier: 3.778A pdb=" N PHE B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 372 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 421 removed outlier: 3.718A pdb=" N GLY B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N HIS B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 452 Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'B' and resid 480 through 480 No H-bonds generated for 'chain 'B' and resid 480 through 480' Processing helix chain 'B' and resid 481 through 499 removed outlier: 3.635A pdb=" N VAL B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 525 through 533 removed outlier: 3.834A pdb=" N ILE B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 562 removed outlier: 3.643A pdb=" N VAL B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 120 Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.520A pdb=" N TYR C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.575A pdb=" N ASP C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 291 removed outlier: 3.858A pdb=" N SER C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 372 removed outlier: 3.778A pdb=" N PHE C 350 " --> pdb=" O ASN C 346 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU C 372 " --> pdb=" O VAL C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 421 removed outlier: 3.718A pdb=" N GLY C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N HIS C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE C 405 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 452 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 480 through 480 No H-bonds generated for 'chain 'C' and resid 480 through 480' Processing helix chain 'C' and resid 481 through 499 removed outlier: 3.635A pdb=" N VAL C 487 " --> pdb=" O MET C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 525 through 533 removed outlier: 3.834A pdb=" N ILE C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN C 533 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 562 removed outlier: 3.644A pdb=" N VAL C 539 " --> pdb=" O ILE C 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.519A pdb=" N TYR D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 162 Processing helix chain 'D' and resid 163 through 168 removed outlier: 3.575A pdb=" N ASP D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 291 removed outlier: 3.858A pdb=" N SER D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY D 291 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 372 removed outlier: 3.779A pdb=" N PHE D 350 " --> pdb=" O ASN D 346 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU D 372 " --> pdb=" O VAL D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 421 removed outlier: 3.718A pdb=" N GLY D 402 " --> pdb=" O ILE D 398 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N HIS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE D 405 " --> pdb=" O VAL D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 452 Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'D' and resid 480 through 480 No H-bonds generated for 'chain 'D' and resid 480 through 480' Processing helix chain 'D' and resid 481 through 499 removed outlier: 3.635A pdb=" N VAL D 487 " --> pdb=" O MET D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 525 through 533 removed outlier: 3.833A pdb=" N ILE D 529 " --> pdb=" O ASP D 525 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 562 removed outlier: 3.643A pdb=" N VAL D 539 " --> pdb=" O ILE D 535 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 removed outlier: 6.832A pdb=" N LEU A 195 " --> pdb=" O TYR A 308 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR A 308 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA A 197 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER A 306 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 300 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 314 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'B' and resid 187 through 188 Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 188 removed outlier: 6.832A pdb=" N LEU B 195 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR B 308 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA B 197 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER B 306 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 300 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 314 " --> pdb=" O ASN B 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 188 Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 188 removed outlier: 6.832A pdb=" N LEU C 195 " --> pdb=" O TYR C 308 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR C 308 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA C 197 " --> pdb=" O SER C 306 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER C 306 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 300 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 314 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 258 through 259 Processing sheet with id=AB1, first strand: chain 'D' and resid 187 through 188 Processing sheet with id=AB2, first strand: chain 'D' and resid 187 through 188 removed outlier: 6.832A pdb=" N LEU D 195 " --> pdb=" O TYR D 308 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR D 308 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA D 197 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER D 306 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 300 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D 314 " --> pdb=" O ASN D 309 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 258 through 259 784 hydrogen bonds defined for protein. 2268 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4214 1.34 - 1.46: 3436 1.46 - 1.57: 6486 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 14216 Sorted by residual: bond pdb=" CA TRP C 259 " pdb=" CB TRP C 259 " ideal model delta sigma weight residual 1.528 1.489 0.039 1.39e-02 5.18e+03 7.86e+00 bond pdb=" CA TRP A 259 " pdb=" CB TRP A 259 " ideal model delta sigma weight residual 1.528 1.489 0.039 1.39e-02 5.18e+03 7.86e+00 bond pdb=" CA TRP B 259 " pdb=" CB TRP B 259 " ideal model delta sigma weight residual 1.528 1.489 0.039 1.39e-02 5.18e+03 7.81e+00 bond pdb=" CA TRP D 259 " pdb=" CB TRP D 259 " ideal model delta sigma weight residual 1.528 1.489 0.038 1.39e-02 5.18e+03 7.55e+00 bond pdb=" C GLN C 234 " pdb=" N LEU C 235 " ideal model delta sigma weight residual 1.329 1.259 0.070 3.03e-02 1.09e+03 5.33e+00 ... (remaining 14211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 17297 1.41 - 2.81: 1721 2.81 - 4.22: 286 4.22 - 5.63: 60 5.63 - 7.03: 20 Bond angle restraints: 19384 Sorted by residual: angle pdb=" N GLY A 183 " pdb=" CA GLY A 183 " pdb=" C GLY A 183 " ideal model delta sigma weight residual 110.97 116.54 -5.57 1.56e+00 4.11e-01 1.28e+01 angle pdb=" N GLY B 183 " pdb=" CA GLY B 183 " pdb=" C GLY B 183 " ideal model delta sigma weight residual 110.97 116.54 -5.57 1.56e+00 4.11e-01 1.28e+01 angle pdb=" N GLY C 183 " pdb=" CA GLY C 183 " pdb=" C GLY C 183 " ideal model delta sigma weight residual 110.97 116.53 -5.56 1.56e+00 4.11e-01 1.27e+01 angle pdb=" N GLY D 183 " pdb=" CA GLY D 183 " pdb=" C GLY D 183 " ideal model delta sigma weight residual 110.97 116.48 -5.51 1.56e+00 4.11e-01 1.25e+01 angle pdb=" C ILE B 451 " pdb=" N LYS B 452 " pdb=" CA LYS B 452 " ideal model delta sigma weight residual 120.63 125.87 -5.24 1.61e+00 3.86e-01 1.06e+01 ... (remaining 19379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 7852 16.28 - 32.57: 232 32.57 - 48.85: 60 48.85 - 65.14: 20 65.14 - 81.42: 12 Dihedral angle restraints: 8176 sinusoidal: 3156 harmonic: 5020 Sorted by residual: dihedral pdb=" CA ASN B 311 " pdb=" C ASN B 311 " pdb=" N ILE B 312 " pdb=" CA ILE B 312 " ideal model delta harmonic sigma weight residual 180.00 158.05 21.95 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASN D 311 " pdb=" C ASN D 311 " pdb=" N ILE D 312 " pdb=" CA ILE D 312 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASN C 311 " pdb=" C ASN C 311 " pdb=" N ILE C 312 " pdb=" CA ILE C 312 " ideal model delta harmonic sigma weight residual 180.00 158.09 21.91 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 8173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1090 0.039 - 0.078: 721 0.078 - 0.116: 295 0.116 - 0.155: 78 0.155 - 0.194: 8 Chirality restraints: 2192 Sorted by residual: chirality pdb=" CA ARG C 299 " pdb=" N ARG C 299 " pdb=" C ARG C 299 " pdb=" CB ARG C 299 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA ARG D 299 " pdb=" N ARG D 299 " pdb=" C ARG D 299 " pdb=" CB ARG D 299 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" CA ARG B 299 " pdb=" N ARG B 299 " pdb=" C ARG B 299 " pdb=" CB ARG B 299 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.05e-01 ... (remaining 2189 not shown) Planarity restraints: 2428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 171 " -0.015 2.00e-02 2.50e+03 1.76e-02 7.73e+00 pdb=" CG TRP C 171 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 171 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 171 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 171 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 171 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 171 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 171 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 171 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP C 171 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 171 " -0.015 2.00e-02 2.50e+03 1.75e-02 7.62e+00 pdb=" CG TRP D 171 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP D 171 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 171 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 171 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 171 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 171 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 171 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 171 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 171 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 171 " -0.015 2.00e-02 2.50e+03 1.74e-02 7.58e+00 pdb=" CG TRP B 171 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 171 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 171 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 171 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 171 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 171 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 171 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 171 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 171 " 0.000 2.00e-02 2.50e+03 ... (remaining 2425 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3259 2.77 - 3.30: 13614 3.30 - 3.84: 22586 3.84 - 4.37: 26689 4.37 - 4.90: 44611 Nonbonded interactions: 110759 Sorted by model distance: nonbonded pdb=" NH2 ARG B 182 " pdb=" NH1 ARG D 296 " model vdw 2.239 3.200 nonbonded pdb=" NH1 ARG A 296 " pdb=" NH2 ARG D 182 " model vdw 2.242 3.200 nonbonded pdb=" NH1 ARG B 296 " pdb=" NH2 ARG C 182 " model vdw 2.242 3.200 nonbonded pdb=" NH2 ARG A 182 " pdb=" NH1 ARG C 296 " model vdw 2.254 3.200 nonbonded pdb=" OD1 ASP B 427 " pdb=" N GLU B 429 " model vdw 2.316 3.120 ... (remaining 110754 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.240 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.011 0.070 14232 Z= 0.498 Angle : 0.954 8.664 19428 Z= 0.548 Chirality : 0.057 0.194 2192 Planarity : 0.006 0.052 2416 Dihedral : 10.296 81.422 4948 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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 are not related in a simple way. whole: -3.34 (0.16), residues: 1692 helix: -2.55 (0.13), residues: 912 sheet: -0.44 (0.33), residues: 184 loop : -1.89 (0.20), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 337 TYR 0.040 0.003 TYR D 129 PHE 0.022 0.003 PHE A 364 TRP 0.044 0.004 TRP C 171 HIS 0.007 0.002 HIS D 213 Details of bonding type rmsd covalent geometry : bond 0.01139 (14216) covalent geometry : angle 0.92816 (19384) SS BOND : bond 0.01462 ( 4) SS BOND : angle 2.57828 ( 8) hydrogen bonds : bond 0.09937 ( 776) hydrogen bonds : angle 8.82455 ( 2268) link_NAG-ASN : bond 0.00957 ( 12) link_NAG-ASN : angle 5.12704 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7967 (tt0) REVERT: A 363 ILE cc_start: 0.8102 (pt) cc_final: 0.7891 (tp) REVERT: A 482 ILE cc_start: 0.9063 (tt) cc_final: 0.8702 (mm) REVERT: A 530 ASP cc_start: 0.8846 (t70) cc_final: 0.8575 (t70) REVERT: B 290 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7967 (tt0) REVERT: B 363 ILE cc_start: 0.8125 (pt) cc_final: 0.7918 (tp) REVERT: B 482 ILE cc_start: 0.9067 (tt) cc_final: 0.8702 (mm) REVERT: B 530 ASP cc_start: 0.8843 (t70) cc_final: 0.8574 (t70) REVERT: C 290 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7969 (tt0) REVERT: C 363 ILE cc_start: 0.8102 (pt) cc_final: 0.7889 (tp) REVERT: C 482 ILE cc_start: 0.9061 (tt) cc_final: 0.8701 (mm) REVERT: C 530 ASP cc_start: 0.8848 (t70) cc_final: 0.8582 (t70) REVERT: D 290 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7980 (tt0) REVERT: D 363 ILE cc_start: 0.8101 (pt) cc_final: 0.7888 (tp) REVERT: D 482 ILE cc_start: 0.9063 (tt) cc_final: 0.8700 (mm) REVERT: D 530 ASP cc_start: 0.8846 (t70) cc_final: 0.8571 (t70) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1086 time to fit residues: 53.0353 Evaluate side-chains 217 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0030 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS A 202 GLN A 437 GLN A 516 GLN A 533 ASN A 554 ASN B 139 HIS B 202 GLN B 437 GLN B 516 GLN B 533 ASN B 554 ASN C 139 HIS C 202 GLN C 437 GLN C 516 GLN C 533 ASN C 554 ASN D 139 HIS D 202 GLN D 437 GLN D 516 GLN D 533 ASN D 554 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.129597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.100649 restraints weight = 21415.394| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.52 r_work: 0.3008 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14232 Z= 0.152 Angle : 0.591 6.276 19428 Z= 0.315 Chirality : 0.044 0.209 2192 Planarity : 0.004 0.032 2416 Dihedral : 6.146 46.977 2120 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.48 % Allowed : 6.16 % Favored : 91.36 % 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 are not related in a simple way. whole: -0.20 (0.19), residues: 1692 helix: 0.48 (0.17), residues: 876 sheet: 0.17 (0.33), residues: 184 loop : -0.99 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 413 TYR 0.023 0.002 TYR D 129 PHE 0.028 0.002 PHE B 550 TRP 0.017 0.002 TRP B 434 HIS 0.009 0.002 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00338 (14216) covalent geometry : angle 0.57033 (19384) SS BOND : bond 0.00486 ( 4) SS BOND : angle 0.50928 ( 8) hydrogen bonds : bond 0.04251 ( 776) hydrogen bonds : angle 4.64753 ( 2268) link_NAG-ASN : bond 0.00399 ( 12) link_NAG-ASN : angle 3.65486 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 260 time to evaluate : 0.511 Fit side-chains REVERT: A 290 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8205 (tt0) REVERT: A 482 ILE cc_start: 0.9027 (tt) cc_final: 0.8518 (mm) REVERT: A 483 MET cc_start: 0.8679 (tmm) cc_final: 0.8272 (tmm) REVERT: B 290 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8208 (tt0) REVERT: B 482 ILE cc_start: 0.9010 (tt) cc_final: 0.8494 (mm) REVERT: B 483 MET cc_start: 0.8688 (tmm) cc_final: 0.8280 (tmm) REVERT: C 290 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8213 (tt0) REVERT: C 429 GLU cc_start: 0.7953 (mp0) cc_final: 0.7592 (mp0) REVERT: C 482 ILE cc_start: 0.9021 (tt) cc_final: 0.8509 (mm) REVERT: C 483 MET cc_start: 0.8689 (tmm) cc_final: 0.8285 (tmm) REVERT: D 290 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8213 (tt0) REVERT: D 397 SER cc_start: 0.8750 (m) cc_final: 0.8549 (m) REVERT: D 429 GLU cc_start: 0.7931 (mp0) cc_final: 0.7575 (mp0) REVERT: D 482 ILE cc_start: 0.9004 (tt) cc_final: 0.8488 (mm) REVERT: D 483 MET cc_start: 0.8658 (tmm) cc_final: 0.8253 (tmm) outliers start: 35 outliers final: 16 residues processed: 277 average time/residue: 0.1022 time to fit residues: 43.7744 Evaluate side-chains 224 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.128942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.099830 restraints weight = 21454.785| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.54 r_work: 0.2986 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14232 Z= 0.156 Angle : 0.555 6.120 19428 Z= 0.298 Chirality : 0.043 0.204 2192 Planarity : 0.004 0.037 2416 Dihedral : 5.272 28.979 2120 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.62 % Allowed : 8.14 % Favored : 89.24 % 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 are not related in a simple way. whole: 0.65 (0.20), residues: 1692 helix: 1.35 (0.17), residues: 876 sheet: 0.34 (0.33), residues: 184 loop : -0.80 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.018 0.001 TYR C 129 PHE 0.023 0.002 PHE C 549 TRP 0.016 0.002 TRP B 434 HIS 0.007 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00357 (14216) covalent geometry : angle 0.53963 (19384) SS BOND : bond 0.00449 ( 4) SS BOND : angle 0.45748 ( 8) hydrogen bonds : bond 0.03986 ( 776) hydrogen bonds : angle 4.17816 ( 2268) link_NAG-ASN : bond 0.00318 ( 12) link_NAG-ASN : angle 3.03269 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.542 Fit side-chains REVERT: A 290 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8265 (tt0) REVERT: A 482 ILE cc_start: 0.8989 (tt) cc_final: 0.8449 (mm) REVERT: A 483 MET cc_start: 0.8729 (tmm) cc_final: 0.8323 (tmm) REVERT: A 557 LEU cc_start: 0.8241 (tp) cc_final: 0.7979 (tp) REVERT: B 290 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8273 (tt0) REVERT: B 482 ILE cc_start: 0.8988 (tt) cc_final: 0.8448 (mm) REVERT: B 483 MET cc_start: 0.8722 (tmm) cc_final: 0.8316 (tmm) REVERT: B 557 LEU cc_start: 0.8222 (tp) cc_final: 0.7976 (tp) REVERT: C 290 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8266 (tt0) REVERT: C 429 GLU cc_start: 0.7840 (mp0) cc_final: 0.7614 (mp0) REVERT: C 482 ILE cc_start: 0.8978 (tt) cc_final: 0.8430 (mm) REVERT: C 483 MET cc_start: 0.8727 (tmm) cc_final: 0.8324 (tmm) REVERT: C 557 LEU cc_start: 0.8225 (tp) cc_final: 0.7977 (tp) REVERT: D 290 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8243 (tt0) REVERT: D 429 GLU cc_start: 0.7839 (mp0) cc_final: 0.7621 (mp0) REVERT: D 482 ILE cc_start: 0.8985 (tt) cc_final: 0.8446 (mm) REVERT: D 483 MET cc_start: 0.8719 (tmm) cc_final: 0.8305 (tmm) REVERT: D 557 LEU cc_start: 0.8213 (tp) cc_final: 0.7960 (tp) outliers start: 37 outliers final: 32 residues processed: 253 average time/residue: 0.1087 time to fit residues: 42.2052 Evaluate side-chains 250 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 112 optimal weight: 9.9990 chunk 90 optimal weight: 0.0030 chunk 140 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN D 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.095789 restraints weight = 21705.528| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.55 r_work: 0.2951 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14232 Z= 0.256 Angle : 0.637 10.637 19428 Z= 0.333 Chirality : 0.046 0.219 2192 Planarity : 0.004 0.049 2416 Dihedral : 5.255 26.961 2120 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.04 % Allowed : 8.07 % Favored : 87.89 % 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 are not related in a simple way. whole: 0.68 (0.20), residues: 1692 helix: 1.33 (0.17), residues: 876 sheet: 0.60 (0.35), residues: 184 loop : -0.81 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 206 TYR 0.016 0.002 TYR B 129 PHE 0.029 0.002 PHE B 549 TRP 0.018 0.002 TRP B 434 HIS 0.007 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00604 (14216) covalent geometry : angle 0.62159 (19384) SS BOND : bond 0.00530 ( 4) SS BOND : angle 0.63321 ( 8) hydrogen bonds : bond 0.04329 ( 776) hydrogen bonds : angle 4.23373 ( 2268) link_NAG-ASN : bond 0.00487 ( 12) link_NAG-ASN : angle 3.29871 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 231 time to evaluate : 0.550 Fit side-chains REVERT: A 290 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8260 (tt0) REVERT: A 482 ILE cc_start: 0.9024 (tt) cc_final: 0.8492 (mm) REVERT: A 483 MET cc_start: 0.8777 (tmm) cc_final: 0.8385 (tmm) REVERT: A 557 LEU cc_start: 0.8233 (tp) cc_final: 0.7965 (tp) REVERT: B 290 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8257 (tt0) REVERT: B 482 ILE cc_start: 0.9030 (tt) cc_final: 0.8502 (mm) REVERT: B 483 MET cc_start: 0.8772 (tmm) cc_final: 0.8387 (tmm) REVERT: B 557 LEU cc_start: 0.8254 (tp) cc_final: 0.7990 (tp) REVERT: C 290 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8275 (tt0) REVERT: C 482 ILE cc_start: 0.9029 (tt) cc_final: 0.8498 (mm) REVERT: C 483 MET cc_start: 0.8784 (tmm) cc_final: 0.8394 (tmm) REVERT: C 557 LEU cc_start: 0.8246 (tp) cc_final: 0.7984 (tp) REVERT: D 290 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8268 (tt0) REVERT: D 482 ILE cc_start: 0.9024 (tt) cc_final: 0.8495 (mm) REVERT: D 483 MET cc_start: 0.8787 (tmm) cc_final: 0.8392 (tmm) REVERT: D 557 LEU cc_start: 0.8236 (tp) cc_final: 0.7968 (tp) outliers start: 57 outliers final: 32 residues processed: 257 average time/residue: 0.1181 time to fit residues: 44.8787 Evaluate side-chains 242 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 86 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 119 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.129727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100169 restraints weight = 21471.297| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.57 r_work: 0.3005 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14232 Z= 0.117 Angle : 0.532 10.496 19428 Z= 0.277 Chirality : 0.042 0.192 2192 Planarity : 0.004 0.042 2416 Dihedral : 4.620 24.427 2120 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.41 % Allowed : 10.20 % Favored : 87.39 % 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 are not related in a simple way. whole: 1.02 (0.20), residues: 1692 helix: 1.61 (0.17), residues: 876 sheet: 0.65 (0.33), residues: 184 loop : -0.61 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 182 TYR 0.012 0.001 TYR C 127 PHE 0.024 0.001 PHE A 549 TRP 0.014 0.001 TRP D 434 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00254 (14216) covalent geometry : angle 0.52148 (19384) SS BOND : bond 0.00322 ( 4) SS BOND : angle 0.30575 ( 8) hydrogen bonds : bond 0.03699 ( 776) hydrogen bonds : angle 3.90498 ( 2268) link_NAG-ASN : bond 0.00319 ( 12) link_NAG-ASN : angle 2.55321 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.581 Fit side-chains REVERT: A 290 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8185 (tt0) REVERT: A 482 ILE cc_start: 0.8889 (tt) cc_final: 0.8311 (mm) REVERT: A 483 MET cc_start: 0.8719 (tmm) cc_final: 0.8312 (tmm) REVERT: A 557 LEU cc_start: 0.8261 (tp) cc_final: 0.8011 (tp) REVERT: B 290 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8191 (tt0) REVERT: B 482 ILE cc_start: 0.8879 (tt) cc_final: 0.8294 (mm) REVERT: B 483 MET cc_start: 0.8713 (tmm) cc_final: 0.8310 (tmm) REVERT: B 557 LEU cc_start: 0.8270 (tp) cc_final: 0.8019 (tp) REVERT: C 290 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8196 (tt0) REVERT: C 429 GLU cc_start: 0.7812 (mp0) cc_final: 0.7591 (mp0) REVERT: C 482 ILE cc_start: 0.8890 (tt) cc_final: 0.8311 (mm) REVERT: C 483 MET cc_start: 0.8721 (tmm) cc_final: 0.8317 (tmm) REVERT: C 557 LEU cc_start: 0.8263 (tp) cc_final: 0.8012 (tp) REVERT: D 290 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8189 (tt0) REVERT: D 429 GLU cc_start: 0.7797 (mp0) cc_final: 0.7584 (mp0) REVERT: D 482 ILE cc_start: 0.8880 (tt) cc_final: 0.8296 (mm) REVERT: D 483 MET cc_start: 0.8724 (tmm) cc_final: 0.8319 (tmm) REVERT: D 557 LEU cc_start: 0.8251 (tp) cc_final: 0.7999 (tp) outliers start: 34 outliers final: 25 residues processed: 250 average time/residue: 0.1085 time to fit residues: 41.5901 Evaluate side-chains 232 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 555 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 81 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 145 optimal weight: 0.0000 chunk 153 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.130669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101526 restraints weight = 21308.057| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.56 r_work: 0.3049 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14232 Z= 0.108 Angle : 0.506 9.891 19428 Z= 0.268 Chirality : 0.041 0.189 2192 Planarity : 0.004 0.040 2416 Dihedral : 4.323 21.356 2120 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.41 % Allowed : 10.84 % Favored : 86.76 % 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 are not related in a simple way. whole: 1.16 (0.20), residues: 1692 helix: 1.69 (0.17), residues: 880 sheet: 0.71 (0.34), residues: 184 loop : -0.50 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 182 TYR 0.012 0.001 TYR C 127 PHE 0.028 0.001 PHE B 549 TRP 0.012 0.001 TRP C 434 HIS 0.004 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00236 (14216) covalent geometry : angle 0.49779 (19384) SS BOND : bond 0.00281 ( 4) SS BOND : angle 0.32127 ( 8) hydrogen bonds : bond 0.03543 ( 776) hydrogen bonds : angle 3.78073 ( 2268) link_NAG-ASN : bond 0.00311 ( 12) link_NAG-ASN : angle 2.22196 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8138 (tt0) REVERT: A 482 ILE cc_start: 0.8810 (tt) cc_final: 0.8215 (mm) REVERT: A 483 MET cc_start: 0.8693 (tmm) cc_final: 0.8272 (tmm) REVERT: A 557 LEU cc_start: 0.8243 (tp) cc_final: 0.8012 (tp) REVERT: B 290 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8145 (tt0) REVERT: B 482 ILE cc_start: 0.8807 (tt) cc_final: 0.8216 (mm) REVERT: B 483 MET cc_start: 0.8691 (tmm) cc_final: 0.8272 (tmm) REVERT: B 557 LEU cc_start: 0.8249 (tp) cc_final: 0.8019 (tp) REVERT: C 290 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8170 (tt0) REVERT: C 482 ILE cc_start: 0.8809 (tt) cc_final: 0.8211 (mm) REVERT: C 483 MET cc_start: 0.8694 (tmm) cc_final: 0.8279 (tmm) REVERT: C 557 LEU cc_start: 0.8252 (tp) cc_final: 0.8021 (tp) REVERT: D 167 ASP cc_start: 0.8436 (m-30) cc_final: 0.8187 (t0) REVERT: D 290 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8125 (tt0) REVERT: D 482 ILE cc_start: 0.8808 (tt) cc_final: 0.8215 (mm) REVERT: D 483 MET cc_start: 0.8700 (tmm) cc_final: 0.8283 (tmm) REVERT: D 557 LEU cc_start: 0.8233 (tp) cc_final: 0.8001 (tp) outliers start: 34 outliers final: 28 residues processed: 249 average time/residue: 0.1085 time to fit residues: 41.5400 Evaluate side-chains 251 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 555 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 17 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 0.0870 chunk 9 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 421 GLN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 421 GLN C 404 HIS D 404 HIS D 445 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.100290 restraints weight = 21268.913| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.55 r_work: 0.3008 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14232 Z= 0.135 Angle : 0.527 9.778 19428 Z= 0.278 Chirality : 0.042 0.196 2192 Planarity : 0.004 0.041 2416 Dihedral : 4.315 20.152 2120 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.62 % Allowed : 11.40 % Favored : 85.98 % 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 are not related in a simple way. whole: 1.25 (0.20), residues: 1692 helix: 1.73 (0.17), residues: 880 sheet: 0.82 (0.35), residues: 184 loop : -0.42 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 199 TYR 0.011 0.001 TYR B 496 PHE 0.028 0.001 PHE A 549 TRP 0.013 0.001 TRP D 434 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00310 (14216) covalent geometry : angle 0.51868 (19384) SS BOND : bond 0.00330 ( 4) SS BOND : angle 0.37786 ( 8) hydrogen bonds : bond 0.03641 ( 776) hydrogen bonds : angle 3.76396 ( 2268) link_NAG-ASN : bond 0.00290 ( 12) link_NAG-ASN : angle 2.24134 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8148 (tt0) REVERT: A 417 LYS cc_start: 0.8749 (tptp) cc_final: 0.8496 (tppt) REVERT: A 482 ILE cc_start: 0.8794 (tt) cc_final: 0.8183 (mm) REVERT: A 483 MET cc_start: 0.8703 (tmm) cc_final: 0.8265 (tmm) REVERT: A 557 LEU cc_start: 0.8240 (tp) cc_final: 0.8008 (tp) REVERT: B 290 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8164 (tt0) REVERT: B 417 LYS cc_start: 0.8755 (tptp) cc_final: 0.8498 (tppt) REVERT: B 482 ILE cc_start: 0.8787 (tt) cc_final: 0.8179 (mm) REVERT: B 483 MET cc_start: 0.8719 (tmm) cc_final: 0.8303 (tmm) REVERT: B 557 LEU cc_start: 0.8247 (tp) cc_final: 0.8019 (tp) REVERT: C 290 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8160 (tt0) REVERT: C 482 ILE cc_start: 0.8787 (tt) cc_final: 0.8173 (mm) REVERT: C 483 MET cc_start: 0.8696 (tmm) cc_final: 0.8283 (tmm) REVERT: C 557 LEU cc_start: 0.8242 (tp) cc_final: 0.8010 (tp) REVERT: D 167 ASP cc_start: 0.8478 (m-30) cc_final: 0.8231 (t0) REVERT: D 290 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8148 (tt0) REVERT: D 482 ILE cc_start: 0.8791 (tt) cc_final: 0.8182 (mm) REVERT: D 483 MET cc_start: 0.8704 (tmm) cc_final: 0.8289 (tmm) REVERT: D 557 LEU cc_start: 0.8231 (tp) cc_final: 0.8002 (tp) outliers start: 37 outliers final: 28 residues processed: 245 average time/residue: 0.1135 time to fit residues: 42.1919 Evaluate side-chains 247 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 555 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 10 optimal weight: 3.9990 chunk 134 optimal weight: 0.0770 chunk 99 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN B 404 HIS B 420 GLN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS D 445 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.100745 restraints weight = 21130.793| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.54 r_work: 0.3022 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14232 Z= 0.127 Angle : 0.526 9.260 19428 Z= 0.279 Chirality : 0.042 0.193 2192 Planarity : 0.004 0.041 2416 Dihedral : 4.242 19.468 2120 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.76 % Allowed : 11.47 % Favored : 85.76 % 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 are not related in a simple way. whole: 1.29 (0.20), residues: 1692 helix: 1.75 (0.17), residues: 880 sheet: 0.87 (0.35), residues: 184 loop : -0.39 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 261 TYR 0.011 0.001 TYR A 496 PHE 0.029 0.001 PHE A 549 TRP 0.012 0.001 TRP B 434 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00290 (14216) covalent geometry : angle 0.51794 (19384) SS BOND : bond 0.00306 ( 4) SS BOND : angle 0.37914 ( 8) hydrogen bonds : bond 0.03602 ( 776) hydrogen bonds : angle 3.72687 ( 2268) link_NAG-ASN : bond 0.00294 ( 12) link_NAG-ASN : angle 2.19812 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 227 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8151 (tt0) REVERT: A 417 LYS cc_start: 0.8811 (tptp) cc_final: 0.8467 (tppt) REVERT: A 482 ILE cc_start: 0.8744 (tt) cc_final: 0.8176 (mm) REVERT: A 483 MET cc_start: 0.8702 (tmm) cc_final: 0.8294 (tmm) REVERT: A 504 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7784 (tm-30) REVERT: A 557 LEU cc_start: 0.8258 (tp) cc_final: 0.8026 (tp) REVERT: B 290 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8170 (tt0) REVERT: B 417 LYS cc_start: 0.8818 (tptp) cc_final: 0.8463 (tppt) REVERT: B 482 ILE cc_start: 0.8743 (tt) cc_final: 0.8178 (mm) REVERT: B 483 MET cc_start: 0.8701 (tmm) cc_final: 0.8295 (tmm) REVERT: B 504 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7775 (tm-30) REVERT: B 557 LEU cc_start: 0.8268 (tp) cc_final: 0.8038 (tp) REVERT: C 290 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8142 (tt0) REVERT: C 482 ILE cc_start: 0.8738 (tt) cc_final: 0.8175 (mm) REVERT: C 483 MET cc_start: 0.8706 (tmm) cc_final: 0.8311 (tmm) REVERT: C 504 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7790 (tm-30) REVERT: C 557 LEU cc_start: 0.8262 (tp) cc_final: 0.8030 (tp) REVERT: D 167 ASP cc_start: 0.8473 (m-30) cc_final: 0.8227 (t0) REVERT: D 290 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8139 (tt0) REVERT: D 482 ILE cc_start: 0.8738 (tt) cc_final: 0.8180 (mm) REVERT: D 483 MET cc_start: 0.8702 (tmm) cc_final: 0.8308 (tmm) REVERT: D 504 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7788 (tm-30) REVERT: D 557 LEU cc_start: 0.8263 (tp) cc_final: 0.8031 (tp) outliers start: 39 outliers final: 29 residues processed: 250 average time/residue: 0.1062 time to fit residues: 40.2911 Evaluate side-chains 242 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 210 CYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 555 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 86 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 69 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN B 404 HIS ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS C 445 ASN D 404 HIS D 420 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099928 restraints weight = 21354.449| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.54 r_work: 0.3001 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14232 Z= 0.148 Angle : 0.549 9.571 19428 Z= 0.290 Chirality : 0.043 0.197 2192 Planarity : 0.004 0.042 2416 Dihedral : 4.331 19.470 2120 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.34 % Allowed : 11.90 % Favored : 85.76 % 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 are not related in a simple way. whole: 1.31 (0.21), residues: 1692 helix: 1.77 (0.17), residues: 880 sheet: 0.86 (0.36), residues: 184 loop : -0.37 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 206 TYR 0.012 0.001 TYR C 496 PHE 0.028 0.001 PHE B 549 TRP 0.013 0.001 TRP D 434 HIS 0.005 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00344 (14216) covalent geometry : angle 0.54048 (19384) SS BOND : bond 0.00339 ( 4) SS BOND : angle 0.40875 ( 8) hydrogen bonds : bond 0.03688 ( 776) hydrogen bonds : angle 3.75252 ( 2268) link_NAG-ASN : bond 0.00302 ( 12) link_NAG-ASN : angle 2.29115 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8137 (tt0) REVERT: A 417 LYS cc_start: 0.8706 (tptp) cc_final: 0.8451 (tppt) REVERT: A 482 ILE cc_start: 0.8710 (tt) cc_final: 0.8156 (mm) REVERT: A 483 MET cc_start: 0.8709 (tmm) cc_final: 0.8309 (tmm) REVERT: A 504 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7790 (tm-30) REVERT: A 557 LEU cc_start: 0.8252 (tp) cc_final: 0.8020 (tp) REVERT: B 290 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8140 (tt0) REVERT: B 417 LYS cc_start: 0.8704 (tptp) cc_final: 0.8451 (tppt) REVERT: B 482 ILE cc_start: 0.8725 (tt) cc_final: 0.8175 (mm) REVERT: B 483 MET cc_start: 0.8701 (tmm) cc_final: 0.8301 (tmm) REVERT: B 504 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7798 (tm-30) REVERT: B 557 LEU cc_start: 0.8259 (tp) cc_final: 0.8030 (tp) REVERT: C 290 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8137 (tt0) REVERT: C 429 GLU cc_start: 0.7931 (mp0) cc_final: 0.7609 (mp0) REVERT: C 482 ILE cc_start: 0.8676 (tt) cc_final: 0.8121 (mm) REVERT: C 483 MET cc_start: 0.8706 (tmm) cc_final: 0.8308 (tmm) REVERT: C 504 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7803 (tm-30) REVERT: C 557 LEU cc_start: 0.8263 (tp) cc_final: 0.8033 (tp) REVERT: D 167 ASP cc_start: 0.8469 (m-30) cc_final: 0.8227 (t0) REVERT: D 290 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8128 (tt0) REVERT: D 429 GLU cc_start: 0.7926 (mp0) cc_final: 0.7612 (mp0) REVERT: D 482 ILE cc_start: 0.8677 (tt) cc_final: 0.8125 (mm) REVERT: D 483 MET cc_start: 0.8701 (tmm) cc_final: 0.8304 (tmm) REVERT: D 504 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7816 (tm-30) REVERT: D 557 LEU cc_start: 0.8250 (tp) cc_final: 0.8019 (tp) outliers start: 33 outliers final: 29 residues processed: 237 average time/residue: 0.1039 time to fit residues: 37.4943 Evaluate side-chains 244 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 210 CYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 420 GLN Chi-restraints excluded: chain D residue 555 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 31 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 61 optimal weight: 0.0370 chunk 92 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 420 GLN B 404 HIS B 420 GLN C 404 HIS D 404 HIS ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.101409 restraints weight = 21077.429| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.53 r_work: 0.3035 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14232 Z= 0.119 Angle : 0.533 9.635 19428 Z= 0.281 Chirality : 0.042 0.190 2192 Planarity : 0.004 0.041 2416 Dihedral : 4.203 19.038 2120 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.12 % Allowed : 12.54 % Favored : 85.34 % 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 are not related in a simple way. whole: 1.44 (0.21), residues: 1692 helix: 1.85 (0.17), residues: 880 sheet: 0.90 (0.35), residues: 184 loop : -0.27 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 182 TYR 0.011 0.001 TYR B 127 PHE 0.030 0.001 PHE B 549 TRP 0.011 0.001 TRP A 434 HIS 0.004 0.001 HIS D 213 Details of bonding type rmsd covalent geometry : bond 0.00269 (14216) covalent geometry : angle 0.52548 (19384) SS BOND : bond 0.00286 ( 4) SS BOND : angle 0.40128 ( 8) hydrogen bonds : bond 0.03543 ( 776) hydrogen bonds : angle 3.70903 ( 2268) link_NAG-ASN : bond 0.00293 ( 12) link_NAG-ASN : angle 2.14744 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8157 (tt0) REVERT: A 417 LYS cc_start: 0.8715 (tptp) cc_final: 0.8446 (tppt) REVERT: A 420 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7296 (pp30) REVERT: A 429 GLU cc_start: 0.7926 (mp0) cc_final: 0.7594 (mp0) REVERT: A 480 PHE cc_start: 0.6804 (t80) cc_final: 0.6359 (m-80) REVERT: A 482 ILE cc_start: 0.8652 (tt) cc_final: 0.8093 (mm) REVERT: A 483 MET cc_start: 0.8689 (tmm) cc_final: 0.8197 (tmm) REVERT: A 504 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 557 LEU cc_start: 0.8249 (tp) cc_final: 0.8013 (tp) REVERT: B 290 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8188 (tt0) REVERT: B 417 LYS cc_start: 0.8717 (tptp) cc_final: 0.8413 (tppt) REVERT: B 420 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7293 (pp30) REVERT: B 429 GLU cc_start: 0.7929 (mp0) cc_final: 0.7597 (mp0) REVERT: B 480 PHE cc_start: 0.6808 (t80) cc_final: 0.6365 (m-80) REVERT: B 482 ILE cc_start: 0.8653 (tt) cc_final: 0.8099 (mm) REVERT: B 483 MET cc_start: 0.8676 (tmm) cc_final: 0.8184 (tmm) REVERT: B 504 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7809 (tm-30) REVERT: B 557 LEU cc_start: 0.8256 (tp) cc_final: 0.8031 (tp) REVERT: C 290 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8161 (tt0) REVERT: C 429 GLU cc_start: 0.7909 (mp0) cc_final: 0.7588 (mp0) REVERT: C 480 PHE cc_start: 0.6857 (t80) cc_final: 0.6437 (m-80) REVERT: C 482 ILE cc_start: 0.8616 (tt) cc_final: 0.8050 (mm) REVERT: C 483 MET cc_start: 0.8677 (tmm) cc_final: 0.8201 (tmm) REVERT: C 504 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7809 (tm-30) REVERT: C 557 LEU cc_start: 0.8260 (tp) cc_final: 0.8036 (tp) REVERT: D 167 ASP cc_start: 0.8489 (m-30) cc_final: 0.8238 (t0) REVERT: D 290 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8155 (tt0) REVERT: D 429 GLU cc_start: 0.7910 (mp0) cc_final: 0.7593 (mp0) REVERT: D 480 PHE cc_start: 0.6882 (t80) cc_final: 0.6505 (m-80) REVERT: D 482 ILE cc_start: 0.8618 (tt) cc_final: 0.8054 (mm) REVERT: D 483 MET cc_start: 0.8678 (tmm) cc_final: 0.8202 (tmm) REVERT: D 504 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7813 (tm-30) REVERT: D 557 LEU cc_start: 0.8251 (tp) cc_final: 0.8021 (tp) outliers start: 30 outliers final: 26 residues processed: 245 average time/residue: 0.1068 time to fit residues: 40.0645 Evaluate side-chains 248 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 420 GLN Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 210 CYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 125 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 69 optimal weight: 0.0000 chunk 2 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS B 404 HIS ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS D 404 HIS D 445 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.130048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.100865 restraints weight = 21254.386| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.54 r_work: 0.3016 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 14232 Z= 0.188 Angle : 0.923 58.839 19428 Z= 0.564 Chirality : 0.049 0.833 2192 Planarity : 0.004 0.040 2416 Dihedral : 4.208 18.683 2120 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.91 % Allowed : 12.89 % Favored : 85.20 % Cbeta Deviations : 0.12 % 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 are not related in a simple way. whole: 1.44 (0.21), residues: 1692 helix: 1.85 (0.17), residues: 880 sheet: 0.90 (0.35), residues: 184 loop : -0.28 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 199 TYR 0.021 0.001 TYR C 119 PHE 0.028 0.001 PHE A 549 TRP 0.011 0.001 TRP A 434 HIS 0.004 0.001 HIS D 213 Details of bonding type rmsd covalent geometry : bond 0.00378 (14216) covalent geometry : angle 0.91950 (19384) SS BOND : bond 0.00300 ( 4) SS BOND : angle 0.40351 ( 8) hydrogen bonds : bond 0.03545 ( 776) hydrogen bonds : angle 3.71601 ( 2268) link_NAG-ASN : bond 0.00288 ( 12) link_NAG-ASN : angle 2.14836 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2855.51 seconds wall clock time: 49 minutes 49.01 seconds (2989.01 seconds total)