Starting phenix.real_space_refine on Thu Jun 12 11:25:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5z1w_6877/06_2025/5z1w_6877_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5z1w_6877/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5z1w_6877/06_2025/5z1w_6877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5z1w_6877/06_2025/5z1w_6877.map" model { file = "/net/cci-nas-00/data/ceres_data/5z1w_6877/06_2025/5z1w_6877_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5z1w_6877/06_2025/5z1w_6877_neut.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 2} 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: C, B, D Time building chain proxies: 7.18, per 1000 atoms: 0.52 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 C 210 " - pdb=" SG CYS C 223 " distance=2.02 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 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: 3.33 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.27 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: 4.04 Time building geometry restraints manager: 3.95 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.250 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.230 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.044 0.004 TRP C 171 HIS 0.007 0.002 HIS D 213 PHE 0.022 0.003 PHE A 364 TYR 0.040 0.003 TYR D 129 ARG 0.006 0.001 ARG B 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00957 ( 12) link_NAG-ASN : angle 5.12704 ( 36) hydrogen bonds : bond 0.09937 ( 776) hydrogen bonds : angle 8.82455 ( 2268) SS BOND : bond 0.01462 ( 4) SS BOND : angle 2.57828 ( 8) covalent geometry : bond 0.01139 (14216) covalent geometry : angle 0.92816 (19384) *********************** 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 : 1.563 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: 0.2308 time to fit residues: 111.8334 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 : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 0.0770 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.3340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS A 185 HIS A 202 GLN A 437 GLN A 493 GLN A 516 GLN A 533 ASN A 554 ASN B 139 HIS B 185 HIS B 202 GLN B 437 GLN B 493 GLN B 516 GLN B 533 ASN B 554 ASN C 139 HIS C 185 HIS C 202 GLN C 437 GLN C 493 GLN C 516 GLN C 533 ASN C 554 ASN D 139 HIS D 185 HIS D 202 GLN D 437 GLN D 493 GLN D 516 GLN D 533 ASN D 554 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101045 restraints weight = 21216.981| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.50 r_work: 0.3018 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14232 Z= 0.149 Angle : 0.585 6.237 19428 Z= 0.312 Chirality : 0.044 0.213 2192 Planarity : 0.004 0.032 2416 Dihedral : 6.084 46.355 2120 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.69 % Allowed : 5.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.19), residues: 1692 helix: 0.54 (0.17), residues: 876 sheet: 0.17 (0.33), residues: 184 loop : -0.97 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 434 HIS 0.008 0.002 HIS C 213 PHE 0.028 0.002 PHE C 550 TYR 0.022 0.002 TYR D 129 ARG 0.002 0.000 ARG A 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 12) link_NAG-ASN : angle 3.57879 ( 36) hydrogen bonds : bond 0.04223 ( 776) hydrogen bonds : angle 4.57843 ( 2268) SS BOND : bond 0.00571 ( 4) SS BOND : angle 0.52341 ( 8) covalent geometry : bond 0.00330 (14216) covalent geometry : angle 0.56494 (19384) *********************** 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 305 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 267 time to evaluate : 1.583 Fit side-chains REVERT: A 290 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8204 (tt0) REVERT: A 482 ILE cc_start: 0.9003 (tt) cc_final: 0.8488 (mm) REVERT: A 483 MET cc_start: 0.8696 (tmm) cc_final: 0.8286 (tmm) REVERT: B 290 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8228 (tt0) REVERT: B 482 ILE cc_start: 0.9002 (tt) cc_final: 0.8486 (mm) REVERT: B 483 MET cc_start: 0.8699 (tmm) cc_final: 0.8289 (tmm) REVERT: C 290 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8207 (tt0) REVERT: C 396 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7303 (mp) REVERT: C 482 ILE cc_start: 0.9007 (tt) cc_final: 0.8490 (mm) REVERT: C 483 MET cc_start: 0.8704 (tmm) cc_final: 0.8296 (tmm) REVERT: D 290 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8213 (tt0) REVERT: D 396 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7339 (mp) REVERT: D 482 ILE cc_start: 0.8994 (tt) cc_final: 0.8476 (mm) REVERT: D 483 MET cc_start: 0.8665 (tmm) cc_final: 0.8257 (tmm) outliers start: 38 outliers final: 17 residues processed: 284 average time/residue: 0.2632 time to fit residues: 113.1267 Evaluate side-chains 230 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU 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 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 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 25 optimal weight: 5.9990 chunk 66 optimal weight: 0.0050 chunk 52 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 133 optimal weight: 0.0570 chunk 153 optimal weight: 6.9990 chunk 57 optimal weight: 0.0370 chunk 45 optimal weight: 0.9980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.133521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.104196 restraints weight = 21112.786| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.57 r_work: 0.3046 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14232 Z= 0.103 Angle : 0.505 6.025 19428 Z= 0.274 Chirality : 0.042 0.187 2192 Planarity : 0.004 0.032 2416 Dihedral : 4.781 25.612 2120 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.05 % Allowed : 8.14 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1692 helix: 1.35 (0.17), residues: 900 sheet: 0.59 (0.32), residues: 184 loop : -0.93 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 434 HIS 0.005 0.001 HIS C 213 PHE 0.021 0.001 PHE C 549 TYR 0.016 0.001 TYR D 107 ARG 0.002 0.000 ARG D 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 12) link_NAG-ASN : angle 2.47863 ( 36) hydrogen bonds : bond 0.03608 ( 776) hydrogen bonds : angle 4.01338 ( 2268) SS BOND : bond 0.00314 ( 4) SS BOND : angle 0.33613 ( 8) covalent geometry : bond 0.00206 (14216) covalent geometry : angle 0.49438 (19384) *********************** 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 292 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 263 time to evaluate : 2.670 Fit side-chains REVERT: A 173 LYS cc_start: 0.8788 (mtmm) cc_final: 0.8300 (mmtp) REVERT: A 290 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8237 (tt0) REVERT: A 330 THR cc_start: 0.9169 (m) cc_final: 0.8949 (m) REVERT: A 482 ILE cc_start: 0.8827 (tt) cc_final: 0.8254 (mm) REVERT: A 483 MET cc_start: 0.8640 (tmm) cc_final: 0.8197 (tmm) REVERT: A 550 PHE cc_start: 0.7181 (t80) cc_final: 0.6949 (t80) REVERT: A 557 LEU cc_start: 0.8211 (tp) cc_final: 0.7934 (tp) REVERT: B 173 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8301 (mmtp) REVERT: B 290 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8263 (tt0) REVERT: B 330 THR cc_start: 0.9165 (m) cc_final: 0.8945 (m) REVERT: B 482 ILE cc_start: 0.8826 (tt) cc_final: 0.8253 (mm) REVERT: B 483 MET cc_start: 0.8634 (tmm) cc_final: 0.8194 (tmm) REVERT: B 550 PHE cc_start: 0.7191 (t80) cc_final: 0.6962 (t80) REVERT: B 557 LEU cc_start: 0.8228 (tp) cc_final: 0.7963 (tp) REVERT: C 173 LYS cc_start: 0.8791 (mtmm) cc_final: 0.8302 (mmtp) REVERT: C 290 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8249 (tt0) REVERT: C 330 THR cc_start: 0.9176 (m) cc_final: 0.8951 (m) REVERT: C 482 ILE cc_start: 0.8860 (tt) cc_final: 0.8287 (mm) REVERT: C 483 MET cc_start: 0.8654 (tmm) cc_final: 0.8213 (tmm) REVERT: C 550 PHE cc_start: 0.7181 (t80) cc_final: 0.6955 (t80) REVERT: C 557 LEU cc_start: 0.8224 (tp) cc_final: 0.7960 (tp) REVERT: D 173 LYS cc_start: 0.8802 (mtmm) cc_final: 0.8303 (mmtp) REVERT: D 290 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8249 (tt0) REVERT: D 330 THR cc_start: 0.9162 (m) cc_final: 0.8938 (m) REVERT: D 482 ILE cc_start: 0.8812 (tt) cc_final: 0.8236 (mm) REVERT: D 483 MET cc_start: 0.8637 (tmm) cc_final: 0.8193 (tmm) REVERT: D 550 PHE cc_start: 0.7200 (t80) cc_final: 0.6981 (t80) REVERT: D 557 LEU cc_start: 0.8218 (tp) cc_final: 0.7955 (tp) outliers start: 29 outliers final: 17 residues processed: 268 average time/residue: 0.3599 time to fit residues: 142.4519 Evaluate side-chains 232 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 214 GLU 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 211 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 423 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 128 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 153 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 HIS C 404 HIS D 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.130042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100490 restraints weight = 21311.056| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.58 r_work: 0.3039 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14232 Z= 0.134 Angle : 0.532 10.847 19428 Z= 0.278 Chirality : 0.042 0.195 2192 Planarity : 0.004 0.036 2416 Dihedral : 4.668 24.102 2120 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.62 % Allowed : 8.99 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.20), residues: 1692 helix: 1.66 (0.17), residues: 876 sheet: 0.75 (0.32), residues: 184 loop : -0.64 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 434 HIS 0.006 0.001 HIS D 213 PHE 0.026 0.002 PHE C 549 TYR 0.015 0.001 TYR A 129 ARG 0.002 0.000 ARG D 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 12) link_NAG-ASN : angle 2.50833 ( 36) hydrogen bonds : bond 0.03622 ( 776) hydrogen bonds : angle 3.89087 ( 2268) SS BOND : bond 0.00346 ( 4) SS BOND : angle 2.54693 ( 8) covalent geometry : bond 0.00308 (14216) covalent geometry : angle 0.51881 (19384) *********************** 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 266 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 2.230 Fit side-chains revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8362 (mmtp) REVERT: A 290 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8220 (tt0) REVERT: A 482 ILE cc_start: 0.8902 (tt) cc_final: 0.8326 (mm) REVERT: A 483 MET cc_start: 0.8707 (tmm) cc_final: 0.8264 (tmm) REVERT: A 550 PHE cc_start: 0.7358 (t80) cc_final: 0.7147 (t80) REVERT: A 557 LEU cc_start: 0.8278 (tp) cc_final: 0.8031 (tp) REVERT: B 173 LYS cc_start: 0.8765 (mtmm) cc_final: 0.8366 (mmtp) REVERT: B 290 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8218 (tt0) REVERT: B 482 ILE cc_start: 0.8897 (tt) cc_final: 0.8317 (mm) REVERT: B 483 MET cc_start: 0.8696 (tmm) cc_final: 0.8261 (tmm) REVERT: B 550 PHE cc_start: 0.7362 (t80) cc_final: 0.7154 (t80) REVERT: B 557 LEU cc_start: 0.8281 (tp) cc_final: 0.8034 (tp) REVERT: C 173 LYS cc_start: 0.8777 (mtmm) cc_final: 0.8367 (mmtp) REVERT: C 290 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8224 (tt0) REVERT: C 482 ILE cc_start: 0.8898 (tt) cc_final: 0.8315 (mm) REVERT: C 483 MET cc_start: 0.8707 (tmm) cc_final: 0.8281 (tmm) REVERT: C 550 PHE cc_start: 0.7356 (t80) cc_final: 0.7146 (t80) REVERT: C 557 LEU cc_start: 0.8265 (tp) cc_final: 0.8009 (tp) REVERT: D 173 LYS cc_start: 0.8802 (mtmm) cc_final: 0.8383 (mmtp) REVERT: D 290 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8178 (tt0) REVERT: D 330 THR cc_start: 0.9270 (m) cc_final: 0.9010 (m) REVERT: D 482 ILE cc_start: 0.8849 (tt) cc_final: 0.8257 (mm) REVERT: D 483 MET cc_start: 0.8720 (tmm) cc_final: 0.8286 (tmm) REVERT: D 550 PHE cc_start: 0.7368 (t80) cc_final: 0.7143 (t80) REVERT: D 557 LEU cc_start: 0.8291 (tp) cc_final: 0.8047 (tp) outliers start: 37 outliers final: 24 residues processed: 246 average time/residue: 0.2694 time to fit residues: 99.8865 Evaluate side-chains 232 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 1.752 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 119 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 C 493 GLN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.131688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.102190 restraints weight = 21157.888| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.59 r_work: 0.3069 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14232 Z= 0.108 Angle : 0.506 10.565 19428 Z= 0.265 Chirality : 0.041 0.185 2192 Planarity : 0.003 0.037 2416 Dihedral : 4.335 21.103 2120 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.20 % Allowed : 9.99 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.20), residues: 1692 helix: 1.79 (0.17), residues: 880 sheet: 0.85 (0.33), residues: 184 loop : -0.53 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 434 HIS 0.004 0.001 HIS C 213 PHE 0.026 0.001 PHE B 549 TYR 0.011 0.001 TYR B 129 ARG 0.001 0.000 ARG B 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 12) link_NAG-ASN : angle 2.21356 ( 36) hydrogen bonds : bond 0.03478 ( 776) hydrogen bonds : angle 3.74445 ( 2268) SS BOND : bond 0.00359 ( 4) SS BOND : angle 2.07987 ( 8) covalent geometry : bond 0.00235 (14216) covalent geometry : angle 0.49597 (19384) *********************** 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 273 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8754 (mtmm) cc_final: 0.8325 (mmtp) REVERT: A 290 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8229 (tt0) REVERT: A 482 ILE cc_start: 0.8762 (tt) cc_final: 0.8181 (mm) REVERT: A 483 MET cc_start: 0.8656 (tmm) cc_final: 0.8224 (tmm) REVERT: A 550 PHE cc_start: 0.7296 (t80) cc_final: 0.7082 (t80) REVERT: A 557 LEU cc_start: 0.8273 (tp) cc_final: 0.8032 (tp) REVERT: B 173 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8354 (mmtp) REVERT: B 290 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8186 (tt0) REVERT: B 482 ILE cc_start: 0.8758 (tt) cc_final: 0.8181 (mm) REVERT: B 483 MET cc_start: 0.8640 (tmm) cc_final: 0.8235 (tmm) REVERT: B 550 PHE cc_start: 0.7301 (t80) cc_final: 0.7087 (t80) REVERT: B 557 LEU cc_start: 0.8301 (tp) cc_final: 0.8052 (tp) REVERT: C 173 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8342 (mmtp) REVERT: C 290 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8180 (tt0) REVERT: C 482 ILE cc_start: 0.8763 (tt) cc_final: 0.8185 (mm) REVERT: C 483 MET cc_start: 0.8661 (tmm) cc_final: 0.8258 (tmm) REVERT: C 550 PHE cc_start: 0.7286 (t80) cc_final: 0.7078 (t80) REVERT: C 557 LEU cc_start: 0.8288 (tp) cc_final: 0.8034 (tp) REVERT: D 173 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8330 (mmtp) REVERT: D 290 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8221 (tt0) REVERT: D 330 THR cc_start: 0.9225 (m) cc_final: 0.8973 (m) REVERT: D 482 ILE cc_start: 0.8784 (tt) cc_final: 0.8199 (mm) REVERT: D 483 MET cc_start: 0.8662 (tmm) cc_final: 0.8259 (tmm) REVERT: D 550 PHE cc_start: 0.7290 (t80) cc_final: 0.7083 (t80) REVERT: D 557 LEU cc_start: 0.8264 (tp) cc_final: 0.8021 (tp) outliers start: 31 outliers final: 26 residues processed: 257 average time/residue: 0.2648 time to fit residues: 99.8267 Evaluate side-chains 245 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 445 ASN B 404 HIS C 404 HIS C 493 GLN D 404 HIS D 493 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.130483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.101182 restraints weight = 21461.627| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.59 r_work: 0.3047 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3475 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= 0.131 Angle : 0.524 9.943 19428 Z= 0.276 Chirality : 0.042 0.191 2192 Planarity : 0.004 0.039 2416 Dihedral : 4.344 20.324 2120 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.98 % Allowed : 10.48 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1692 helix: 1.90 (0.17), residues: 880 sheet: 0.76 (0.34), residues: 184 loop : -0.43 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 434 HIS 0.004 0.001 HIS B 213 PHE 0.028 0.001 PHE C 549 TYR 0.011 0.001 TYR C 129 ARG 0.002 0.000 ARG C 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 12) link_NAG-ASN : angle 2.27567 ( 36) hydrogen bonds : bond 0.03558 ( 776) hydrogen bonds : angle 3.72704 ( 2268) SS BOND : bond 0.00388 ( 4) SS BOND : angle 2.16834 ( 8) covalent geometry : bond 0.00300 (14216) covalent geometry : angle 0.51366 (19384) *********************** 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 257 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8736 (mtmm) cc_final: 0.8354 (mmtp) REVERT: A 290 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8198 (tt0) REVERT: A 482 ILE cc_start: 0.8706 (tt) cc_final: 0.8169 (mm) REVERT: A 483 MET cc_start: 0.8692 (tmm) cc_final: 0.8295 (tmm) REVERT: A 557 LEU cc_start: 0.8273 (tp) cc_final: 0.8034 (tp) REVERT: B 119 TYR cc_start: 0.8727 (m-10) cc_final: 0.8328 (m-10) REVERT: B 173 LYS cc_start: 0.8728 (mtmm) cc_final: 0.8362 (mmtp) REVERT: B 290 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8198 (tt0) REVERT: B 482 ILE cc_start: 0.8706 (tt) cc_final: 0.8171 (mm) REVERT: B 483 MET cc_start: 0.8680 (tmm) cc_final: 0.8289 (tmm) REVERT: B 557 LEU cc_start: 0.8283 (tp) cc_final: 0.8041 (tp) REVERT: C 173 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8358 (mmtp) REVERT: C 290 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8183 (tt0) REVERT: C 482 ILE cc_start: 0.8716 (tt) cc_final: 0.8170 (mm) REVERT: C 483 MET cc_start: 0.8694 (tmm) cc_final: 0.8300 (tmm) REVERT: C 557 LEU cc_start: 0.8282 (tp) cc_final: 0.8041 (tp) REVERT: D 173 LYS cc_start: 0.8741 (mtmm) cc_final: 0.8345 (mmtp) REVERT: D 290 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8159 (tt0) REVERT: D 482 ILE cc_start: 0.8757 (tt) cc_final: 0.8159 (mm) REVERT: D 483 MET cc_start: 0.8687 (tmm) cc_final: 0.8292 (tmm) REVERT: D 557 LEU cc_start: 0.8275 (tp) cc_final: 0.8036 (tp) outliers start: 28 outliers final: 24 residues processed: 243 average time/residue: 0.3074 time to fit residues: 113.1787 Evaluate side-chains 245 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 123 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 25 optimal weight: 30.0000 chunk 124 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 C 404 HIS D 404 HIS D 421 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.130630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.101727 restraints weight = 21239.279| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.54 r_work: 0.3053 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14232 Z= 0.127 Angle : 0.524 9.810 19428 Z= 0.276 Chirality : 0.042 0.189 2192 Planarity : 0.003 0.039 2416 Dihedral : 4.267 19.531 2120 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.84 % Allowed : 11.05 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.21), residues: 1692 helix: 1.89 (0.17), residues: 880 sheet: 0.82 (0.34), residues: 184 loop : -0.35 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 434 HIS 0.004 0.001 HIS D 213 PHE 0.028 0.001 PHE C 549 TYR 0.010 0.001 TYR B 129 ARG 0.002 0.000 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 12) link_NAG-ASN : angle 2.19983 ( 36) hydrogen bonds : bond 0.03542 ( 776) hydrogen bonds : angle 3.69871 ( 2268) SS BOND : bond 0.00384 ( 4) SS BOND : angle 1.98735 ( 8) covalent geometry : bond 0.00291 (14216) covalent geometry : angle 0.51403 (19384) *********************** 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 262 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8360 (mmtp) REVERT: A 290 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8197 (tt0) REVERT: A 482 ILE cc_start: 0.8680 (tt) cc_final: 0.8135 (mm) REVERT: A 483 MET cc_start: 0.8679 (tmm) cc_final: 0.8270 (tmm) REVERT: A 557 LEU cc_start: 0.8268 (tp) cc_final: 0.8033 (tp) REVERT: B 119 TYR cc_start: 0.8535 (m-10) cc_final: 0.8254 (m-10) REVERT: B 173 LYS cc_start: 0.8718 (mtmm) cc_final: 0.8348 (mmtp) REVERT: B 290 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8185 (tt0) REVERT: B 482 ILE cc_start: 0.8684 (tt) cc_final: 0.8146 (mm) REVERT: B 483 MET cc_start: 0.8665 (tmm) cc_final: 0.8259 (tmm) REVERT: B 557 LEU cc_start: 0.8262 (tp) cc_final: 0.8021 (tp) REVERT: C 173 LYS cc_start: 0.8728 (mtmm) cc_final: 0.8351 (mmtp) REVERT: C 290 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8177 (tt0) REVERT: C 482 ILE cc_start: 0.8690 (tt) cc_final: 0.8148 (mm) REVERT: C 483 MET cc_start: 0.8674 (tmm) cc_final: 0.8265 (tmm) REVERT: C 557 LEU cc_start: 0.8268 (tp) cc_final: 0.8029 (tp) REVERT: D 173 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8349 (mmtp) REVERT: D 290 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8193 (tt0) REVERT: D 417 LYS cc_start: 0.8728 (tptp) cc_final: 0.8406 (tppt) REVERT: D 482 ILE cc_start: 0.8689 (tt) cc_final: 0.8145 (mm) REVERT: D 483 MET cc_start: 0.8664 (tmm) cc_final: 0.8254 (tmm) REVERT: D 557 LEU cc_start: 0.8261 (tp) cc_final: 0.8023 (tp) outliers start: 26 outliers final: 22 residues processed: 248 average time/residue: 0.2379 time to fit residues: 88.4931 Evaluate side-chains 245 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 404 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.099640 restraints weight = 21285.209| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.55 r_work: 0.3015 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14232 Z= 0.163 Angle : 0.559 9.508 19428 Z= 0.294 Chirality : 0.043 0.200 2192 Planarity : 0.004 0.040 2416 Dihedral : 4.452 20.683 2120 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.91 % Allowed : 11.12 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1692 helix: 1.82 (0.17), residues: 880 sheet: 0.85 (0.35), residues: 184 loop : -0.30 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 434 HIS 0.005 0.001 HIS A 213 PHE 0.029 0.002 PHE A 549 TYR 0.011 0.001 TYR B 491 ARG 0.003 0.000 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 12) link_NAG-ASN : angle 2.39828 ( 36) hydrogen bonds : bond 0.03778 ( 776) hydrogen bonds : angle 3.79743 ( 2268) SS BOND : bond 0.00431 ( 4) SS BOND : angle 2.17086 ( 8) covalent geometry : bond 0.00382 (14216) covalent geometry : angle 0.54855 (19384) *********************** 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 252 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 1.777 Fit side-chains REVERT: A 173 LYS cc_start: 0.8762 (mtmm) cc_final: 0.8357 (mmtp) REVERT: A 290 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8172 (tt0) REVERT: A 482 ILE cc_start: 0.8706 (tt) cc_final: 0.8151 (mm) REVERT: A 483 MET cc_start: 0.8703 (tmm) cc_final: 0.8309 (tmm) REVERT: A 557 LEU cc_start: 0.8269 (tp) cc_final: 0.8024 (tp) REVERT: B 173 LYS cc_start: 0.8753 (mtmm) cc_final: 0.8365 (mmtp) REVERT: B 290 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8176 (tt0) REVERT: B 482 ILE cc_start: 0.8686 (tt) cc_final: 0.8138 (mm) REVERT: B 483 MET cc_start: 0.8703 (tmm) cc_final: 0.8299 (tmm) REVERT: B 557 LEU cc_start: 0.8264 (tp) cc_final: 0.8018 (tp) REVERT: C 173 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8366 (mmtp) REVERT: C 290 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8176 (tt0) REVERT: C 429 GLU cc_start: 0.7950 (mp0) cc_final: 0.7600 (mp0) REVERT: C 482 ILE cc_start: 0.8695 (tt) cc_final: 0.8148 (mm) REVERT: C 483 MET cc_start: 0.8712 (tmm) cc_final: 0.8309 (tmm) REVERT: C 557 LEU cc_start: 0.8273 (tp) cc_final: 0.8029 (tp) REVERT: D 173 LYS cc_start: 0.8767 (mtmm) cc_final: 0.8380 (mmtp) REVERT: D 290 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8174 (tt0) REVERT: D 417 LYS cc_start: 0.8839 (tptp) cc_final: 0.8485 (tppt) REVERT: D 429 GLU cc_start: 0.7972 (mp0) cc_final: 0.7600 (mp0) REVERT: D 482 ILE cc_start: 0.8708 (tt) cc_final: 0.8154 (mm) REVERT: D 483 MET cc_start: 0.8711 (tmm) cc_final: 0.8311 (tmm) REVERT: D 557 LEU cc_start: 0.8260 (tp) cc_final: 0.8015 (tp) outliers start: 27 outliers final: 20 residues processed: 237 average time/residue: 0.2625 time to fit residues: 92.1115 Evaluate side-chains 228 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 1.943 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 70 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 92 optimal weight: 0.0270 chunk 54 optimal weight: 5.9990 chunk 5 optimal weight: 0.3980 chunk 68 optimal weight: 6.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS D 404 HIS D 420 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.132209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.103345 restraints weight = 20936.402| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.53 r_work: 0.3081 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14232 Z= 0.107 Angle : 0.517 9.483 19428 Z= 0.273 Chirality : 0.041 0.178 2192 Planarity : 0.003 0.037 2416 Dihedral : 4.085 18.918 2120 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.35 % Allowed : 11.76 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.21), residues: 1692 helix: 1.89 (0.17), residues: 880 sheet: 0.88 (0.35), residues: 184 loop : -0.19 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 434 HIS 0.003 0.001 HIS A 213 PHE 0.027 0.001 PHE C 549 TYR 0.011 0.001 TYR D 127 ARG 0.002 0.000 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 12) link_NAG-ASN : angle 1.96777 ( 36) hydrogen bonds : bond 0.03361 ( 776) hydrogen bonds : angle 3.65700 ( 2268) SS BOND : bond 0.00303 ( 4) SS BOND : angle 1.78510 ( 8) covalent geometry : bond 0.00240 (14216) covalent geometry : angle 0.50958 (19384) *********************** 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 264 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 245 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8741 (mtmm) cc_final: 0.8379 (mmtp) REVERT: A 290 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8154 (tt0) REVERT: A 480 PHE cc_start: 0.6887 (t80) cc_final: 0.6494 (m-80) REVERT: A 482 ILE cc_start: 0.8600 (tt) cc_final: 0.8005 (mm) REVERT: A 483 MET cc_start: 0.8652 (tmm) cc_final: 0.8175 (tmm) REVERT: A 557 LEU cc_start: 0.8286 (tp) cc_final: 0.8054 (tp) REVERT: B 173 LYS cc_start: 0.8739 (mtmm) cc_final: 0.8405 (mmtp) REVERT: B 290 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8142 (tt0) REVERT: B 429 GLU cc_start: 0.7917 (mp0) cc_final: 0.7580 (mp0) REVERT: B 480 PHE cc_start: 0.6879 (t80) cc_final: 0.6497 (m-80) REVERT: B 482 ILE cc_start: 0.8611 (tt) cc_final: 0.8020 (mm) REVERT: B 483 MET cc_start: 0.8646 (tmm) cc_final: 0.8170 (tmm) REVERT: B 557 LEU cc_start: 0.8286 (tp) cc_final: 0.8052 (tp) REVERT: C 173 LYS cc_start: 0.8748 (mtmm) cc_final: 0.8403 (mmtp) REVERT: C 290 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8146 (tt0) REVERT: C 480 PHE cc_start: 0.6830 (t80) cc_final: 0.6465 (m-80) REVERT: C 482 ILE cc_start: 0.8602 (tt) cc_final: 0.8013 (mm) REVERT: C 483 MET cc_start: 0.8655 (tmm) cc_final: 0.8156 (tmm) REVERT: C 557 LEU cc_start: 0.8290 (tp) cc_final: 0.8057 (tp) REVERT: D 167 ASP cc_start: 0.8676 (m-30) cc_final: 0.8261 (t0) REVERT: D 173 LYS cc_start: 0.8755 (mtmm) cc_final: 0.8406 (mmtp) REVERT: D 290 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8149 (tt0) REVERT: D 417 LYS cc_start: 0.8764 (tptp) cc_final: 0.8441 (tppt) REVERT: D 480 PHE cc_start: 0.6832 (t80) cc_final: 0.6503 (m-80) REVERT: D 482 ILE cc_start: 0.8602 (tt) cc_final: 0.8006 (mm) REVERT: D 483 MET cc_start: 0.8649 (tmm) cc_final: 0.8174 (tmm) REVERT: D 557 LEU cc_start: 0.8282 (tp) cc_final: 0.8047 (tp) outliers start: 19 outliers final: 16 residues processed: 253 average time/residue: 0.2363 time to fit residues: 90.3099 Evaluate side-chains 237 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 264 SER 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 264 SER 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 264 SER 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 264 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 55 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS D 404 HIS ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.132860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103801 restraints weight = 21065.439| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.55 r_work: 0.3089 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14232 Z= 0.107 Angle : 0.522 9.830 19428 Z= 0.276 Chirality : 0.041 0.182 2192 Planarity : 0.003 0.037 2416 Dihedral : 4.028 25.997 2120 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.20 % Allowed : 12.54 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.21), residues: 1692 helix: 1.99 (0.17), residues: 880 sheet: 1.02 (0.35), residues: 184 loop : -0.20 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 434 HIS 0.003 0.000 HIS A 213 PHE 0.029 0.001 PHE A 549 TYR 0.011 0.001 TYR C 127 ARG 0.002 0.000 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 12) link_NAG-ASN : angle 1.89376 ( 36) hydrogen bonds : bond 0.03303 ( 776) hydrogen bonds : angle 3.57439 ( 2268) SS BOND : bond 0.00295 ( 4) SS BOND : angle 2.04454 ( 8) covalent geometry : bond 0.00238 (14216) covalent geometry : angle 0.51447 (19384) ********************** 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 250 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8736 (mtmm) cc_final: 0.8380 (mmtp) REVERT: A 290 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8131 (tt0) REVERT: A 429 GLU cc_start: 0.7914 (mp0) cc_final: 0.7594 (mp0) REVERT: A 480 PHE cc_start: 0.6911 (t80) cc_final: 0.6519 (m-80) REVERT: A 482 ILE cc_start: 0.8509 (tt) cc_final: 0.7950 (mm) REVERT: A 483 MET cc_start: 0.8634 (tmm) cc_final: 0.8161 (tmm) REVERT: A 504 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 557 LEU cc_start: 0.8289 (tp) cc_final: 0.8061 (tp) REVERT: B 173 LYS cc_start: 0.8726 (mtmm) cc_final: 0.8392 (mmtp) REVERT: B 290 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8127 (tt0) REVERT: B 480 PHE cc_start: 0.6882 (t80) cc_final: 0.6502 (m-80) REVERT: B 482 ILE cc_start: 0.8524 (tt) cc_final: 0.7967 (mm) REVERT: B 483 MET cc_start: 0.8617 (tmm) cc_final: 0.8149 (tmm) REVERT: B 504 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 557 LEU cc_start: 0.8292 (tp) cc_final: 0.8065 (tp) REVERT: C 173 LYS cc_start: 0.8734 (mtmm) cc_final: 0.8397 (mmtp) REVERT: C 290 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8117 (tt0) REVERT: C 480 PHE cc_start: 0.6880 (t80) cc_final: 0.6492 (m-80) REVERT: C 482 ILE cc_start: 0.8517 (tt) cc_final: 0.7956 (mm) REVERT: C 483 MET cc_start: 0.8625 (tmm) cc_final: 0.8135 (tmm) REVERT: C 504 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7803 (tm-30) REVERT: C 557 LEU cc_start: 0.8291 (tp) cc_final: 0.8064 (tp) REVERT: D 167 ASP cc_start: 0.8691 (m-30) cc_final: 0.8268 (t0) REVERT: D 173 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8395 (mmtp) REVERT: D 290 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8141 (tt0) REVERT: D 417 LYS cc_start: 0.8709 (tptp) cc_final: 0.8421 (tppt) REVERT: D 480 PHE cc_start: 0.6891 (t80) cc_final: 0.6541 (m-80) REVERT: D 482 ILE cc_start: 0.8519 (tt) cc_final: 0.7961 (mm) REVERT: D 483 MET cc_start: 0.8632 (tmm) cc_final: 0.8153 (tmm) REVERT: D 504 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7781 (tm-30) REVERT: D 557 LEU cc_start: 0.8275 (tp) cc_final: 0.8044 (tp) outliers start: 17 outliers final: 16 residues processed: 242 average time/residue: 0.2407 time to fit residues: 87.0357 Evaluate side-chains 244 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 264 SER 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 264 SER 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 264 SER 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 264 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 66 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 126 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS D 404 HIS D 420 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.099547 restraints weight = 21594.287| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.57 r_work: 0.3017 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14232 Z= 0.161 Angle : 0.564 9.641 19428 Z= 0.297 Chirality : 0.043 0.200 2192 Planarity : 0.004 0.041 2416 Dihedral : 4.371 24.238 2120 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.63 % Allowed : 13.17 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.21), residues: 1692 helix: 1.75 (0.17), residues: 908 sheet: 0.91 (0.35), residues: 184 loop : -0.23 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 434 HIS 0.004 0.001 HIS C 213 PHE 0.031 0.002 PHE C 549 TYR 0.011 0.001 TYR A 491 ARG 0.003 0.000 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 12) link_NAG-ASN : angle 2.24521 ( 36) hydrogen bonds : bond 0.03667 ( 776) hydrogen bonds : angle 3.73328 ( 2268) SS BOND : bond 0.00539 ( 4) SS BOND : angle 2.48992 ( 8) covalent geometry : bond 0.00379 (14216) covalent geometry : angle 0.55441 (19384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6054.03 seconds wall clock time: 109 minutes 19.28 seconds (6559.28 seconds total)