Starting phenix.real_space_refine on Thu Sep 26 19:17:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1w_6877/09_2024/5z1w_6877_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1w_6877/09_2024/5z1w_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1w_6877/09_2024/5z1w_6877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1w_6877/09_2024/5z1w_6877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1w_6877/09_2024/5z1w_6877_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1w_6877/09_2024/5z1w_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-5461/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: 7.49, per 1000 atoms: 0.54 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 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: 3.80 Conformation dependent library (CDL) restraints added in 1.9 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: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.573A pdb=" N VAL A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.520A pdb=" N TYR A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.575A pdb=" N ASP A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.859A pdb=" N SER A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 372 removed outlier: 3.778A pdb=" N PHE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 372 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 421 removed outlier: 3.718A pdb=" N GLY A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N HIS A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 452 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 480 through 480 No H-bonds generated for 'chain 'A' and resid 480 through 480' Processing helix chain 'A' and resid 481 through 499 removed outlier: 3.636A pdb=" N VAL A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.834A pdb=" N ILE A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 562 removed outlier: 3.644A pdb=" N VAL A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.520A pdb=" N TYR B 129 " --> pdb=" O SER B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 163 through 168 removed outlier: 3.575A pdb=" N ASP B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.860A pdb=" N SER B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 372 removed outlier: 3.778A pdb=" N PHE B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 372 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 421 removed outlier: 3.718A pdb=" N GLY B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N HIS B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 452 Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'B' and resid 480 through 480 No H-bonds generated for 'chain 'B' and resid 480 through 480' Processing helix chain 'B' and resid 481 through 499 removed outlier: 3.635A pdb=" N VAL B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 525 through 533 removed outlier: 3.834A pdb=" N ILE B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 562 removed outlier: 3.643A pdb=" N VAL B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 120 Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.520A pdb=" N TYR C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.575A pdb=" N ASP C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 291 removed outlier: 3.858A pdb=" N SER C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 372 removed outlier: 3.778A pdb=" N PHE C 350 " --> pdb=" O ASN C 346 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU C 372 " --> pdb=" O VAL C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 421 removed outlier: 3.718A pdb=" N GLY C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N HIS C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE C 405 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 452 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 480 through 480 No H-bonds generated for 'chain 'C' and resid 480 through 480' Processing helix chain 'C' and resid 481 through 499 removed outlier: 3.635A pdb=" N VAL C 487 " --> pdb=" O MET C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 525 through 533 removed outlier: 3.834A pdb=" N ILE C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN C 533 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 562 removed outlier: 3.644A pdb=" N VAL C 539 " --> pdb=" O ILE C 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.519A pdb=" N TYR D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 162 Processing helix chain 'D' and resid 163 through 168 removed outlier: 3.575A pdb=" N ASP D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 291 removed outlier: 3.858A pdb=" N SER D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY D 291 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 372 removed outlier: 3.779A pdb=" N PHE D 350 " --> pdb=" O ASN D 346 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU D 372 " --> pdb=" O VAL D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 421 removed outlier: 3.718A pdb=" N GLY D 402 " --> pdb=" O ILE D 398 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N HIS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE D 405 " --> pdb=" O VAL D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 452 Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'D' and resid 480 through 480 No H-bonds generated for 'chain 'D' and resid 480 through 480' Processing helix chain 'D' and resid 481 through 499 removed outlier: 3.635A pdb=" N VAL D 487 " --> pdb=" O MET D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 525 through 533 removed outlier: 3.833A pdb=" N ILE D 529 " --> pdb=" O ASP D 525 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 562 removed outlier: 3.643A pdb=" N VAL D 539 " --> pdb=" O ILE D 535 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 removed outlier: 6.832A pdb=" N LEU A 195 " --> pdb=" O TYR A 308 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR A 308 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA A 197 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER A 306 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 300 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 314 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'B' and resid 187 through 188 Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 188 removed outlier: 6.832A pdb=" N LEU B 195 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR B 308 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA B 197 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER B 306 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 300 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 314 " --> pdb=" O ASN B 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 188 Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 188 removed outlier: 6.832A pdb=" N LEU C 195 " --> pdb=" O TYR C 308 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR C 308 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA C 197 " --> pdb=" O SER C 306 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER C 306 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 300 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 314 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 258 through 259 Processing sheet with id=AB1, first strand: chain 'D' and resid 187 through 188 Processing sheet with id=AB2, first strand: chain 'D' and resid 187 through 188 removed outlier: 6.832A pdb=" N LEU D 195 " --> pdb=" O TYR D 308 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR D 308 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA D 197 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER D 306 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 300 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D 314 " --> pdb=" O ASN D 309 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 258 through 259 784 hydrogen bonds defined for protein. 2268 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 4.41 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: 7843 16.28 - 32.57: 232 32.57 - 48.85: 60 48.85 - 65.14: 20 65.14 - 81.42: 12 Dihedral angle restraints: 8167 sinusoidal: 3147 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 8164 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: 2.02 - 2.59: 107 2.59 - 3.17: 12951 3.17 - 3.75: 20662 3.75 - 4.32: 29449 4.32 - 4.90: 47599 Nonbonded interactions: 110768 Sorted by model distance: nonbonded pdb=" SG CYS D 210 " pdb=" SG CYS D 223 " model vdw 2.016 3.760 nonbonded pdb=" SG CYS B 210 " pdb=" SG CYS B 223 " model vdw 2.016 3.760 nonbonded pdb=" SG CYS C 210 " pdb=" SG CYS C 223 " model vdw 2.017 3.760 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 ... (remaining 110763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.700 Find NCS groups from input model: 0.500 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.790 ------------------------------------------------------------------------------- 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 14216 Z= 0.727 Angle : 0.928 7.032 19384 Z= 0.543 Chirality : 0.057 0.194 2192 Planarity : 0.006 0.052 2416 Dihedral : 10.296 81.422 4948 Min Nonbonded Distance : 2.016 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.921 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: 0.2458 time to fit residues: 119.2669 Evaluate side-chains 217 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14216 Z= 0.221 Angle : 0.569 5.641 19384 Z= 0.310 Chirality : 0.044 0.213 2192 Planarity : 0.004 0.032 2416 Dihedral : 6.192 47.704 2120 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.48 % Allowed : 6.16 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.25 (0.19), residues: 1692 helix: 0.45 (0.17), residues: 880 sheet: 0.17 (0.33), residues: 184 loop : -1.05 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 434 HIS 0.009 0.002 HIS C 213 PHE 0.028 0.002 PHE A 550 TYR 0.021 0.002 TYR A 129 ARG 0.002 0.000 ARG B 206 *********************** 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 302 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 267 time to evaluate : 1.558 Fit side-chains REVERT: A 290 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7951 (tt0) REVERT: A 482 ILE cc_start: 0.9034 (tt) cc_final: 0.8525 (mm) REVERT: A 483 MET cc_start: 0.8343 (tmm) cc_final: 0.7959 (tmm) REVERT: B 290 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7952 (tt0) REVERT: B 482 ILE cc_start: 0.9035 (tt) cc_final: 0.8526 (mm) REVERT: B 483 MET cc_start: 0.8343 (tmm) cc_final: 0.7955 (tmm) REVERT: B 496 TYR cc_start: 0.9105 (t80) cc_final: 0.8899 (t80) REVERT: C 290 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7948 (tt0) REVERT: C 482 ILE cc_start: 0.9028 (tt) cc_final: 0.8518 (mm) REVERT: C 483 MET cc_start: 0.8352 (tmm) cc_final: 0.7966 (tmm) REVERT: D 290 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7947 (tt0) REVERT: D 429 GLU cc_start: 0.7975 (mp0) cc_final: 0.7570 (mp0) REVERT: D 482 ILE cc_start: 0.9012 (tt) cc_final: 0.8490 (mm) REVERT: D 483 MET cc_start: 0.8330 (tmm) cc_final: 0.7950 (tmm) REVERT: D 496 TYR cc_start: 0.9089 (t80) cc_final: 0.8882 (t80) outliers start: 35 outliers final: 16 residues processed: 284 average time/residue: 0.2237 time to fit residues: 96.8290 Evaluate side-chains 220 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 204 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14216 Z= 0.323 Angle : 0.587 5.418 19384 Z= 0.320 Chirality : 0.045 0.212 2192 Planarity : 0.004 0.041 2416 Dihedral : 5.581 31.685 2120 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.76 % Allowed : 7.44 % 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: 0.47 (0.20), residues: 1692 helix: 1.19 (0.17), residues: 876 sheet: 0.42 (0.34), residues: 184 loop : -0.92 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 434 HIS 0.007 0.001 HIS C 213 PHE 0.023 0.002 PHE B 549 TYR 0.018 0.002 TYR C 129 ARG 0.002 0.000 ARG D 206 *********************** 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 278 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 239 time to evaluate : 1.559 Fit side-chains REVERT: A 482 ILE cc_start: 0.9024 (tt) cc_final: 0.8489 (mm) REVERT: A 483 MET cc_start: 0.8398 (tmm) cc_final: 0.8027 (tmm) REVERT: A 557 LEU cc_start: 0.8346 (tp) cc_final: 0.8056 (tp) REVERT: B 482 ILE cc_start: 0.9025 (tt) cc_final: 0.8492 (mm) REVERT: B 483 MET cc_start: 0.8396 (tmm) cc_final: 0.8025 (tmm) REVERT: B 496 TYR cc_start: 0.9123 (t80) cc_final: 0.8897 (t80) REVERT: B 557 LEU cc_start: 0.8373 (tp) cc_final: 0.8081 (tp) REVERT: C 482 ILE cc_start: 0.9027 (tt) cc_final: 0.8494 (mm) REVERT: C 483 MET cc_start: 0.8399 (tmm) cc_final: 0.8032 (tmm) REVERT: C 557 LEU cc_start: 0.8373 (tp) cc_final: 0.8081 (tp) REVERT: D 429 GLU cc_start: 0.8023 (mp0) cc_final: 0.7650 (mp0) REVERT: D 482 ILE cc_start: 0.9017 (tt) cc_final: 0.8483 (mm) REVERT: D 483 MET cc_start: 0.8390 (tmm) cc_final: 0.8009 (tmm) REVERT: D 496 TYR cc_start: 0.9114 (t80) cc_final: 0.8886 (t80) REVERT: D 557 LEU cc_start: 0.8361 (tp) cc_final: 0.8078 (tp) outliers start: 39 outliers final: 35 residues processed: 256 average time/residue: 0.2360 time to fit residues: 90.2546 Evaluate side-chains 257 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 222 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 555 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 79 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 7.9990 chunk 162 optimal weight: 0.0980 chunk 80 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14216 Z= 0.147 Angle : 0.509 10.979 19384 Z= 0.269 Chirality : 0.042 0.187 2192 Planarity : 0.004 0.036 2416 Dihedral : 4.540 24.895 2120 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.62 % Allowed : 9.35 % Favored : 88.03 % 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: 0.88 (0.20), residues: 1692 helix: 1.50 (0.17), residues: 876 sheet: 0.57 (0.33), residues: 184 loop : -0.68 (0.25), residues: 632 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 0.022 0.001 PHE A 549 TYR 0.014 0.001 TYR C 129 ARG 0.001 0.000 ARG A 182 *********************** 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 290 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 253 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8136 (mmtp) REVERT: A 482 ILE cc_start: 0.8825 (tt) cc_final: 0.8234 (mm) REVERT: A 483 MET cc_start: 0.8345 (tmm) cc_final: 0.7961 (tmm) REVERT: A 557 LEU cc_start: 0.8328 (tp) cc_final: 0.8070 (tp) REVERT: B 173 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8133 (mmtp) REVERT: B 482 ILE cc_start: 0.8825 (tt) cc_final: 0.8236 (mm) REVERT: B 483 MET cc_start: 0.8344 (tmm) cc_final: 0.7961 (tmm) REVERT: B 557 LEU cc_start: 0.8338 (tp) cc_final: 0.8064 (tp) REVERT: C 173 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8134 (mmtp) REVERT: C 482 ILE cc_start: 0.8826 (tt) cc_final: 0.8237 (mm) REVERT: C 483 MET cc_start: 0.8343 (tmm) cc_final: 0.7963 (tmm) REVERT: C 557 LEU cc_start: 0.8339 (tp) cc_final: 0.8066 (tp) REVERT: D 173 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8134 (mmtp) REVERT: D 482 ILE cc_start: 0.8821 (tt) cc_final: 0.8232 (mm) REVERT: D 483 MET cc_start: 0.8338 (tmm) cc_final: 0.7950 (tmm) REVERT: D 557 LEU cc_start: 0.8316 (tp) cc_final: 0.8060 (tp) outliers start: 37 outliers final: 20 residues processed: 269 average time/residue: 0.2543 time to fit residues: 103.5416 Evaluate side-chains 245 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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 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 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 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 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 135 optimal weight: 7.9990 chunk 92 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 138 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 0.4980 chunk 145 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14216 Z= 0.239 Angle : 0.531 10.309 19384 Z= 0.284 Chirality : 0.043 0.201 2192 Planarity : 0.004 0.042 2416 Dihedral : 4.591 23.475 2120 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.20 % Allowed : 10.20 % Favored : 87.61 % 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: 0.87 (0.20), residues: 1692 helix: 1.36 (0.17), residues: 904 sheet: 0.90 (0.33), residues: 184 loop : -0.69 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 434 HIS 0.006 0.001 HIS B 213 PHE 0.027 0.002 PHE B 549 TYR 0.012 0.001 TYR C 129 ARG 0.002 0.000 ARG A 206 *********************** 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 258 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 227 time to evaluate : 1.678 Fit side-chains REVERT: A 173 LYS cc_start: 0.8639 (mtmm) cc_final: 0.8154 (mmtp) REVERT: A 482 ILE cc_start: 0.8886 (tt) cc_final: 0.8298 (mm) REVERT: A 483 MET cc_start: 0.8391 (tmm) cc_final: 0.8012 (tmm) REVERT: A 557 LEU cc_start: 0.8371 (tp) cc_final: 0.8121 (tp) REVERT: B 173 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8119 (mmtp) REVERT: B 482 ILE cc_start: 0.8878 (tt) cc_final: 0.8288 (mm) REVERT: B 483 MET cc_start: 0.8383 (tmm) cc_final: 0.8005 (tmm) REVERT: B 557 LEU cc_start: 0.8358 (tp) cc_final: 0.8103 (tp) REVERT: C 173 LYS cc_start: 0.8610 (mtmm) cc_final: 0.8121 (mmtp) REVERT: C 482 ILE cc_start: 0.8879 (tt) cc_final: 0.8290 (mm) REVERT: C 483 MET cc_start: 0.8384 (tmm) cc_final: 0.8010 (tmm) REVERT: C 557 LEU cc_start: 0.8358 (tp) cc_final: 0.8104 (tp) REVERT: D 173 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8152 (mmtp) REVERT: D 482 ILE cc_start: 0.8871 (tt) cc_final: 0.8279 (mm) REVERT: D 483 MET cc_start: 0.8384 (tmm) cc_final: 0.8001 (tmm) REVERT: D 557 LEU cc_start: 0.8351 (tp) cc_final: 0.8104 (tp) outliers start: 31 outliers final: 26 residues processed: 241 average time/residue: 0.2369 time to fit residues: 85.6637 Evaluate side-chains 242 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 216 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 B residue 520 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 C residue 520 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 D 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14216 Z= 0.172 Angle : 0.507 10.157 19384 Z= 0.269 Chirality : 0.042 0.190 2192 Planarity : 0.004 0.041 2416 Dihedral : 4.332 21.947 2120 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.27 % Allowed : 11.54 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.20 (0.20), residues: 1692 helix: 1.70 (0.17), residues: 880 sheet: 0.91 (0.34), residues: 184 loop : -0.49 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 434 HIS 0.005 0.001 HIS C 213 PHE 0.027 0.001 PHE A 549 TYR 0.011 0.001 TYR D 127 ARG 0.001 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 241 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8129 (mmtp) REVERT: A 482 ILE cc_start: 0.8801 (tt) cc_final: 0.8201 (mm) REVERT: A 483 MET cc_start: 0.8353 (tmm) cc_final: 0.7980 (tmm) REVERT: A 557 LEU cc_start: 0.8357 (tp) cc_final: 0.8104 (tp) REVERT: B 173 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8100 (mmtp) REVERT: B 482 ILE cc_start: 0.8788 (tt) cc_final: 0.8186 (mm) REVERT: B 483 MET cc_start: 0.8347 (tmm) cc_final: 0.7980 (tmm) REVERT: B 557 LEU cc_start: 0.8364 (tp) cc_final: 0.8117 (tp) REVERT: C 173 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8127 (mmtp) REVERT: C 482 ILE cc_start: 0.8791 (tt) cc_final: 0.8187 (mm) REVERT: C 483 MET cc_start: 0.8349 (tmm) cc_final: 0.7983 (tmm) REVERT: C 557 LEU cc_start: 0.8353 (tp) cc_final: 0.8108 (tp) REVERT: D 173 LYS cc_start: 0.8590 (mtmm) cc_final: 0.8095 (mmtp) REVERT: D 482 ILE cc_start: 0.8785 (tt) cc_final: 0.8181 (mm) REVERT: D 483 MET cc_start: 0.8369 (tmm) cc_final: 0.7998 (tmm) REVERT: D 557 LEU cc_start: 0.8341 (tp) cc_final: 0.8091 (tp) outliers start: 32 outliers final: 23 residues processed: 258 average time/residue: 0.2358 time to fit residues: 91.2212 Evaluate side-chains 245 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 222 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 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 D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 421 GLN C 404 HIS C 493 GLN D 404 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14216 Z= 0.188 Angle : 0.512 9.735 19384 Z= 0.273 Chirality : 0.042 0.193 2192 Planarity : 0.004 0.041 2416 Dihedral : 4.278 20.875 2120 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.70 % Allowed : 11.61 % Favored : 86.69 % 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: 1.32 (0.21), residues: 1692 helix: 1.79 (0.17), residues: 880 sheet: 0.96 (0.34), residues: 184 loop : -0.42 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 434 HIS 0.005 0.001 HIS B 213 PHE 0.028 0.001 PHE B 549 TYR 0.010 0.001 TYR C 127 ARG 0.001 0.000 ARG D 199 *********************** 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 254 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 230 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8610 (mtmm) cc_final: 0.8151 (mmtp) REVERT: A 482 ILE cc_start: 0.8727 (tt) cc_final: 0.8165 (mm) REVERT: A 483 MET cc_start: 0.8371 (tmm) cc_final: 0.8010 (tmm) REVERT: A 557 LEU cc_start: 0.8354 (tp) cc_final: 0.8104 (tp) REVERT: B 173 LYS cc_start: 0.8615 (mtmm) cc_final: 0.8129 (mmtp) REVERT: B 417 LYS cc_start: 0.8711 (tptp) cc_final: 0.8341 (tppt) REVERT: B 482 ILE cc_start: 0.8721 (tt) cc_final: 0.8164 (mm) REVERT: B 483 MET cc_start: 0.8363 (tmm) cc_final: 0.7999 (tmm) REVERT: B 557 LEU cc_start: 0.8382 (tp) cc_final: 0.8138 (tp) REVERT: C 173 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8150 (mmtp) REVERT: C 482 ILE cc_start: 0.8726 (tt) cc_final: 0.8169 (mm) REVERT: C 483 MET cc_start: 0.8367 (tmm) cc_final: 0.8003 (tmm) REVERT: C 557 LEU cc_start: 0.8382 (tp) cc_final: 0.8139 (tp) REVERT: D 173 LYS cc_start: 0.8609 (mtmm) cc_final: 0.8124 (mmtp) REVERT: D 482 ILE cc_start: 0.8719 (tt) cc_final: 0.8162 (mm) REVERT: D 483 MET cc_start: 0.8363 (tmm) cc_final: 0.7997 (tmm) REVERT: D 557 LEU cc_start: 0.8328 (tp) cc_final: 0.8070 (tp) outliers start: 24 outliers final: 20 residues processed: 242 average time/residue: 0.2259 time to fit residues: 81.6999 Evaluate side-chains 239 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 219 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.0970 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.0870 chunk 102 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 147 optimal weight: 0.7980 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14216 Z= 0.142 Angle : 0.490 9.552 19384 Z= 0.260 Chirality : 0.041 0.178 2192 Planarity : 0.003 0.039 2416 Dihedral : 3.917 17.275 2120 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.98 % Allowed : 11.69 % Favored : 86.33 % 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: 1.55 (0.20), residues: 1692 helix: 1.96 (0.17), residues: 880 sheet: 0.97 (0.35), residues: 184 loop : -0.26 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 434 HIS 0.004 0.001 HIS A 213 PHE 0.027 0.001 PHE A 549 TYR 0.012 0.001 TYR D 127 ARG 0.001 0.000 ARG D 296 *********************** 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 285 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 257 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8127 (mmtp) REVERT: A 330 THR cc_start: 0.9149 (m) cc_final: 0.8860 (m) REVERT: A 429 GLU cc_start: 0.7723 (mp0) cc_final: 0.7388 (mp0) REVERT: A 480 PHE cc_start: 0.6809 (t80) cc_final: 0.6545 (m-80) REVERT: A 482 ILE cc_start: 0.8640 (tt) cc_final: 0.8068 (mm) REVERT: A 483 MET cc_start: 0.8330 (tmm) cc_final: 0.7929 (tmm) REVERT: A 557 LEU cc_start: 0.8372 (tp) cc_final: 0.8116 (tp) REVERT: B 173 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8126 (mmtp) REVERT: B 330 THR cc_start: 0.9144 (m) cc_final: 0.8856 (m) REVERT: B 417 LYS cc_start: 0.8805 (tptp) cc_final: 0.8463 (tppt) REVERT: B 429 GLU cc_start: 0.7734 (mp0) cc_final: 0.7372 (mp0) REVERT: B 480 PHE cc_start: 0.6811 (t80) cc_final: 0.6540 (m-80) REVERT: B 482 ILE cc_start: 0.8624 (tt) cc_final: 0.8036 (mm) REVERT: B 483 MET cc_start: 0.8319 (tmm) cc_final: 0.7919 (tmm) REVERT: B 557 LEU cc_start: 0.8368 (tp) cc_final: 0.8112 (tp) REVERT: C 173 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8128 (mmtp) REVERT: C 330 THR cc_start: 0.9143 (m) cc_final: 0.8857 (m) REVERT: C 429 GLU cc_start: 0.7729 (mp0) cc_final: 0.7398 (mp0) REVERT: C 480 PHE cc_start: 0.6811 (t80) cc_final: 0.6539 (m-80) REVERT: C 482 ILE cc_start: 0.8633 (tt) cc_final: 0.8032 (mm) REVERT: C 483 MET cc_start: 0.8329 (tmm) cc_final: 0.7928 (tmm) REVERT: C 557 LEU cc_start: 0.8368 (tp) cc_final: 0.8115 (tp) REVERT: D 173 LYS cc_start: 0.8567 (mtmm) cc_final: 0.8123 (mmtp) REVERT: D 330 THR cc_start: 0.9144 (m) cc_final: 0.8852 (m) REVERT: D 429 GLU cc_start: 0.7785 (mp0) cc_final: 0.7513 (mp0) REVERT: D 480 PHE cc_start: 0.6831 (t80) cc_final: 0.6553 (m-80) REVERT: D 482 ILE cc_start: 0.8629 (tt) cc_final: 0.8041 (mm) REVERT: D 483 MET cc_start: 0.8330 (tmm) cc_final: 0.7932 (tmm) REVERT: D 557 LEU cc_start: 0.8361 (tp) cc_final: 0.8127 (tp) outliers start: 28 outliers final: 17 residues processed: 272 average time/residue: 0.2617 time to fit residues: 104.2740 Evaluate side-chains 253 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 236 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 A residue 396 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 142 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS C 493 GLN D 404 HIS D 493 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14216 Z= 0.156 Angle : 0.501 9.581 19384 Z= 0.267 Chirality : 0.041 0.185 2192 Planarity : 0.004 0.051 2416 Dihedral : 3.919 15.786 2120 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.49 % Allowed : 13.03 % Favored : 85.48 % 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: 1.44 (0.20), residues: 1692 helix: 1.84 (0.17), residues: 904 sheet: 0.93 (0.34), residues: 184 loop : -0.36 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 434 HIS 0.006 0.001 HIS B 213 PHE 0.028 0.001 PHE B 549 TYR 0.011 0.001 TYR C 127 ARG 0.005 0.000 ARG D 204 *********************** 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 266 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8158 (mmtp) REVERT: A 330 THR cc_start: 0.9197 (m) cc_final: 0.8915 (m) REVERT: A 480 PHE cc_start: 0.6833 (t80) cc_final: 0.6549 (m-80) REVERT: A 482 ILE cc_start: 0.8597 (tt) cc_final: 0.8010 (mm) REVERT: A 483 MET cc_start: 0.8346 (tmm) cc_final: 0.7934 (tmm) REVERT: A 504 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7704 (tm-30) REVERT: A 557 LEU cc_start: 0.8383 (tp) cc_final: 0.8134 (tp) REVERT: B 173 LYS cc_start: 0.8598 (mtmm) cc_final: 0.8156 (mmtp) REVERT: B 330 THR cc_start: 0.9193 (m) cc_final: 0.8913 (m) REVERT: B 417 LYS cc_start: 0.8811 (tptp) cc_final: 0.8440 (tppt) REVERT: B 480 PHE cc_start: 0.6861 (t80) cc_final: 0.6571 (m-80) REVERT: B 482 ILE cc_start: 0.8567 (tt) cc_final: 0.7965 (mm) REVERT: B 483 MET cc_start: 0.8332 (tmm) cc_final: 0.7926 (tmm) REVERT: B 504 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7727 (tm-30) REVERT: B 557 LEU cc_start: 0.8382 (tp) cc_final: 0.8140 (tp) REVERT: C 173 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8155 (mmtp) REVERT: C 330 THR cc_start: 0.9193 (m) cc_final: 0.8911 (m) REVERT: C 480 PHE cc_start: 0.6832 (t80) cc_final: 0.6547 (m-80) REVERT: C 482 ILE cc_start: 0.8561 (tt) cc_final: 0.7973 (mm) REVERT: C 483 MET cc_start: 0.8330 (tmm) cc_final: 0.7936 (tmm) REVERT: C 504 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7723 (tm-30) REVERT: C 557 LEU cc_start: 0.8383 (tp) cc_final: 0.8135 (tp) REVERT: D 173 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8151 (mmtp) REVERT: D 330 THR cc_start: 0.9190 (m) cc_final: 0.8910 (m) REVERT: D 429 GLU cc_start: 0.7803 (mp0) cc_final: 0.7542 (mp0) REVERT: D 480 PHE cc_start: 0.6884 (t80) cc_final: 0.6589 (m-80) REVERT: D 482 ILE cc_start: 0.8571 (tt) cc_final: 0.7968 (mm) REVERT: D 483 MET cc_start: 0.8337 (tmm) cc_final: 0.7933 (tmm) REVERT: D 504 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7731 (tm-30) REVERT: D 557 LEU cc_start: 0.8359 (tp) cc_final: 0.8127 (tp) outliers start: 21 outliers final: 18 residues processed: 257 average time/residue: 0.2290 time to fit residues: 88.1194 Evaluate side-chains 254 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 236 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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 A residue 396 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 264 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 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 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS C 493 GLN D 404 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14216 Z= 0.189 Angle : 0.524 9.512 19384 Z= 0.279 Chirality : 0.042 0.188 2192 Planarity : 0.004 0.042 2416 Dihedral : 4.059 26.892 2120 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.77 % Allowed : 13.24 % Favored : 84.99 % 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: 1.58 (0.20), residues: 1692 helix: 2.03 (0.17), residues: 880 sheet: 0.91 (0.34), residues: 184 loop : -0.29 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 434 HIS 0.005 0.001 HIS C 213 PHE 0.029 0.001 PHE C 549 TYR 0.010 0.001 TYR C 127 ARG 0.005 0.000 ARG D 204 ********************** 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 260 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 235 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8142 (mmtp) REVERT: A 480 PHE cc_start: 0.6925 (t80) cc_final: 0.6598 (m-80) REVERT: A 482 ILE cc_start: 0.8574 (tt) cc_final: 0.7995 (mm) REVERT: A 483 MET cc_start: 0.8351 (tmm) cc_final: 0.7953 (tmm) REVERT: A 504 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7707 (tm-30) REVERT: A 557 LEU cc_start: 0.8408 (tp) cc_final: 0.8162 (tp) REVERT: B 173 LYS cc_start: 0.8578 (mtmm) cc_final: 0.8139 (mmtp) REVERT: B 417 LYS cc_start: 0.8706 (tptp) cc_final: 0.8398 (tppt) REVERT: B 480 PHE cc_start: 0.6944 (t80) cc_final: 0.6607 (m-80) REVERT: B 482 ILE cc_start: 0.8522 (tt) cc_final: 0.7975 (mm) REVERT: B 483 MET cc_start: 0.8339 (tmm) cc_final: 0.7947 (tmm) REVERT: B 504 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 557 LEU cc_start: 0.8396 (tp) cc_final: 0.8144 (tp) REVERT: C 173 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8113 (mmtp) REVERT: C 480 PHE cc_start: 0.6927 (t80) cc_final: 0.6592 (m-80) REVERT: C 482 ILE cc_start: 0.8532 (tt) cc_final: 0.7986 (mm) REVERT: C 483 MET cc_start: 0.8341 (tmm) cc_final: 0.7929 (tmm) REVERT: C 504 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7700 (tm-30) REVERT: C 557 LEU cc_start: 0.8408 (tp) cc_final: 0.8160 (tp) REVERT: D 173 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8109 (mmtp) REVERT: D 429 GLU cc_start: 0.7833 (mp0) cc_final: 0.7560 (mp0) REVERT: D 482 ILE cc_start: 0.8531 (tt) cc_final: 0.7977 (mm) REVERT: D 483 MET cc_start: 0.8347 (tmm) cc_final: 0.8006 (tmm) REVERT: D 504 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7695 (tm-30) REVERT: D 557 LEU cc_start: 0.8380 (tp) cc_final: 0.8134 (tp) outliers start: 25 outliers final: 22 residues processed: 246 average time/residue: 0.2408 time to fit residues: 88.6833 Evaluate side-chains 253 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 231 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 A residue 283 GLU Chi-restraints excluded: chain A residue 396 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 264 SER Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 283 GLU 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 Chi-restraints excluded: chain D residue 283 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** A 493 GLN B 404 HIS B 420 GLN C 404 HIS D 404 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.132220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102856 restraints weight = 20950.976| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.55 r_work: 0.3068 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14216 Z= 0.166 Angle : 0.510 10.202 19384 Z= 0.272 Chirality : 0.041 0.181 2192 Planarity : 0.004 0.041 2416 Dihedral : 3.936 22.599 2120 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.77 % Allowed : 13.39 % Favored : 84.84 % 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: 1.50 (0.20), residues: 1692 helix: 1.87 (0.17), residues: 904 sheet: 0.98 (0.35), residues: 184 loop : -0.30 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 434 HIS 0.005 0.001 HIS D 213 PHE 0.029 0.001 PHE B 549 TYR 0.012 0.001 TYR D 119 ARG 0.006 0.000 ARG A 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2839.77 seconds wall clock time: 51 minutes 35.21 seconds (3095.21 seconds total)