Starting phenix.real_space_refine on Wed Sep 17 15:17:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygs_39261/09_2025/8ygs_39261_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygs_39261/09_2025/8ygs_39261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ygs_39261/09_2025/8ygs_39261_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygs_39261/09_2025/8ygs_39261_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ygs_39261/09_2025/8ygs_39261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygs_39261/09_2025/8ygs_39261.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.033 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 26 5.16 5 C 5920 2.51 5 N 1555 2.21 5 O 1790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9291 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2158 Classifications: {'peptide': 274} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 259} Chain breaks: 1 Chain: "B" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2049 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 246} Chain breaks: 1 Chain: "C" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1675 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 202} Chain: "H" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 899 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "N" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N SER H 17 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER H 17 " occ=0.50 residue: pdb=" N SER H 61 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER H 61 " occ=0.50 residue: pdb=" N MET L 11 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET L 11 " occ=0.50 residue: pdb=" N ARG L 18 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG L 18 " occ=0.50 residue: pdb=" N GLN L 27 " occ=0.83 ... (7 atoms not shown) pdb=" NE2 GLN L 27 " occ=0.83 residue: pdb=" N SER L 43 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER L 43 " occ=0.50 residue: pdb=" N SER L 50 " occ=0.90 ... (4 atoms not shown) pdb=" OG SER L 50 " occ=0.90 residue: pdb=" N SER L 67 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER L 67 " occ=0.50 residue: pdb=" N GLU L 105 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU L 105 " occ=0.50 residue: pdb=" N SER M 17 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER M 17 " occ=0.50 residue: pdb=" N SER M 61 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER M 61 " occ=0.50 residue: pdb=" N MET N 11 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET N 11 " occ=0.50 ... (remaining 6 not shown) Time building chain proxies: 2.45, per 1000 atoms: 0.26 Number of scatterers: 9291 At special positions: 0 Unit cell: (108, 130, 131, 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 26 16.00 O 1790 8.00 N 1555 7.00 C 5920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.28 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.28 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 357.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2186 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 22 sheets defined 3.0% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 360 through 365 removed outlier: 3.539A pdb=" N VAL A 365 " --> pdb=" O PHE A 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.880A pdb=" N ARG B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 364 Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.314A pdb=" N SER H 65 " --> pdb=" O ALA H 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 76 Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 33 through 34 current: chain 'C' and resid 290 through 296 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 290 through 296 current: chain 'C' and resid 338 through 345 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 48 through 50 current: chain 'A' and resid 311 through 321 removed outlier: 3.556A pdb=" N TRP A 356 " --> pdb=" O HIS A 315 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 350 through 357 current: chain 'A' and resid 396 through 415 removed outlier: 6.454A pdb=" N VAL A 396 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU A 439 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR A 398 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE A 437 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY A 400 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL A 402 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU A 433 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU A 404 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA A 431 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N SER A 406 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ARG A 429 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLY A 408 " --> pdb=" O ARG A 427 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 420 through 439 current: chain 'B' and resid 311 through 321 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 350 through 357 current: chain 'B' and resid 401 through 415 removed outlier: 5.233A pdb=" N VAL B 402 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU B 433 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU B 404 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA B 431 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N SER B 406 " --> pdb=" O ARG B 429 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARG B 429 " --> pdb=" O SER B 406 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY B 408 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 60 removed outlier: 7.145A pdb=" N THR A 59 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 275 removed outlier: 6.825A pdb=" N LEU A 473 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL A 368 " --> pdb=" O LEU A 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 279 through 283 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 329 removed outlier: 5.570A pdb=" N PHE A 328 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER A 340 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 345 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 262 through 275 removed outlier: 6.709A pdb=" N ALA B 465 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU B 375 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG B 467 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA B 373 " --> pdb=" O ARG B 467 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER B 469 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU B 371 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE B 471 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 279 through 283 removed outlier: 6.434A pdb=" N THR B 280 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE B 294 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE B 282 " --> pdb=" O SER B 292 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 384 through 386 Processing sheet with id=AB1, first strand: chain 'C' and resid 266 through 275 removed outlier: 4.052A pdb=" N SER C 370 " --> pdb=" O ILE C 471 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 299 through 307 removed outlier: 6.091A pdb=" N ASP C 357 " --> pdb=" O ASN C 422 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ASN C 422 " --> pdb=" O ASP C 357 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY C 408 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ARG C 429 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N SER C 406 " --> pdb=" O ARG C 429 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA C 431 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU C 404 " --> pdb=" O ALA C 431 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 378 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 384 through 386 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB5, first strand: chain 'H' and resid 34 through 39 removed outlier: 3.714A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 104 through 107 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.007A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB8, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AB9, first strand: chain 'M' and resid 19 through 20 removed outlier: 3.935A pdb=" N GLN M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 33 through 39 removed outlier: 3.730A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 104 through 107 Processing sheet with id=AC2, first strand: chain 'N' and resid 4 through 6 removed outlier: 4.113A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.455A pdb=" N MET N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.420A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 585 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: 1.49 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1496 1.28 - 1.41: 2580 1.41 - 1.55: 5358 1.55 - 1.68: 53 1.68 - 1.81: 38 Bond restraints: 9525 Sorted by residual: bond pdb=" C ILE M 20 " pdb=" O ILE M 20 " ideal model delta sigma weight residual 1.235 1.144 0.091 9.90e-03 1.02e+04 8.39e+01 bond pdb=" CA VAL A 33 " pdb=" C VAL A 33 " ideal model delta sigma weight residual 1.525 1.450 0.075 1.22e-02 6.72e+03 3.76e+01 bond pdb=" CA LYS H 64 " pdb=" C LYS H 64 " ideal model delta sigma weight residual 1.523 1.444 0.079 1.30e-02 5.92e+03 3.73e+01 bond pdb=" CA ASN H 60 " pdb=" C ASN H 60 " ideal model delta sigma weight residual 1.524 1.445 0.078 1.33e-02 5.65e+03 3.46e+01 bond pdb=" CA VAL A 33 " pdb=" CB VAL A 33 " ideal model delta sigma weight residual 1.540 1.477 0.063 1.10e-02 8.26e+03 3.29e+01 ... (remaining 9520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 12310 3.20 - 6.41: 563 6.41 - 9.61: 65 9.61 - 12.81: 12 12.81 - 16.01: 3 Bond angle restraints: 12953 Sorted by residual: angle pdb=" N VAL L 58 " pdb=" CA VAL L 58 " pdb=" C VAL L 58 " ideal model delta sigma weight residual 109.19 97.67 11.52 8.20e-01 1.49e+00 1.97e+02 angle pdb=" N SER B 445 " pdb=" CA SER B 445 " pdb=" C SER B 445 " ideal model delta sigma weight residual 109.62 125.63 -16.01 1.50e+00 4.44e-01 1.14e+02 angle pdb=" N SER L 7 " pdb=" CA SER L 7 " pdb=" C SER L 7 " ideal model delta sigma weight residual 111.07 122.41 -11.34 1.07e+00 8.73e-01 1.12e+02 angle pdb=" N ALA B 41 " pdb=" CA ALA B 41 " pdb=" C ALA B 41 " ideal model delta sigma weight residual 110.53 123.67 -13.14 1.32e+00 5.74e-01 9.91e+01 angle pdb=" CA ASP A 354 " pdb=" C ASP A 354 " pdb=" O ASP A 354 " ideal model delta sigma weight residual 121.87 111.81 10.06 1.16e+00 7.43e-01 7.53e+01 ... (remaining 12948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 5151 17.08 - 34.17: 340 34.17 - 51.25: 47 51.25 - 68.34: 15 68.34 - 85.42: 6 Dihedral angle restraints: 5559 sinusoidal: 2133 harmonic: 3426 Sorted by residual: dihedral pdb=" C SER H 65 " pdb=" N SER H 65 " pdb=" CA SER H 65 " pdb=" CB SER H 65 " ideal model delta harmonic sigma weight residual -122.60 -151.24 28.64 0 2.50e+00 1.60e-01 1.31e+02 dihedral pdb=" C ALA B 41 " pdb=" N ALA B 41 " pdb=" CA ALA B 41 " pdb=" CB ALA B 41 " ideal model delta harmonic sigma weight residual -122.60 -151.14 28.54 0 2.50e+00 1.60e-01 1.30e+02 dihedral pdb=" N ALA B 41 " pdb=" C ALA B 41 " pdb=" CA ALA B 41 " pdb=" CB ALA B 41 " ideal model delta harmonic sigma weight residual 122.90 151.17 -28.27 0 2.50e+00 1.60e-01 1.28e+02 ... (remaining 5556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.255: 1403 0.255 - 0.510: 18 0.510 - 0.765: 0 0.765 - 1.020: 0 1.020 - 1.275: 5 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CA SER H 65 " pdb=" N SER H 65 " pdb=" C SER H 65 " pdb=" CB SER H 65 " both_signs ideal model delta sigma weight residual False 2.51 1.24 1.28 2.00e-01 2.50e+01 4.06e+01 chirality pdb=" CA ALA B 41 " pdb=" N ALA B 41 " pdb=" C ALA B 41 " pdb=" CB ALA B 41 " both_signs ideal model delta sigma weight residual False 2.48 1.23 1.25 2.00e-01 2.50e+01 3.91e+01 chirality pdb=" CB THR A 34 " pdb=" CA THR A 34 " pdb=" OG1 THR A 34 " pdb=" CG2 THR A 34 " both_signs ideal model delta sigma weight residual False 2.55 1.30 1.25 2.00e-01 2.50e+01 3.89e+01 ... (remaining 1423 not shown) Planarity restraints: 1660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 342 " -0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C PHE C 342 " 0.066 2.00e-02 2.50e+03 pdb=" O PHE C 342 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU C 343 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 354 " -0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C ASP A 354 " 0.065 2.00e-02 2.50e+03 pdb=" O ASP A 354 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR A 355 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 412 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C SER C 412 " -0.058 2.00e-02 2.50e+03 pdb=" O SER C 412 " 0.022 2.00e-02 2.50e+03 pdb=" N THR C 413 " 0.019 2.00e-02 2.50e+03 ... (remaining 1657 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3049 2.84 - 3.35: 7880 3.35 - 3.87: 13950 3.87 - 4.38: 16150 4.38 - 4.90: 28975 Nonbonded interactions: 70004 Sorted by model distance: nonbonded pdb=" N ASN H 60 " pdb=" O ASN H 60 " model vdw 2.320 2.496 nonbonded pdb=" N SER L 50 " pdb=" O SER L 50 " model vdw 2.329 2.496 nonbonded pdb=" OE1 GLN B 266 " pdb=" OG SER H 56 " model vdw 2.334 3.040 nonbonded pdb=" OD1 ASP B 57 " pdb=" N SER B 58 " model vdw 2.389 3.120 nonbonded pdb=" O ASN C 300 " pdb=" OD1 ASN C 300 " model vdw 2.389 3.040 ... (remaining 69999 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' and resid 32 through 476) selection = chain 'B' } ncs_group { reference = chain 'H' selection = (chain 'M' and resid 2 through 115) } ncs_group { reference = (chain 'L' and resid 1 through 106) selection = chain 'N' } 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=0.50 max=1.00 mean=0.99 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: 5.280 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.300 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 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 0.248 9529 Z= 0.704 Angle : 1.498 20.501 12961 Z= 0.992 Chirality : 0.112 1.275 1426 Planarity : 0.007 0.084 1660 Dihedral : 11.765 85.422 3361 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.41 (0.21), residues: 1169 helix: -2.90 (1.13), residues: 12 sheet: -1.68 (0.21), residues: 521 loop : -2.81 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 54 TYR 0.022 0.002 TYR C 355 PHE 0.031 0.003 PHE A 437 TRP 0.026 0.002 TRP B 356 HIS 0.013 0.003 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.01063 ( 9525) covalent geometry : angle 1.47078 (12953) SS BOND : bond 0.17519 ( 4) SS BOND : angle 11.47473 ( 8) hydrogen bonds : bond 0.21547 ( 230) hydrogen bonds : angle 8.40341 ( 585) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 42 GLN cc_start: 0.7361 (mm110) cc_final: 0.7088 (mm-40) REVERT: A 49 ASN cc_start: 0.6692 (t0) cc_final: 0.6435 (p0) REVERT: A 254 ILE cc_start: 0.7512 (mm) cc_final: 0.7173 (mm) REVERT: A 256 ILE cc_start: 0.7300 (tt) cc_final: 0.6868 (pt) REVERT: A 267 TYR cc_start: 0.6885 (m-80) cc_final: 0.6658 (m-80) REVERT: A 274 ARG cc_start: 0.6968 (mtt180) cc_final: 0.6351 (mtp85) REVERT: A 326 PHE cc_start: 0.6673 (m-80) cc_final: 0.6093 (m-80) REVERT: A 474 VAL cc_start: 0.6921 (t) cc_final: 0.6380 (m) REVERT: B 55 ILE cc_start: 0.7041 (pt) cc_final: 0.6633 (mt) REVERT: B 281 ILE cc_start: 0.7114 (pt) cc_final: 0.6820 (mt) REVERT: B 282 ILE cc_start: 0.7453 (pt) cc_final: 0.7237 (pt) REVERT: B 352 TYR cc_start: 0.7375 (m-10) cc_final: 0.7157 (m-10) REVERT: B 378 VAL cc_start: 0.8251 (p) cc_final: 0.7757 (m) REVERT: B 412 SER cc_start: 0.7134 (p) cc_final: 0.6823 (m) REVERT: C 289 TYR cc_start: 0.6859 (m-80) cc_final: 0.6557 (m-80) REVERT: C 303 TYR cc_start: 0.7909 (p90) cc_final: 0.6799 (p90) REVERT: C 305 TYR cc_start: 0.7807 (p90) cc_final: 0.7423 (p90) REVERT: C 329 ASN cc_start: 0.7430 (t0) cc_final: 0.7090 (t0) REVERT: C 441 ARG cc_start: 0.7489 (ttt90) cc_final: 0.7202 (ttt90) REVERT: C 469 SER cc_start: 0.7416 (m) cc_final: 0.7178 (t) REVERT: H 19 SER cc_start: 0.7003 (p) cc_final: 0.6799 (m) REVERT: H 58 ASP cc_start: 0.6753 (t70) cc_final: 0.6374 (t70) REVERT: M 33 SER cc_start: 0.7040 (p) cc_final: 0.6448 (t) REVERT: M 50 MET cc_start: 0.7173 (ttt) cc_final: 0.6907 (ttt) REVERT: M 68 SER cc_start: 0.6942 (m) cc_final: 0.6276 (p) REVERT: N 79 GLN cc_start: 0.7310 (mt0) cc_final: 0.6917 (mt0) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.0824 time to fit residues: 31.9656 Evaluate side-chains 175 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 266 GLN B 300 ASN B 376 ASN B 454 ASN C 324 ASN H 53 ASN H 98 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101119 restraints weight = 15278.625| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.16 r_work: 0.3148 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9529 Z= 0.130 Angle : 0.616 7.322 12961 Z= 0.326 Chirality : 0.046 0.168 1426 Planarity : 0.004 0.047 1660 Dihedral : 5.170 20.833 1291 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.24 % Allowed : 7.20 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.22), residues: 1169 helix: -3.94 (0.81), residues: 12 sheet: -0.95 (0.22), residues: 523 loop : -2.26 (0.20), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 363 TYR 0.018 0.001 TYR L 92 PHE 0.024 0.002 PHE M 27 TRP 0.017 0.001 TRP B 356 HIS 0.005 0.002 HIS N 91 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9525) covalent geometry : angle 0.61549 (12953) SS BOND : bond 0.00854 ( 4) SS BOND : angle 1.33362 ( 8) hydrogen bonds : bond 0.03603 ( 230) hydrogen bonds : angle 6.26773 ( 585) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 254 ILE cc_start: 0.8466 (mm) cc_final: 0.8264 (mm) REVERT: A 256 ILE cc_start: 0.8248 (tt) cc_final: 0.8040 (pt) REVERT: A 265 MET cc_start: 0.8252 (mtp) cc_final: 0.8034 (mtp) REVERT: A 316 THR cc_start: 0.8400 (p) cc_final: 0.8075 (m) REVERT: A 323 VAL cc_start: 0.8677 (p) cc_final: 0.8389 (m) REVERT: B 55 ILE cc_start: 0.7803 (pt) cc_final: 0.7425 (mm) REVERT: B 257 SER cc_start: 0.8191 (m) cc_final: 0.7560 (p) REVERT: B 265 MET cc_start: 0.8254 (mtp) cc_final: 0.7980 (mtp) REVERT: B 282 ILE cc_start: 0.8433 (pt) cc_final: 0.8096 (mt) REVERT: B 326 PHE cc_start: 0.8229 (m-80) cc_final: 0.7896 (m-80) REVERT: B 338 VAL cc_start: 0.8602 (t) cc_final: 0.8260 (p) REVERT: B 421 LEU cc_start: 0.7640 (tt) cc_final: 0.7435 (tp) REVERT: C 303 TYR cc_start: 0.8337 (p90) cc_final: 0.7921 (p90) REVERT: C 305 TYR cc_start: 0.8479 (p90) cc_final: 0.8185 (p90) REVERT: C 307 ARG cc_start: 0.8228 (ttp-170) cc_final: 0.7900 (tmm160) REVERT: C 344 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.7700 (m) REVERT: C 355 TYR cc_start: 0.8250 (t80) cc_final: 0.7719 (t80) REVERT: C 376 ASN cc_start: 0.7858 (m110) cc_final: 0.7560 (m-40) REVERT: C 432 VAL cc_start: 0.8062 (p) cc_final: 0.7733 (m) REVERT: L 52 SER cc_start: 0.8222 (p) cc_final: 0.7951 (m) REVERT: M 33 SER cc_start: 0.8137 (p) cc_final: 0.7723 (t) REVERT: N 52 SER cc_start: 0.7427 (p) cc_final: 0.7038 (t) outliers start: 23 outliers final: 20 residues processed: 214 average time/residue: 0.0986 time to fit residues: 29.7046 Evaluate side-chains 192 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 76 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 0.0980 chunk 72 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 111 optimal weight: 0.0970 chunk 103 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 ASN C 456 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.100725 restraints weight = 15185.531| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.11 r_work: 0.3088 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9529 Z= 0.103 Angle : 0.554 6.799 12961 Z= 0.292 Chirality : 0.044 0.221 1426 Planarity : 0.004 0.035 1660 Dihedral : 4.712 19.388 1291 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.92 % Allowed : 10.02 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.22), residues: 1169 helix: -3.03 (1.12), residues: 12 sheet: -0.57 (0.22), residues: 532 loop : -1.87 (0.21), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 363 TYR 0.024 0.001 TYR N 92 PHE 0.015 0.001 PHE M 27 TRP 0.016 0.001 TRP B 356 HIS 0.004 0.001 HIS N 91 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9525) covalent geometry : angle 0.55384 (12953) SS BOND : bond 0.00879 ( 4) SS BOND : angle 0.88747 ( 8) hydrogen bonds : bond 0.03448 ( 230) hydrogen bonds : angle 5.65527 ( 585) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 474 VAL cc_start: 0.7887 (t) cc_final: 0.7612 (m) REVERT: B 55 ILE cc_start: 0.7806 (pt) cc_final: 0.7423 (mm) REVERT: B 257 SER cc_start: 0.8188 (m) cc_final: 0.7570 (p) REVERT: B 260 SER cc_start: 0.8442 (p) cc_final: 0.7891 (m) REVERT: B 265 MET cc_start: 0.8176 (mtp) cc_final: 0.7968 (mtp) REVERT: B 282 ILE cc_start: 0.8440 (pt) cc_final: 0.8047 (mt) REVERT: B 326 PHE cc_start: 0.8211 (m-80) cc_final: 0.7926 (m-80) REVERT: B 338 VAL cc_start: 0.8616 (t) cc_final: 0.8317 (p) REVERT: B 378 VAL cc_start: 0.8741 (p) cc_final: 0.8392 (m) REVERT: B 421 LEU cc_start: 0.7508 (tt) cc_final: 0.7133 (mt) REVERT: B 424 LEU cc_start: 0.7601 (tt) cc_final: 0.7311 (tp) REVERT: C 303 TYR cc_start: 0.8288 (p90) cc_final: 0.8024 (p90) REVERT: C 305 TYR cc_start: 0.8487 (p90) cc_final: 0.8194 (p90) REVERT: C 307 ARG cc_start: 0.8238 (ttp-170) cc_final: 0.7954 (tmm160) REVERT: C 344 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.7734 (m) REVERT: C 355 TYR cc_start: 0.8268 (t80) cc_final: 0.7684 (t80) REVERT: L 52 SER cc_start: 0.8296 (p) cc_final: 0.8020 (m) REVERT: N 52 SER cc_start: 0.7185 (p) cc_final: 0.6874 (t) outliers start: 30 outliers final: 23 residues processed: 192 average time/residue: 0.0974 time to fit residues: 26.4727 Evaluate side-chains 192 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 79 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 454 ASN B 364 ASN C 436 HIS L 6 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.094750 restraints weight = 15287.486| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.09 r_work: 0.2997 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9529 Z= 0.259 Angle : 0.700 7.403 12961 Z= 0.374 Chirality : 0.049 0.213 1426 Planarity : 0.004 0.037 1660 Dihedral : 5.609 20.689 1291 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.70 % Allowed : 10.80 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.22), residues: 1169 helix: -3.54 (1.03), residues: 12 sheet: -0.54 (0.21), residues: 555 loop : -2.01 (0.21), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 363 TYR 0.023 0.003 TYR M 94 PHE 0.022 0.003 PHE B 468 TRP 0.016 0.002 TRP B 356 HIS 0.009 0.002 HIS N 91 Details of bonding type rmsd covalent geometry : bond 0.00625 ( 9525) covalent geometry : angle 0.70009 (12953) SS BOND : bond 0.00989 ( 4) SS BOND : angle 1.16086 ( 8) hydrogen bonds : bond 0.04613 ( 230) hydrogen bonds : angle 5.99127 ( 585) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.415 Fit side-chains REVERT: B 282 ILE cc_start: 0.8449 (pt) cc_final: 0.8139 (mt) REVERT: B 338 VAL cc_start: 0.8637 (t) cc_final: 0.8378 (p) REVERT: B 378 VAL cc_start: 0.8760 (p) cc_final: 0.8425 (m) REVERT: B 421 LEU cc_start: 0.7613 (tt) cc_final: 0.7356 (mt) REVERT: B 424 LEU cc_start: 0.7857 (tt) cc_final: 0.7542 (tp) REVERT: C 274 ARG cc_start: 0.8282 (mtt180) cc_final: 0.8016 (mtt180) REVERT: C 280 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7837 (p) REVERT: C 305 TYR cc_start: 0.8494 (p90) cc_final: 0.8177 (p90) REVERT: C 344 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.7758 (m) REVERT: C 440 THR cc_start: 0.8490 (m) cc_final: 0.7958 (p) REVERT: C 441 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7802 (mtt90) REVERT: H 58 ASP cc_start: 0.7610 (m-30) cc_final: 0.7403 (m-30) REVERT: L 52 SER cc_start: 0.8572 (p) cc_final: 0.8370 (m) REVERT: L 92 TYR cc_start: 0.8433 (t80) cc_final: 0.8223 (t80) REVERT: M 25 SER cc_start: 0.8104 (OUTLIER) cc_final: 0.7859 (t) REVERT: M 50 MET cc_start: 0.7985 (ttp) cc_final: 0.7341 (ttp) REVERT: M 68 SER cc_start: 0.7960 (m) cc_final: 0.7494 (p) REVERT: N 5 THR cc_start: 0.7745 (p) cc_final: 0.7410 (m) outliers start: 38 outliers final: 28 residues processed: 194 average time/residue: 0.1016 time to fit residues: 27.2677 Evaluate side-chains 179 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 49 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 79 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN B 364 ASN C 324 ASN ** N 90 GLN ** 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 = 0.3353 r_free = 0.3353 target = 0.110725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.096087 restraints weight = 15258.264| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.13 r_work: 0.3013 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9529 Z= 0.152 Angle : 0.589 7.489 12961 Z= 0.313 Chirality : 0.044 0.194 1426 Planarity : 0.004 0.034 1660 Dihedral : 5.145 18.498 1291 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.09 % Allowed : 12.55 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.23), residues: 1169 helix: -3.04 (1.14), residues: 12 sheet: -0.38 (0.22), residues: 537 loop : -1.72 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 446 TYR 0.023 0.002 TYR N 92 PHE 0.015 0.002 PHE A 342 TRP 0.015 0.001 TRP B 356 HIS 0.006 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9525) covalent geometry : angle 0.58928 (12953) SS BOND : bond 0.00789 ( 4) SS BOND : angle 0.84210 ( 8) hydrogen bonds : bond 0.03781 ( 230) hydrogen bonds : angle 5.67479 ( 585) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.327 Fit side-chains REVERT: A 457 ASN cc_start: 0.8329 (t0) cc_final: 0.8082 (t0) REVERT: B 265 MET cc_start: 0.8004 (mmm) cc_final: 0.7773 (mmm) REVERT: B 282 ILE cc_start: 0.8478 (pt) cc_final: 0.8140 (mt) REVERT: B 326 PHE cc_start: 0.8316 (m-80) cc_final: 0.7982 (m-80) REVERT: B 338 VAL cc_start: 0.8629 (t) cc_final: 0.8349 (p) REVERT: B 378 VAL cc_start: 0.8725 (p) cc_final: 0.8393 (m) REVERT: B 424 LEU cc_start: 0.7892 (tt) cc_final: 0.7599 (tp) REVERT: C 274 ARG cc_start: 0.8254 (mtt180) cc_final: 0.7998 (mtt180) REVERT: C 280 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7822 (p) REVERT: C 305 TYR cc_start: 0.8422 (p90) cc_final: 0.8115 (p90) REVERT: C 344 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.7737 (m) REVERT: C 349 SER cc_start: 0.8176 (OUTLIER) cc_final: 0.7939 (p) REVERT: C 440 THR cc_start: 0.8501 (m) cc_final: 0.7945 (p) REVERT: C 441 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7806 (mtt90) REVERT: L 92 TYR cc_start: 0.8447 (t80) cc_final: 0.8193 (t80) REVERT: M 50 MET cc_start: 0.7996 (ttp) cc_final: 0.7295 (ttp) REVERT: M 68 SER cc_start: 0.7927 (m) cc_final: 0.7468 (p) outliers start: 42 outliers final: 35 residues processed: 175 average time/residue: 0.1070 time to fit residues: 25.7482 Evaluate side-chains 185 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 ASN C 324 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095401 restraints weight = 15286.580| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.14 r_work: 0.3014 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9529 Z= 0.137 Angle : 0.571 8.078 12961 Z= 0.302 Chirality : 0.044 0.232 1426 Planarity : 0.004 0.040 1660 Dihedral : 4.956 17.345 1291 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.99 % Allowed : 13.62 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.23), residues: 1169 helix: -2.75 (1.26), residues: 12 sheet: -0.13 (0.22), residues: 567 loop : -1.63 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 441 TYR 0.023 0.002 TYR N 92 PHE 0.021 0.002 PHE H 27 TRP 0.014 0.001 TRP B 356 HIS 0.005 0.002 HIS N 91 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9525) covalent geometry : angle 0.57068 (12953) SS BOND : bond 0.00776 ( 4) SS BOND : angle 0.86738 ( 8) hydrogen bonds : bond 0.03653 ( 230) hydrogen bonds : angle 5.57750 ( 585) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.368 Fit side-chains REVERT: A 55 ILE cc_start: 0.7693 (mm) cc_final: 0.7470 (mm) REVERT: A 457 ASN cc_start: 0.8394 (t0) cc_final: 0.8120 (t0) REVERT: B 55 ILE cc_start: 0.7861 (pt) cc_final: 0.7627 (mm) REVERT: B 265 MET cc_start: 0.7984 (mmm) cc_final: 0.7747 (mmm) REVERT: B 282 ILE cc_start: 0.8479 (pt) cc_final: 0.8156 (mt) REVERT: B 326 PHE cc_start: 0.8333 (m-80) cc_final: 0.7989 (m-80) REVERT: B 338 VAL cc_start: 0.8622 (t) cc_final: 0.8340 (p) REVERT: B 378 VAL cc_start: 0.8716 (p) cc_final: 0.8402 (m) REVERT: B 424 LEU cc_start: 0.7911 (tt) cc_final: 0.7606 (tp) REVERT: C 274 ARG cc_start: 0.8274 (mtt180) cc_final: 0.8011 (mtt180) REVERT: C 280 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7806 (p) REVERT: C 305 TYR cc_start: 0.8414 (p90) cc_final: 0.8101 (p90) REVERT: C 344 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.7756 (m) REVERT: C 349 SER cc_start: 0.8155 (OUTLIER) cc_final: 0.7937 (p) REVERT: C 440 THR cc_start: 0.8497 (m) cc_final: 0.7942 (p) REVERT: C 441 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7823 (mtt90) REVERT: L 92 TYR cc_start: 0.8455 (t80) cc_final: 0.8142 (t80) REVERT: M 50 MET cc_start: 0.8008 (ttp) cc_final: 0.7315 (ttp) REVERT: M 68 SER cc_start: 0.7897 (m) cc_final: 0.7475 (p) outliers start: 41 outliers final: 34 residues processed: 174 average time/residue: 0.1120 time to fit residues: 26.5736 Evaluate side-chains 185 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 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 386 ASN B 300 ASN B 364 ASN C 324 ASN ** N 90 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 = 0.3354 r_free = 0.3354 target = 0.110833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.096176 restraints weight = 15194.403| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.14 r_work: 0.3016 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9529 Z= 0.139 Angle : 0.567 8.541 12961 Z= 0.300 Chirality : 0.044 0.285 1426 Planarity : 0.004 0.037 1660 Dihedral : 4.920 17.133 1291 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.18 % Allowed : 14.20 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.23), residues: 1169 helix: -2.74 (1.26), residues: 12 sheet: -0.23 (0.21), residues: 590 loop : -1.59 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 441 TYR 0.023 0.002 TYR N 92 PHE 0.015 0.002 PHE A 342 TRP 0.014 0.001 TRP B 356 HIS 0.005 0.002 HIS N 91 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9525) covalent geometry : angle 0.56662 (12953) SS BOND : bond 0.00768 ( 4) SS BOND : angle 0.85299 ( 8) hydrogen bonds : bond 0.03557 ( 230) hydrogen bonds : angle 5.60030 ( 585) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.350 Fit side-chains REVERT: A 457 ASN cc_start: 0.8399 (t0) cc_final: 0.8156 (t0) REVERT: B 34 THR cc_start: 0.8192 (m) cc_final: 0.7793 (p) REVERT: B 42 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8283 (mm-40) REVERT: B 55 ILE cc_start: 0.7862 (pt) cc_final: 0.7616 (mm) REVERT: B 265 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7724 (mmm) REVERT: B 282 ILE cc_start: 0.8484 (pt) cc_final: 0.8168 (mt) REVERT: B 338 VAL cc_start: 0.8620 (t) cc_final: 0.8342 (p) REVERT: B 378 VAL cc_start: 0.8736 (p) cc_final: 0.8420 (m) REVERT: B 424 LEU cc_start: 0.7956 (tt) cc_final: 0.7638 (tp) REVERT: C 274 ARG cc_start: 0.8284 (mtt180) cc_final: 0.8019 (mtt180) REVERT: C 280 THR cc_start: 0.8073 (t) cc_final: 0.7840 (p) REVERT: C 344 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.7816 (m) REVERT: C 349 SER cc_start: 0.8145 (OUTLIER) cc_final: 0.7924 (p) REVERT: C 440 THR cc_start: 0.8489 (m) cc_final: 0.7934 (p) REVERT: C 441 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7827 (mtt90) REVERT: L 92 TYR cc_start: 0.8481 (t80) cc_final: 0.8188 (t80) REVERT: M 50 MET cc_start: 0.7993 (ttp) cc_final: 0.7162 (ttp) REVERT: M 68 SER cc_start: 0.7921 (m) cc_final: 0.7471 (p) outliers start: 43 outliers final: 36 residues processed: 176 average time/residue: 0.1061 time to fit residues: 25.6517 Evaluate side-chains 185 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 9 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 82 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 ASN C 324 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.094230 restraints weight = 15186.245| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.20 r_work: 0.3002 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9529 Z= 0.124 Angle : 0.554 8.028 12961 Z= 0.292 Chirality : 0.043 0.284 1426 Planarity : 0.004 0.036 1660 Dihedral : 4.768 17.388 1291 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.47 % Allowed : 14.30 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.23), residues: 1169 helix: -2.52 (1.28), residues: 12 sheet: -0.12 (0.22), residues: 569 loop : -1.61 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 441 TYR 0.023 0.001 TYR N 92 PHE 0.014 0.002 PHE A 342 TRP 0.013 0.001 TRP B 356 HIS 0.005 0.001 HIS N 91 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9525) covalent geometry : angle 0.55430 (12953) SS BOND : bond 0.00719 ( 4) SS BOND : angle 0.80507 ( 8) hydrogen bonds : bond 0.03421 ( 230) hydrogen bonds : angle 5.51773 ( 585) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 147 time to evaluate : 0.294 Fit side-chains REVERT: A 457 ASN cc_start: 0.8391 (t0) cc_final: 0.8139 (t0) REVERT: B 34 THR cc_start: 0.8178 (m) cc_final: 0.7787 (p) REVERT: B 42 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8259 (mm-40) REVERT: B 55 ILE cc_start: 0.7875 (pt) cc_final: 0.7597 (mm) REVERT: B 265 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7720 (mmm) REVERT: B 274 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8382 (mtt180) REVERT: B 282 ILE cc_start: 0.8502 (pt) cc_final: 0.8189 (mt) REVERT: B 326 PHE cc_start: 0.8340 (m-80) cc_final: 0.8067 (m-80) REVERT: B 338 VAL cc_start: 0.8622 (t) cc_final: 0.8334 (p) REVERT: B 378 VAL cc_start: 0.8735 (p) cc_final: 0.8415 (m) REVERT: B 424 LEU cc_start: 0.7988 (tt) cc_final: 0.7656 (tp) REVERT: C 280 THR cc_start: 0.8038 (OUTLIER) cc_final: 0.7803 (p) REVERT: C 300 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7831 (m-40) REVERT: C 344 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.7814 (m) REVERT: C 349 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7916 (p) REVERT: C 440 THR cc_start: 0.8493 (m) cc_final: 0.7933 (p) REVERT: C 441 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7796 (mtt90) REVERT: L 92 TYR cc_start: 0.8487 (t80) cc_final: 0.8261 (t80) REVERT: M 50 MET cc_start: 0.7985 (ttp) cc_final: 0.7145 (ttp) REVERT: M 68 SER cc_start: 0.7917 (m) cc_final: 0.7472 (p) REVERT: N 11 MET cc_start: 0.7016 (mmm) cc_final: 0.5587 (mtp) outliers start: 46 outliers final: 38 residues processed: 173 average time/residue: 0.1015 time to fit residues: 24.0905 Evaluate side-chains 191 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN B 364 ASN ** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** 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 = 0.3320 r_free = 0.3320 target = 0.108693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.094007 restraints weight = 15088.718| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.17 r_work: 0.3001 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9529 Z= 0.166 Angle : 0.599 9.139 12961 Z= 0.316 Chirality : 0.045 0.284 1426 Planarity : 0.004 0.034 1660 Dihedral : 5.025 17.626 1291 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.47 % Allowed : 14.88 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.23), residues: 1169 helix: -2.88 (1.13), residues: 12 sheet: -0.17 (0.22), residues: 565 loop : -1.64 (0.22), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 441 TYR 0.023 0.002 TYR N 92 PHE 0.018 0.002 PHE A 342 TRP 0.014 0.001 TRP B 356 HIS 0.006 0.002 HIS N 91 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9525) covalent geometry : angle 0.59912 (12953) SS BOND : bond 0.00843 ( 4) SS BOND : angle 0.97774 ( 8) hydrogen bonds : bond 0.03755 ( 230) hydrogen bonds : angle 5.66421 ( 585) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.315 Fit side-chains REVERT: A 457 ASN cc_start: 0.8415 (t0) cc_final: 0.8166 (t0) REVERT: B 34 THR cc_start: 0.8177 (m) cc_final: 0.7788 (p) REVERT: B 42 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8309 (mm-40) REVERT: B 55 ILE cc_start: 0.7875 (pt) cc_final: 0.7632 (mm) REVERT: B 265 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7732 (mmm) REVERT: B 274 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8356 (mtt180) REVERT: B 282 ILE cc_start: 0.8506 (pt) cc_final: 0.8194 (mt) REVERT: B 338 VAL cc_start: 0.8622 (t) cc_final: 0.8334 (p) REVERT: B 378 VAL cc_start: 0.8742 (p) cc_final: 0.8421 (m) REVERT: B 424 LEU cc_start: 0.8008 (tt) cc_final: 0.7694 (tp) REVERT: C 280 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7845 (p) REVERT: C 344 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.7829 (m) REVERT: C 349 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7886 (p) REVERT: C 440 THR cc_start: 0.8480 (m) cc_final: 0.7920 (p) REVERT: C 441 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7787 (mtt90) REVERT: L 92 TYR cc_start: 0.8513 (t80) cc_final: 0.8186 (t80) REVERT: M 50 MET cc_start: 0.8008 (ttp) cc_final: 0.7177 (ttp) REVERT: M 68 SER cc_start: 0.7937 (m) cc_final: 0.7514 (p) REVERT: N 11 MET cc_start: 0.6862 (mmm) cc_final: 0.5606 (mtp) outliers start: 46 outliers final: 39 residues processed: 173 average time/residue: 0.1048 time to fit residues: 24.9872 Evaluate side-chains 189 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 70 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 108 optimal weight: 0.0170 chunk 26 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN ** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.109321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094668 restraints weight = 15083.992| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.17 r_work: 0.2998 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9529 Z= 0.136 Angle : 0.571 8.934 12961 Z= 0.301 Chirality : 0.043 0.246 1426 Planarity : 0.004 0.030 1660 Dihedral : 4.866 17.329 1291 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.28 % Allowed : 15.27 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.23), residues: 1169 helix: -2.83 (1.11), residues: 12 sheet: -0.13 (0.22), residues: 565 loop : -1.67 (0.22), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 446 TYR 0.023 0.002 TYR N 92 PHE 0.015 0.002 PHE A 342 TRP 0.013 0.001 TRP B 356 HIS 0.005 0.001 HIS N 91 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9525) covalent geometry : angle 0.57115 (12953) SS BOND : bond 0.00758 ( 4) SS BOND : angle 0.85668 ( 8) hydrogen bonds : bond 0.03528 ( 230) hydrogen bonds : angle 5.56917 ( 585) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 0.338 Fit side-chains REVERT: A 457 ASN cc_start: 0.8486 (t0) cc_final: 0.8238 (t0) REVERT: B 34 THR cc_start: 0.8175 (m) cc_final: 0.7790 (p) REVERT: B 42 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8303 (mm-40) REVERT: B 55 ILE cc_start: 0.7856 (pt) cc_final: 0.7602 (mm) REVERT: B 265 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7719 (mmm) REVERT: B 274 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8272 (mtt180) REVERT: B 282 ILE cc_start: 0.8501 (pt) cc_final: 0.8184 (mt) REVERT: B 338 VAL cc_start: 0.8616 (t) cc_final: 0.8324 (p) REVERT: B 378 VAL cc_start: 0.8740 (p) cc_final: 0.8425 (m) REVERT: B 424 LEU cc_start: 0.7991 (tt) cc_final: 0.7670 (tp) REVERT: C 280 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7819 (p) REVERT: C 335 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.7938 (t) REVERT: C 344 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.7843 (m) REVERT: C 349 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7872 (p) REVERT: C 396 VAL cc_start: 0.8285 (m) cc_final: 0.7816 (p) REVERT: C 440 THR cc_start: 0.8479 (m) cc_final: 0.7910 (p) REVERT: C 441 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7803 (mtt90) REVERT: L 92 TYR cc_start: 0.8497 (t80) cc_final: 0.8231 (t80) REVERT: M 50 MET cc_start: 0.7992 (ttp) cc_final: 0.7148 (ttp) REVERT: M 68 SER cc_start: 0.7920 (m) cc_final: 0.7494 (p) REVERT: N 11 MET cc_start: 0.6893 (mmm) cc_final: 0.5650 (mtp) outliers start: 44 outliers final: 36 residues processed: 174 average time/residue: 0.1004 time to fit residues: 24.1733 Evaluate side-chains 187 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 75 optimal weight: 0.0370 chunk 86 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.094849 restraints weight = 15036.313| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.18 r_work: 0.3030 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9529 Z= 0.107 Angle : 0.540 7.372 12961 Z= 0.284 Chirality : 0.043 0.221 1426 Planarity : 0.003 0.029 1660 Dihedral : 4.606 17.219 1291 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.79 % Allowed : 15.86 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.23), residues: 1169 helix: -2.68 (1.14), residues: 12 sheet: 0.01 (0.22), residues: 558 loop : -1.61 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 446 TYR 0.023 0.001 TYR N 92 PHE 0.013 0.001 PHE B 468 TRP 0.014 0.001 TRP B 356 HIS 0.004 0.001 HIS B 436 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9525) covalent geometry : angle 0.53976 (12953) SS BOND : bond 0.00681 ( 4) SS BOND : angle 0.76208 ( 8) hydrogen bonds : bond 0.03256 ( 230) hydrogen bonds : angle 5.41174 ( 585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2809.09 seconds wall clock time: 48 minutes 47.87 seconds (2927.87 seconds total)