Starting phenix.real_space_refine on Mon May 12 21:27:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygs_39261/05_2025/8ygs_39261_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygs_39261/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ygs_39261/05_2025/8ygs_39261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygs_39261/05_2025/8ygs_39261.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygs_39261/05_2025/8ygs_39261_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygs_39261/05_2025/8ygs_39261_neut.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.01, per 1000 atoms: 0.65 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: 2.13 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.04 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: 2.47 Time building geometry restraints manager: 2.57 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: 2.900 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.630 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (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 TRP 0.026 0.002 TRP B 356 HIS 0.013 0.003 HIS A 436 PHE 0.031 0.003 PHE A 437 TYR 0.022 0.002 TYR C 355 ARG 0.007 0.001 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.21547 ( 230) hydrogen bonds : angle 8.40341 ( 585) SS BOND : bond 0.17519 ( 4) SS BOND : angle 11.47473 ( 8) covalent geometry : bond 0.01063 ( 9525) covalent geometry : angle 1.47078 (12953) *********************** 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 : 1.079 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: 0.1708 time to fit residues: 65.3921 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 : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 0.0670 chunk 59 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN B 300 ASN B 376 ASN B 454 ASN C 324 ASN H 53 ASN H 98 ASN L 6 GLN ** 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 = 0.3443 r_free = 0.3443 target = 0.116479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102217 restraints weight = 15125.550| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.13 r_work: 0.3157 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9529 Z= 0.130 Angle : 0.625 7.436 12961 Z= 0.333 Chirality : 0.046 0.167 1426 Planarity : 0.004 0.045 1660 Dihedral : 5.214 21.308 1291 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.53 % Allowed : 6.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.22), residues: 1169 helix: -4.10 (0.72), residues: 12 sheet: -0.99 (0.22), residues: 530 loop : -2.27 (0.20), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 356 HIS 0.005 0.002 HIS B 436 PHE 0.023 0.002 PHE M 27 TYR 0.021 0.001 TYR L 92 ARG 0.008 0.001 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 230) hydrogen bonds : angle 6.37103 ( 585) SS BOND : bond 0.00920 ( 4) SS BOND : angle 1.52225 ( 8) covalent geometry : bond 0.00290 ( 9525) covalent geometry : angle 0.62375 (12953) *********************** 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 242 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 49 ASN cc_start: 0.7969 (t0) cc_final: 0.7754 (t0) REVERT: A 254 ILE cc_start: 0.8459 (mm) cc_final: 0.8250 (mm) REVERT: A 256 ILE cc_start: 0.8227 (tt) cc_final: 0.8012 (pt) REVERT: A 316 THR cc_start: 0.8405 (p) cc_final: 0.8048 (m) REVERT: A 323 VAL cc_start: 0.8727 (p) cc_final: 0.8428 (m) REVERT: A 369 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7665 (ttt90) REVERT: A 474 VAL cc_start: 0.7667 (t) cc_final: 0.7292 (m) REVERT: B 55 ILE cc_start: 0.7779 (pt) cc_final: 0.7356 (mm) REVERT: B 257 SER cc_start: 0.8189 (m) cc_final: 0.7591 (p) REVERT: B 265 MET cc_start: 0.8268 (mtp) cc_final: 0.7990 (mtp) REVERT: B 282 ILE cc_start: 0.8417 (pt) cc_final: 0.8044 (mt) REVERT: B 326 PHE cc_start: 0.8237 (m-80) cc_final: 0.7884 (m-80) REVERT: B 338 VAL cc_start: 0.8600 (t) cc_final: 0.8252 (p) REVERT: B 378 VAL cc_start: 0.8778 (p) cc_final: 0.8391 (m) REVERT: B 421 LEU cc_start: 0.7617 (tt) cc_final: 0.7405 (tp) REVERT: C 303 TYR cc_start: 0.8340 (p90) cc_final: 0.7886 (p90) REVERT: C 305 TYR cc_start: 0.8476 (p90) cc_final: 0.8156 (p90) REVERT: C 307 ARG cc_start: 0.8208 (ttp-170) cc_final: 0.7877 (tmm160) REVERT: C 344 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7692 (m) REVERT: C 355 TYR cc_start: 0.8206 (t80) cc_final: 0.7606 (t80) REVERT: C 376 ASN cc_start: 0.7817 (m110) cc_final: 0.7514 (m-40) REVERT: C 391 VAL cc_start: 0.7819 (t) cc_final: 0.7608 (p) REVERT: C 432 VAL cc_start: 0.8044 (p) cc_final: 0.7695 (m) REVERT: L 52 SER cc_start: 0.8230 (p) cc_final: 0.7933 (m) REVERT: M 33 SER cc_start: 0.8119 (p) cc_final: 0.7713 (t) outliers start: 26 outliers final: 22 residues processed: 230 average time/residue: 0.2032 time to fit residues: 64.5312 Evaluate side-chains 205 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 402 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 317 THR 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 10 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN C 456 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN 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 = 0.108503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.094160 restraints weight = 15201.443| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.07 r_work: 0.2985 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 9529 Z= 0.281 Angle : 0.754 8.602 12961 Z= 0.401 Chirality : 0.050 0.175 1426 Planarity : 0.005 0.039 1660 Dihedral : 6.002 21.707 1291 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.18 % Allowed : 10.60 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.22), residues: 1169 helix: -3.56 (1.15), residues: 12 sheet: -0.77 (0.21), residues: 539 loop : -2.31 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 356 HIS 0.011 0.003 HIS N 91 PHE 0.024 0.003 PHE B 428 TYR 0.028 0.003 TYR M 94 ARG 0.005 0.001 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.04930 ( 230) hydrogen bonds : angle 6.31520 ( 585) SS BOND : bond 0.00822 ( 4) SS BOND : angle 1.85163 ( 8) covalent geometry : bond 0.00678 ( 9525) covalent geometry : angle 0.75267 (12953) *********************** 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 208 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 1.003 Fit side-chains REVERT: B 257 SER cc_start: 0.8337 (m) cc_final: 0.7768 (p) REVERT: B 260 SER cc_start: 0.8177 (p) cc_final: 0.7964 (m) REVERT: B 282 ILE cc_start: 0.8417 (pt) cc_final: 0.8101 (mt) REVERT: B 338 VAL cc_start: 0.8645 (t) cc_final: 0.8397 (p) REVERT: B 378 VAL cc_start: 0.8786 (p) cc_final: 0.8439 (m) REVERT: B 424 LEU cc_start: 0.7934 (tt) cc_final: 0.7628 (tp) REVERT: C 274 ARG cc_start: 0.8270 (mtt180) cc_final: 0.7924 (mtt180) REVERT: C 280 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7770 (p) REVERT: C 305 TYR cc_start: 0.8510 (p90) cc_final: 0.8169 (p90) REVERT: C 344 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.7730 (m) REVERT: C 349 SER cc_start: 0.8160 (OUTLIER) cc_final: 0.7935 (p) REVERT: C 440 THR cc_start: 0.8452 (m) cc_final: 0.7919 (p) REVERT: C 441 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7701 (mtt90) REVERT: M 50 MET cc_start: 0.8018 (ttp) cc_final: 0.7372 (ttp) REVERT: M 68 SER cc_start: 0.7940 (m) cc_final: 0.7478 (p) REVERT: N 5 THR cc_start: 0.7876 (OUTLIER) cc_final: 0.7502 (m) outliers start: 43 outliers final: 33 residues processed: 193 average time/residue: 0.2125 time to fit residues: 57.2811 Evaluate side-chains 181 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 280 THR Chi-restraints excluded: chain B residue 311 GLU 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 316 THR Chi-restraints excluded: chain C residue 338 VAL 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 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 58 ASP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 93 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 5 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 88 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN C 324 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN ** 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 = 0.3336 r_free = 0.3336 target = 0.109504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094944 restraints weight = 15129.438| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.13 r_work: 0.2996 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4186 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= 0.180 Angle : 0.629 8.825 12961 Z= 0.335 Chirality : 0.046 0.176 1426 Planarity : 0.004 0.036 1660 Dihedral : 5.471 19.843 1291 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.67 % Allowed : 12.06 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.22), residues: 1169 helix: -3.42 (1.04), residues: 12 sheet: -0.39 (0.22), residues: 550 loop : -2.11 (0.20), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 356 HIS 0.007 0.002 HIS N 91 PHE 0.020 0.002 PHE H 27 TYR 0.017 0.002 TYR B 355 ARG 0.005 0.001 ARG C 446 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 230) hydrogen bonds : angle 5.98807 ( 585) SS BOND : bond 0.00861 ( 4) SS BOND : angle 1.14612 ( 8) covalent geometry : bond 0.00426 ( 9525) covalent geometry : angle 0.62897 (12953) *********************** 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 204 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: B 257 SER cc_start: 0.8344 (m) cc_final: 0.7804 (p) REVERT: B 260 SER cc_start: 0.8158 (p) cc_final: 0.7932 (m) REVERT: B 265 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7807 (mmm) REVERT: B 268 ASN cc_start: 0.7759 (t0) cc_final: 0.7461 (m-40) REVERT: B 282 ILE cc_start: 0.8457 (pt) cc_final: 0.8113 (mt) REVERT: B 338 VAL cc_start: 0.8619 (t) cc_final: 0.8348 (p) REVERT: B 378 VAL cc_start: 0.8769 (p) cc_final: 0.8445 (m) REVERT: B 424 LEU cc_start: 0.7949 (tt) cc_final: 0.7642 (tp) REVERT: C 274 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7949 (mtt180) REVERT: C 280 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7789 (p) REVERT: C 305 TYR cc_start: 0.8479 (p90) cc_final: 0.8137 (p90) REVERT: C 344 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.7773 (m) REVERT: C 349 SER cc_start: 0.8146 (OUTLIER) cc_final: 0.7893 (p) REVERT: C 440 THR cc_start: 0.8477 (m) cc_final: 0.7944 (p) REVERT: C 441 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7793 (mtt90) REVERT: M 50 MET cc_start: 0.8055 (ttp) cc_final: 0.7230 (ttp) REVERT: M 68 SER cc_start: 0.7928 (m) cc_final: 0.7473 (p) outliers start: 48 outliers final: 35 residues processed: 183 average time/residue: 0.2179 time to fit residues: 55.4210 Evaluate side-chains 192 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 349 SER Chi-restraints excluded: chain A residue 364 ASN 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 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 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 434 GLU 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 L residue 22 THR Chi-restraints excluded: chain L residue 52 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 78 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 0.0170 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS A 386 ASN B 364 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 = 0.3380 r_free = 0.3380 target = 0.112495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097890 restraints weight = 15057.515| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.14 r_work: 0.3042 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9529 Z= 0.091 Angle : 0.528 6.384 12961 Z= 0.280 Chirality : 0.043 0.152 1426 Planarity : 0.003 0.031 1660 Dihedral : 4.750 18.216 1291 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.50 % Allowed : 13.91 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.23), residues: 1169 helix: -2.58 (1.24), residues: 12 sheet: -0.18 (0.22), residues: 551 loop : -1.78 (0.21), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 356 HIS 0.004 0.001 HIS B 436 PHE 0.013 0.001 PHE H 79 TYR 0.018 0.001 TYR A 305 ARG 0.003 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 230) hydrogen bonds : angle 5.49601 ( 585) SS BOND : bond 0.00708 ( 4) SS BOND : angle 0.71523 ( 8) covalent geometry : bond 0.00196 ( 9525) covalent geometry : angle 0.52810 (12953) *********************** 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 188 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.907 Fit side-chains REVERT: A 55 ILE cc_start: 0.7754 (mm) cc_final: 0.7527 (mm) REVERT: A 457 ASN cc_start: 0.8275 (t0) cc_final: 0.8039 (t0) REVERT: B 42 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8249 (mm-40) REVERT: B 257 SER cc_start: 0.8321 (m) cc_final: 0.7800 (p) REVERT: B 260 SER cc_start: 0.8248 (p) cc_final: 0.7942 (m) REVERT: B 265 MET cc_start: 0.8001 (mmm) cc_final: 0.7744 (mmm) REVERT: B 282 ILE cc_start: 0.8475 (pt) cc_final: 0.8115 (mt) REVERT: B 326 PHE cc_start: 0.8287 (m-80) cc_final: 0.7960 (m-80) REVERT: B 338 VAL cc_start: 0.8623 (t) cc_final: 0.8323 (p) REVERT: B 378 VAL cc_start: 0.8725 (p) cc_final: 0.8421 (m) REVERT: B 424 LEU cc_start: 0.7891 (tt) cc_final: 0.7580 (tp) REVERT: C 274 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7921 (mtt180) REVERT: C 305 TYR cc_start: 0.8416 (p90) cc_final: 0.8054 (p90) REVERT: C 344 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.7765 (m) REVERT: C 355 TYR cc_start: 0.8198 (t80) cc_final: 0.7697 (t80) REVERT: C 440 THR cc_start: 0.8492 (m) cc_final: 0.7925 (p) REVERT: C 441 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7794 (mtt90) REVERT: M 50 MET cc_start: 0.7995 (ttp) cc_final: 0.7181 (ttp) REVERT: M 68 SER cc_start: 0.7911 (m) cc_final: 0.7458 (p) outliers start: 36 outliers final: 31 residues processed: 176 average time/residue: 0.2154 time to fit residues: 52.1641 Evaluate side-chains 185 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 349 SER Chi-restraints excluded: chain A residue 358 ASP 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 447 LEU Chi-restraints excluded: chain B residue 456 ASN 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 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 L residue 49 SER Chi-restraints excluded: chain L residue 52 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 49 SER 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 106 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 107 optimal weight: 0.0470 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 ASN B 364 ASN C 324 ASN L 42 GLN ** 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 = 0.3370 r_free = 0.3370 target = 0.111579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.096900 restraints weight = 15058.324| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.13 r_work: 0.3033 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9529 Z= 0.102 Angle : 0.532 6.436 12961 Z= 0.281 Chirality : 0.042 0.149 1426 Planarity : 0.004 0.043 1660 Dihedral : 4.655 17.921 1291 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.89 % Allowed : 13.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.23), residues: 1169 helix: -2.38 (1.32), residues: 12 sheet: -0.15 (0.22), residues: 551 loop : -1.57 (0.22), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 356 HIS 0.004 0.001 HIS B 436 PHE 0.022 0.001 PHE H 27 TYR 0.014 0.001 TYR A 301 ARG 0.010 0.001 ARG A 441 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 230) hydrogen bonds : angle 5.34860 ( 585) SS BOND : bond 0.00797 ( 4) SS BOND : angle 1.07047 ( 8) covalent geometry : bond 0.00228 ( 9525) covalent geometry : angle 0.53182 (12953) *********************** 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 180 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.955 Fit side-chains REVERT: A 457 ASN cc_start: 0.8361 (t0) cc_final: 0.8114 (t0) REVERT: B 55 ILE cc_start: 0.7867 (pt) cc_final: 0.7637 (mm) REVERT: B 257 SER cc_start: 0.8334 (m) cc_final: 0.7818 (p) REVERT: B 260 SER cc_start: 0.8238 (p) cc_final: 0.7925 (m) REVERT: B 265 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7765 (mmm) REVERT: B 274 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8350 (mtt180) REVERT: B 282 ILE cc_start: 0.8458 (pt) cc_final: 0.8118 (mt) REVERT: B 326 PHE cc_start: 0.8327 (m-80) cc_final: 0.8061 (m-80) REVERT: B 338 VAL cc_start: 0.8613 (t) cc_final: 0.8344 (p) REVERT: B 378 VAL cc_start: 0.8724 (p) cc_final: 0.8423 (m) REVERT: B 424 LEU cc_start: 0.7904 (tt) cc_final: 0.7603 (tp) REVERT: C 344 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.7749 (m) REVERT: C 349 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7931 (p) REVERT: C 441 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7850 (mtt90) REVERT: H 27 PHE cc_start: 0.8014 (p90) cc_final: 0.7766 (p90) REVERT: M 50 MET cc_start: 0.8011 (ttp) cc_final: 0.7169 (ttp) REVERT: M 68 SER cc_start: 0.7897 (m) cc_final: 0.7456 (p) outliers start: 40 outliers final: 34 residues processed: 166 average time/residue: 0.2418 time to fit residues: 55.3827 Evaluate side-chains 177 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 260 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 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 311 GLU 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093084 restraints weight = 15236.388| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.21 r_work: 0.2994 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9529 Z= 0.153 Angle : 0.590 8.468 12961 Z= 0.311 Chirality : 0.044 0.153 1426 Planarity : 0.004 0.038 1660 Dihedral : 4.988 17.379 1291 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.57 % Allowed : 13.72 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.23), residues: 1169 helix: -2.65 (1.27), residues: 12 sheet: -0.24 (0.22), residues: 543 loop : -1.63 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 356 HIS 0.006 0.002 HIS N 91 PHE 0.018 0.002 PHE B 468 TYR 0.018 0.002 TYR A 305 ARG 0.008 0.001 ARG A 441 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 230) hydrogen bonds : angle 5.57462 ( 585) SS BOND : bond 0.00913 ( 4) SS BOND : angle 1.36848 ( 8) covalent geometry : bond 0.00359 ( 9525) covalent geometry : angle 0.58887 (12953) *********************** 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 186 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 1.028 Fit side-chains REVERT: A 457 ASN cc_start: 0.8387 (t0) cc_final: 0.8128 (t0) REVERT: B 34 THR cc_start: 0.8180 (m) cc_final: 0.7795 (p) REVERT: B 55 ILE cc_start: 0.7873 (pt) cc_final: 0.7595 (mm) REVERT: B 260 SER cc_start: 0.8177 (p) cc_final: 0.7903 (m) REVERT: B 265 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7801 (mmm) REVERT: B 274 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8378 (mtt180) REVERT: B 282 ILE cc_start: 0.8485 (pt) cc_final: 0.8171 (mt) REVERT: B 338 VAL cc_start: 0.8627 (t) cc_final: 0.8349 (p) REVERT: B 378 VAL cc_start: 0.8764 (p) cc_final: 0.8446 (m) REVERT: B 424 LEU cc_start: 0.7984 (tt) cc_final: 0.7665 (tp) REVERT: C 274 ARG cc_start: 0.8283 (mtt180) cc_final: 0.7982 (mtt180) REVERT: C 305 TYR cc_start: 0.8467 (p90) cc_final: 0.8122 (p90) REVERT: C 344 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.7819 (m) REVERT: C 349 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7927 (p) REVERT: H 27 PHE cc_start: 0.8065 (p90) cc_final: 0.7735 (p90) REVERT: M 50 MET cc_start: 0.8022 (ttp) cc_final: 0.7349 (ttp) REVERT: M 68 SER cc_start: 0.7895 (m) cc_final: 0.7467 (p) REVERT: N 11 MET cc_start: 0.6966 (mmm) cc_final: 0.5506 (mtt) outliers start: 47 outliers final: 38 residues processed: 171 average time/residue: 0.2235 time to fit residues: 52.5525 Evaluate side-chains 176 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 260 SER 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 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 470 LEU 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 45 LEU 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 112 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 0.0980 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 ASN B 364 ASN N 79 GLN ** 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 = 0.3290 r_free = 0.3290 target = 0.106800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.091972 restraints weight = 15473.390| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.22 r_work: 0.2959 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9529 Z= 0.224 Angle : 0.659 12.097 12961 Z= 0.347 Chirality : 0.046 0.153 1426 Planarity : 0.004 0.034 1660 Dihedral : 5.454 18.704 1291 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.47 % Allowed : 14.01 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.23), residues: 1169 helix: -3.35 (1.53), residues: 6 sheet: -0.35 (0.21), residues: 578 loop : -1.80 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 356 HIS 0.008 0.002 HIS N 91 PHE 0.023 0.002 PHE A 342 TYR 0.017 0.002 TYR M 94 ARG 0.008 0.001 ARG A 441 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 230) hydrogen bonds : angle 5.86552 ( 585) SS BOND : bond 0.00993 ( 4) SS BOND : angle 1.56905 ( 8) covalent geometry : bond 0.00535 ( 9525) covalent geometry : angle 0.65769 (12953) *********************** 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 192 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 1.029 Fit side-chains REVERT: A 56 ASN cc_start: 0.7394 (t0) cc_final: 0.7191 (t0) REVERT: A 61 VAL cc_start: 0.8455 (t) cc_final: 0.8207 (m) REVERT: A 290 LYS cc_start: 0.8514 (ptpt) cc_final: 0.8290 (ptmt) REVERT: A 457 ASN cc_start: 0.8412 (t0) cc_final: 0.8165 (t0) REVERT: B 34 THR cc_start: 0.8188 (m) cc_final: 0.7782 (p) REVERT: B 55 ILE cc_start: 0.7809 (pt) cc_final: 0.7597 (mm) REVERT: B 260 SER cc_start: 0.8167 (p) cc_final: 0.7923 (m) REVERT: B 265 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7857 (mmm) REVERT: B 274 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8365 (mtt180) REVERT: B 282 ILE cc_start: 0.8503 (pt) cc_final: 0.8200 (mt) REVERT: B 338 VAL cc_start: 0.8627 (t) cc_final: 0.8330 (p) REVERT: B 378 VAL cc_start: 0.8765 (p) cc_final: 0.8443 (m) REVERT: B 424 LEU cc_start: 0.8011 (tt) cc_final: 0.7684 (tp) REVERT: C 274 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7975 (mtt180) REVERT: C 344 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.7847 (m) REVERT: C 349 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7849 (p) REVERT: H 27 PHE cc_start: 0.8103 (p90) cc_final: 0.7822 (p90) REVERT: M 68 SER cc_start: 0.7913 (m) cc_final: 0.7473 (p) REVERT: N 11 MET cc_start: 0.6856 (mmm) cc_final: 0.5726 (mtp) outliers start: 46 outliers final: 39 residues processed: 176 average time/residue: 0.2198 time to fit residues: 53.2416 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 : 0.896 ------------------------------------------------------------------------------- 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 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 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 348 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 423 SER 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 H residue 112 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093103 restraints weight = 15127.479| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.20 r_work: 0.3000 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- 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 = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4916 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= 0.134 Angle : 0.576 9.108 12961 Z= 0.304 Chirality : 0.043 0.153 1426 Planarity : 0.004 0.047 1660 Dihedral : 5.046 21.113 1291 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.09 % Allowed : 14.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.23), residues: 1169 helix: -2.97 (1.66), residues: 6 sheet: -0.25 (0.22), residues: 550 loop : -1.72 (0.21), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 356 HIS 0.005 0.002 HIS N 91 PHE 0.016 0.002 PHE B 468 TYR 0.015 0.001 TYR A 301 ARG 0.008 0.001 ARG A 441 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 230) hydrogen bonds : angle 5.62731 ( 585) SS BOND : bond 0.00781 ( 4) SS BOND : angle 1.10043 ( 8) covalent geometry : bond 0.00312 ( 9525) covalent geometry : angle 0.57603 (12953) *********************** 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 190 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 1.027 Fit side-chains REVERT: A 56 ASN cc_start: 0.7342 (t0) cc_final: 0.7127 (t0) REVERT: A 61 VAL cc_start: 0.8420 (t) cc_final: 0.8197 (m) REVERT: A 447 LEU cc_start: 0.7673 (mt) cc_final: 0.7454 (mt) REVERT: A 457 ASN cc_start: 0.8476 (t0) cc_final: 0.8202 (t0) REVERT: B 34 THR cc_start: 0.8171 (m) cc_final: 0.7783 (p) REVERT: B 55 ILE cc_start: 0.7813 (pt) cc_final: 0.7554 (mm) REVERT: B 265 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7738 (mmm) REVERT: B 274 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8256 (mtt180) REVERT: B 282 ILE cc_start: 0.8483 (pt) cc_final: 0.8161 (mt) REVERT: B 338 VAL cc_start: 0.8615 (t) cc_final: 0.8322 (p) REVERT: B 378 VAL cc_start: 0.8734 (p) cc_final: 0.8422 (m) REVERT: B 424 LEU cc_start: 0.7979 (tt) cc_final: 0.7642 (tp) REVERT: C 274 ARG cc_start: 0.8237 (mtt180) cc_final: 0.7923 (mtt180) REVERT: C 307 ARG cc_start: 0.8210 (ttp-170) cc_final: 0.7797 (tmm160) REVERT: C 344 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.7831 (m) REVERT: C 349 SER cc_start: 0.8112 (OUTLIER) cc_final: 0.7878 (p) REVERT: H 27 PHE cc_start: 0.8088 (p90) cc_final: 0.7808 (p90) REVERT: M 50 MET cc_start: 0.8018 (ttp) cc_final: 0.7170 (ttp) REVERT: M 68 SER cc_start: 0.7891 (m) cc_final: 0.7444 (p) REVERT: N 11 MET cc_start: 0.6839 (mmm) cc_final: 0.5736 (mtp) outliers start: 42 outliers final: 37 residues processed: 177 average time/residue: 0.2205 time to fit residues: 53.7413 Evaluate side-chains 187 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 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 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 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 H residue 112 THR 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 70 SER Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain N residue 49 SER 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: 1.9990 chunk 61 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 0.0020 chunk 109 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.093757 restraints weight = 15188.876| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.15 r_work: 0.2968 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9529 Z= 0.239 Angle : 0.676 12.137 12961 Z= 0.356 Chirality : 0.046 0.158 1426 Planarity : 0.004 0.059 1660 Dihedral : 5.577 21.761 1291 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.77 % Allowed : 14.30 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.23), residues: 1169 helix: -3.58 (1.32), residues: 6 sheet: -0.34 (0.22), residues: 568 loop : -1.88 (0.22), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 262 HIS 0.008 0.002 HIS N 91 PHE 0.024 0.002 PHE A 342 TYR 0.019 0.002 TYR A 301 ARG 0.010 0.001 ARG C 441 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 230) hydrogen bonds : angle 5.91663 ( 585) SS BOND : bond 0.01014 ( 4) SS BOND : angle 1.58482 ( 8) covalent geometry : bond 0.00575 ( 9525) covalent geometry : angle 0.67537 (12953) ********************** 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 191 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 1.022 Fit side-chains REVERT: A 56 ASN cc_start: 0.7422 (t0) cc_final: 0.7175 (t0) REVERT: A 61 VAL cc_start: 0.8500 (t) cc_final: 0.8270 (m) REVERT: A 457 ASN cc_start: 0.8419 (t0) cc_final: 0.8178 (t0) REVERT: B 55 ILE cc_start: 0.7823 (pt) cc_final: 0.7581 (mm) REVERT: B 265 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7833 (mmm) REVERT: B 274 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8373 (mtt180) REVERT: B 282 ILE cc_start: 0.8485 (pt) cc_final: 0.8192 (mt) REVERT: B 338 VAL cc_start: 0.8599 (t) cc_final: 0.8286 (p) REVERT: B 370 SER cc_start: 0.8366 (t) cc_final: 0.8090 (m) REVERT: B 378 VAL cc_start: 0.8783 (p) cc_final: 0.8464 (m) REVERT: B 424 LEU cc_start: 0.8026 (tt) cc_final: 0.7703 (tp) REVERT: C 344 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.7874 (m) REVERT: C 349 SER cc_start: 0.8095 (OUTLIER) cc_final: 0.7842 (p) REVERT: C 470 LEU cc_start: 0.8280 (tt) cc_final: 0.8071 (tp) REVERT: H 27 PHE cc_start: 0.8093 (p90) cc_final: 0.7852 (p90) REVERT: M 50 MET cc_start: 0.8020 (ttp) cc_final: 0.7251 (ttp) REVERT: M 68 SER cc_start: 0.7886 (m) cc_final: 0.7463 (p) REVERT: N 11 MET cc_start: 0.6991 (mmm) cc_final: 0.5982 (mtp) outliers start: 49 outliers final: 43 residues processed: 176 average time/residue: 0.2185 time to fit residues: 53.1818 Evaluate side-chains 188 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 317 THR Chi-restraints excluded: chain A residue 327 SER 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 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 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 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 H residue 112 THR 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 49 SER 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 32 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 ASN ** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092264 restraints weight = 15250.016| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.22 r_work: 0.2982 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9529 Z= 0.187 Angle : 0.625 10.371 12961 Z= 0.330 Chirality : 0.045 0.154 1426 Planarity : 0.004 0.052 1660 Dihedral : 5.366 21.378 1291 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.28 % Allowed : 14.98 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.23), residues: 1169 helix: -3.63 (1.30), residues: 6 sheet: -0.38 (0.22), residues: 552 loop : -1.81 (0.22), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 356 HIS 0.007 0.002 HIS N 91 PHE 0.020 0.002 PHE A 342 TYR 0.024 0.002 TYR B 461 ARG 0.009 0.001 ARG C 441 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 230) hydrogen bonds : angle 5.78771 ( 585) SS BOND : bond 0.00879 ( 4) SS BOND : angle 1.30928 ( 8) covalent geometry : bond 0.00446 ( 9525) covalent geometry : angle 0.62405 (12953) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5101.66 seconds wall clock time: 89 minutes 16.11 seconds (5356.11 seconds total)