Starting phenix.real_space_refine on Sat Oct 24 07:26:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wtz_66228/10_2026/9wtz_66228.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wtz_66228/10_2026/9wtz_66228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wtz_66228/10_2026/9wtz_66228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wtz_66228/10_2026/9wtz_66228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wtz_66228/10_2026/9wtz_66228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wtz_66228/10_2026/9wtz_66228.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.178 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 84 5.16 5 C 7863 2.51 5 N 2091 2.21 5 O 2403 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12441 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4091 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 14, 'TRANS': 488} Chain breaks: 1 Chain: "B" Number of atoms: 4091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4091 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 14, 'TRANS': 488} Chain breaks: 1 Chain: "C" Number of atoms: 4091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4091 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 14, 'TRANS': 488} Chain breaks: 1 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.85, per 1000 atoms: 0.23 Number of scatterers: 12441 At special positions: 0 Unit cell: (87.4, 88.35, 135.85, 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 84 16.00 O 2403 8.00 N 2091 7.00 C 7863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 393 " - pdb=" SG CYS A 403 " distance=2.04 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 436 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 403 " distance=2.04 Simple disulfide: pdb=" SG CYS B 418 " - pdb=" SG CYS B 436 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 365 " distance=2.03 Simple disulfide: pdb=" SG CYS C 393 " - pdb=" SG CYS C 403 " distance=2.04 Simple disulfide: pdb=" SG CYS C 418 " - pdb=" SG CYS C 436 " distance=2.03 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 495 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 104 " " NAG A 702 " - " ASN A 293 " " NAG A 703 " - " ASN A 361 " " NAG A 704 " - " ASN A 526 " " NAG B 701 " - " ASN B 104 " " NAG B 702 " - " ASN B 293 " " NAG B 703 " - " ASN B 361 " " NAG B 704 " - " ASN B 526 " " NAG C 701 " - " ASN C 104 " " NAG C 702 " - " ASN C 293 " " NAG C 703 " - " ASN C 361 " " NAG C 704 " - " ASN C 526 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 525.4 milliseconds 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 36.5% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 79 through 102 removed outlier: 3.563A pdb=" N PHE A 83 " --> pdb=" O HIS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 122 through 137 Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.613A pdb=" N LYS A 204 " --> pdb=" O HIS A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 211 Processing helix chain 'A' and resid 226 through 237 Processing helix chain 'A' and resid 239 through 274 removed outlier: 3.715A pdb=" N TYR A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 295 through 298 Processing helix chain 'A' and resid 309 through 320 removed outlier: 4.229A pdb=" N HIS A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 562 through 568 Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'B' and resid 79 through 102 removed outlier: 3.568A pdb=" N PHE B 83 " --> pdb=" O HIS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 122 Processing helix chain 'B' and resid 122 through 137 Processing helix chain 'B' and resid 192 through 204 removed outlier: 3.603A pdb=" N LYS B 204 " --> pdb=" O HIS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 211 Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 239 through 274 removed outlier: 3.729A pdb=" N TYR B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.506A pdb=" N MET B 313 " --> pdb=" O ASN B 309 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N HIS B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 417 through 424 Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 551 through 558 Processing helix chain 'B' and resid 562 through 568 Processing helix chain 'C' and resid 40 through 44 Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.571A pdb=" N PHE C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 122 Processing helix chain 'C' and resid 122 through 137 Processing helix chain 'C' and resid 192 through 204 removed outlier: 3.624A pdb=" N LYS C 204 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 211 Processing helix chain 'C' and resid 226 through 237 Processing helix chain 'C' and resid 239 through 274 removed outlier: 3.724A pdb=" N TYR C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 294 Processing helix chain 'C' and resid 311 through 320 removed outlier: 4.182A pdb=" N ALA C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 417 through 424 Processing helix chain 'C' and resid 431 through 436 removed outlier: 3.994A pdb=" N ASP C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 514 Processing helix chain 'C' and resid 526 through 531 Processing helix chain 'C' and resid 551 through 558 Processing helix chain 'C' and resid 562 through 568 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 50 removed outlier: 4.748A pdb=" N VAL A 484 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 77 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 77 current: chain 'A' and resid 332 through 343 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 332 through 343 current: chain 'A' and resid 374 through 378 removed outlier: 5.946A pdb=" N ASN A 383 " --> pdb=" O SER A 378 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 383 through 387 current: chain 'A' and resid 401 through 403 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 401 through 403 current: chain 'B' and resid 475 through 480 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 475 through 480 current: chain 'B' and resid 502 through 506 Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 358 removed outlier: 9.016A pdb=" N ASN A 547 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ARG A 442 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 465 through 471 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 475 through 480 current: chain 'A' and resid 502 through 506 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 502 through 506 current: chain 'C' and resid 332 through 343 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 332 through 343 current: chain 'C' and resid 374 through 378 removed outlier: 5.891A pdb=" N ASN C 383 " --> pdb=" O SER C 378 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 383 through 387 current: chain 'C' and resid 401 through 403 Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 50 removed outlier: 4.764A pdb=" N VAL B 484 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 77 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 77 current: chain 'B' and resid 332 through 343 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 332 through 343 current: chain 'B' and resid 374 through 378 removed outlier: 5.880A pdb=" N ASN B 383 " --> pdb=" O SER B 378 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 383 through 387 current: chain 'B' and resid 401 through 403 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 401 through 403 current: chain 'C' and resid 475 through 480 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 475 through 480 current: chain 'C' and resid 502 through 506 Processing sheet with id=AA7, first strand: chain 'B' and resid 357 through 358 removed outlier: 9.072A pdb=" N ASN B 547 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARG B 442 " --> pdb=" O ASN B 547 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 46 through 50 removed outlier: 4.756A pdb=" N VAL C 484 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 358 removed outlier: 9.090A pdb=" N ASN C 547 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG C 442 " --> pdb=" O ASN C 547 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4110 1.34 - 1.46: 2713 1.46 - 1.58: 5699 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 12657 Sorted by residual: bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" C1 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" C1 NAG C 704 " pdb=" O5 NAG C 704 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" C1 NAG C 702 " pdb=" O5 NAG C 702 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 ... (remaining 12652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 16331 1.20 - 2.40: 642 2.40 - 3.60: 148 3.60 - 4.79: 18 4.79 - 5.99: 9 Bond angle restraints: 17148 Sorted by residual: angle pdb=" CA CYS A 393 " pdb=" CB CYS A 393 " pdb=" SG CYS A 393 " ideal model delta sigma weight residual 114.40 119.85 -5.45 2.30e+00 1.89e-01 5.60e+00 angle pdb=" CA CYS B 393 " pdb=" CB CYS B 393 " pdb=" SG CYS B 393 " ideal model delta sigma weight residual 114.40 119.81 -5.41 2.30e+00 1.89e-01 5.54e+00 angle pdb=" C LEU C 402 " pdb=" N CYS C 403 " pdb=" CA CYS C 403 " ideal model delta sigma weight residual 123.00 119.69 3.31 1.41e+00 5.03e-01 5.50e+00 angle pdb=" C LEU B 402 " pdb=" N CYS B 403 " pdb=" CA CYS B 403 " ideal model delta sigma weight residual 123.00 119.79 3.21 1.41e+00 5.03e-01 5.18e+00 angle pdb=" N ASN C 104 " pdb=" CA ASN C 104 " pdb=" CB ASN C 104 " ideal model delta sigma weight residual 109.95 113.24 -3.29 1.55e+00 4.16e-01 4.50e+00 ... (remaining 17143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.83: 7384 22.83 - 45.65: 394 45.65 - 68.48: 59 68.48 - 91.31: 23 91.31 - 114.14: 72 Dihedral angle restraints: 7932 sinusoidal: 3429 harmonic: 4503 Sorted by residual: dihedral pdb=" CA CYS C 393 " pdb=" C CYS C 393 " pdb=" N LYS C 394 " pdb=" CA LYS C 394 " ideal model delta harmonic sigma weight residual -180.00 -158.68 -21.32 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA CYS C 403 " pdb=" C CYS C 403 " pdb=" N TYR C 404 " pdb=" CA TYR C 404 " ideal model delta harmonic sigma weight residual 180.00 -158.88 -21.12 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA CYS A 403 " pdb=" C CYS A 403 " pdb=" N TYR A 404 " pdb=" CA TYR A 404 " ideal model delta harmonic sigma weight residual -180.00 -158.93 -21.07 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 7929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1471 0.045 - 0.089: 411 0.089 - 0.133: 115 0.133 - 0.178: 14 0.178 - 0.222: 2 Chirality restraints: 2013 Sorted by residual: chirality pdb=" C1 NAG B 702 " pdb=" ND2 ASN B 293 " pdb=" C2 NAG B 702 " pdb=" O5 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 293 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" C1 NAG C 701 " pdb=" ND2 ASN C 104 " pdb=" C2 NAG C 701 " pdb=" O5 NAG C 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 2010 not shown) Planarity restraints: 2202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 104 " -0.000 2.00e-02 2.50e+03 1.77e-02 3.93e+00 pdb=" CG ASN A 104 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 104 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 104 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 104 " 0.000 2.00e-02 2.50e+03 1.73e-02 3.73e+00 pdb=" CG ASN C 104 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN C 104 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN C 104 " -0.018 2.00e-02 2.50e+03 pdb=" C1 NAG C 701 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 104 " -0.000 2.00e-02 2.50e+03 1.71e-02 3.64e+00 pdb=" CG ASN B 104 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 104 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 104 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " -0.017 2.00e-02 2.50e+03 ... (remaining 2199 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 65 2.58 - 3.16: 10076 3.16 - 3.74: 18996 3.74 - 4.32: 27797 4.32 - 4.90: 45739 Nonbonded interactions: 102673 Sorted by model distance: nonbonded pdb=" OE2 GLU C 466 " pdb=" OG SER C 477 " model vdw 2.005 3.040 nonbonded pdb=" OE2 GLU A 466 " pdb=" OG SER A 477 " model vdw 2.020 3.040 nonbonded pdb=" OE2 GLU B 466 " pdb=" OG SER B 477 " model vdw 2.020 3.040 nonbonded pdb=" NE2 GLN B 63 " pdb=" OD1 ASP B 348 " model vdw 2.243 3.120 nonbonded pdb=" NE2 GLN A 63 " pdb=" OD1 ASP A 348 " model vdw 2.244 3.120 ... (remaining 102668 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.760 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 0.004 0.052 12684 Z= 0.166 Angle : 0.599 6.780 17214 Z= 0.308 Chirality : 0.045 0.222 2013 Planarity : 0.003 0.027 2190 Dihedral : 19.020 114.136 4947 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1497 helix: 2.16 (0.24), residues: 498 sheet: 0.53 (0.26), residues: 384 loop : -1.29 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 124 TYR 0.009 0.001 TYR B 459 PHE 0.019 0.001 PHE B 260 TRP 0.005 0.001 TRP C 71 HIS 0.006 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (12657) covalent geometry : angle 0.57267 / 0.30 (17148) SS BOND : bond 0.00361 / 0.19 ( 15) SS BOND : angle 2.40061 / 1.71 ( 30) hydrogen bonds : bond 0.12309 / 7.30 ( 432) hydrogen bonds : angle 5.55390 / 3.92 ( 1200) link_NAG-ASN : bond 0.00853 / 0.55 ( 12) link_NAG-ASN : angle 3.27563 / 1.86 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 529 ARG cc_start: 0.7698 (ttt180) cc_final: 0.7299 (tmt90) REVERT: B 42 THR cc_start: 0.8689 (m) cc_final: 0.8382 (p) REVERT: B 128 GLU cc_start: 0.7215 (mt-10) cc_final: 0.7014 (mt-10) REVERT: B 313 MET cc_start: 0.8580 (mmp) cc_final: 0.8258 (mmp) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.6249 time to fit residues: 159.9430 Evaluate side-chains 185 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 HIS A 229 HIS A 479 GLN A 512 ASN B 138 HIS B 229 HIS B 246 ASN B 479 GLN B 511 ASN B 512 ASN ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS C 512 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.142772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.102900 restraints weight = 12767.997| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.86 r_work: 0.2916 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12684 Z= 0.195 Angle : 0.654 9.235 17214 Z= 0.321 Chirality : 0.047 0.235 2013 Planarity : 0.003 0.036 2190 Dihedral : 11.383 99.958 1884 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.99 % Allowed : 9.74 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1497 helix: 2.26 (0.24), residues: 495 sheet: 0.07 (0.26), residues: 414 loop : -1.07 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 276 TYR 0.013 0.001 TYR B 459 PHE 0.012 0.002 PHE A 260 TRP 0.007 0.001 TRP C 71 HIS 0.006 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.19 (12657) covalent geometry : angle 0.64312 / 0.32 (17148) SS BOND : bond 0.00304 / 0.17 ( 15) SS BOND : angle 1.43127 / 1.00 ( 30) hydrogen bonds : bond 0.04136 / 2.73 ( 432) hydrogen bonds : angle 4.75188 / 3.35 ( 1200) link_NAG-ASN : bond 0.00619 / 0.44 ( 12) link_NAG-ASN : angle 2.41975 / 1.55 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8622 (tt0) REVERT: A 382 ARG cc_start: 0.8707 (mtp180) cc_final: 0.8337 (mtp85) REVERT: A 488 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8476 (mm-30) REVERT: A 529 ARG cc_start: 0.8118 (ttt180) cc_final: 0.7719 (tmt90) REVERT: B 377 MET cc_start: 0.9231 (tpp) cc_final: 0.8994 (tpp) REVERT: B 540 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7957 (mm-30) REVERT: C 124 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7770 (mmp80) REVERT: C 246 ASN cc_start: 0.8535 (m110) cc_final: 0.8202 (m-40) REVERT: C 249 LYS cc_start: 0.8139 (tttp) cc_final: 0.7930 (tttt) REVERT: C 382 ARG cc_start: 0.8536 (mtp180) cc_final: 0.8194 (mtp85) REVERT: C 488 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8461 (mm-30) outliers start: 28 outliers final: 8 residues processed: 215 average time/residue: 0.6244 time to fit residues: 144.9505 Evaluate side-chains 188 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 524 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [13, 16, 81, 85, 78, 42, 32, 7, 61, 23, 75] chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 0.0030 chunk 61 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN B 229 HIS B 548 ASN C 138 HIS C 246 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.145437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.105064 restraints weight = 13206.928| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.05 r_work: 0.2888 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12684 Z= 0.106 Angle : 0.526 7.332 17214 Z= 0.262 Chirality : 0.042 0.163 2013 Planarity : 0.003 0.039 2190 Dihedral : 9.164 91.228 1884 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.49 % Allowed : 11.73 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.22), residues: 1497 helix: 2.37 (0.24), residues: 495 sheet: 0.34 (0.27), residues: 399 loop : -1.02 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.011 0.001 TYR A 274 PHE 0.010 0.001 PHE C 539 TRP 0.004 0.001 TRP A 71 HIS 0.004 0.001 HIS C 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (12657) covalent geometry : angle 0.50967 / 0.26 (17148) SS BOND : bond 0.00165 / 0.12 ( 15) SS BOND : angle 1.01763 / 0.81 ( 30) hydrogen bonds : bond 0.03160 / 2.07 ( 432) hydrogen bonds : angle 4.48199 / 3.17 ( 1200) link_NAG-ASN : bond 0.00722 / 0.46 ( 12) link_NAG-ASN : angle 2.74164 / 1.76 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.482 Fit side-chains REVERT: A 64 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8800 (pp-130) REVERT: A 76 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8600 (tt0) REVERT: A 124 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7336 (tpp-160) REVERT: A 488 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8458 (mm-30) REVERT: B 42 THR cc_start: 0.8502 (m) cc_final: 0.8134 (p) REVERT: B 124 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7388 (mmp80) REVERT: B 307 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: B 377 MET cc_start: 0.9165 (tpp) cc_final: 0.8952 (tpp) REVERT: B 488 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7930 (mm-30) REVERT: B 540 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7895 (mm-30) REVERT: C 124 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7644 (mmp80) REVERT: C 382 ARG cc_start: 0.8469 (mtp180) cc_final: 0.8077 (mtp85) REVERT: C 488 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8424 (mm-30) REVERT: C 529 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7489 (mtp-110) REVERT: C 532 ARG cc_start: 0.6759 (mpt180) cc_final: 0.6447 (mtt180) outliers start: 21 outliers final: 5 residues processed: 202 average time/residue: 0.6115 time to fit residues: 133.6474 Evaluate side-chains 191 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 403 CYS Chi-restraints excluded: chain B residue 405 LYS Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 498 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [1, 22, 41, 20, 52, 29, 97, 108, 17, 96, 64] chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.0570 chunk 97 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 ASN B 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.142832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.103260 restraints weight = 12883.299| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.87 r_work: 0.2899 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12684 Z= 0.135 Angle : 0.542 8.039 17214 Z= 0.271 Chirality : 0.043 0.223 2013 Planarity : 0.003 0.040 2190 Dihedral : 8.562 89.314 1884 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.56 % Allowed : 12.30 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1497 helix: 2.39 (0.24), residues: 495 sheet: 0.45 (0.26), residues: 399 loop : -1.06 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 456 TYR 0.012 0.001 TYR A 274 PHE 0.008 0.001 PHE C 260 TRP 0.006 0.001 TRP C 71 HIS 0.004 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (12657) covalent geometry : angle 0.52656 / 0.27 (17148) SS BOND : bond 0.00159 / 0.08 ( 15) SS BOND : angle 0.98642 / 0.70 ( 30) hydrogen bonds : bond 0.03399 / 2.23 ( 432) hydrogen bonds : angle 4.44084 / 3.15 ( 1200) link_NAG-ASN : bond 0.00623 / 0.42 ( 12) link_NAG-ASN : angle 2.77351 / 1.77 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8809 (pp-130) REVERT: A 124 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7552 (tpp-160) REVERT: A 466 GLU cc_start: 0.7815 (tp30) cc_final: 0.7435 (tp30) REVERT: A 488 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8452 (mm-30) REVERT: B 88 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: B 124 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7455 (mmp80) REVERT: B 307 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: B 488 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7908 (mm-30) REVERT: B 529 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7611 (ttt90) REVERT: C 124 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7753 (mmp80) REVERT: C 382 ARG cc_start: 0.8506 (mtp180) cc_final: 0.8178 (mtp85) REVERT: C 488 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8356 (mm-30) outliers start: 36 outliers final: 11 residues processed: 207 average time/residue: 0.6045 time to fit residues: 135.4205 Evaluate side-chains 197 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 405 LYS Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 524 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [35, 13, 10, 33, 15, 24, 60, 75, 4, 49, 19] chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 548 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.143748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.104440 restraints weight = 12913.342| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.86 r_work: 0.2903 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12684 Z= 0.119 Angle : 0.528 8.030 17214 Z= 0.264 Chirality : 0.042 0.163 2013 Planarity : 0.003 0.040 2190 Dihedral : 8.185 86.769 1884 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.20 % Allowed : 14.21 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.22), residues: 1497 helix: 2.36 (0.23), residues: 504 sheet: 0.71 (0.27), residues: 384 loop : -1.02 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 529 TYR 0.012 0.001 TYR B 374 PHE 0.007 0.001 PHE C 260 TRP 0.005 0.001 TRP C 71 HIS 0.004 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (12657) covalent geometry : angle 0.51296 / 0.26 (17148) SS BOND : bond 0.00148 / 0.09 ( 15) SS BOND : angle 0.97415 / 0.69 ( 30) hydrogen bonds : bond 0.03155 / 2.07 ( 432) hydrogen bonds : angle 4.36331 / 3.09 ( 1200) link_NAG-ASN : bond 0.00668 / 0.43 ( 12) link_NAG-ASN : angle 2.66043 / 1.66 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8836 (pp-130) REVERT: A 307 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: A 466 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: A 488 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8465 (mm-30) REVERT: B 42 THR cc_start: 0.8533 (m) cc_final: 0.8166 (p) REVERT: B 124 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7315 (mmp80) REVERT: B 194 ASP cc_start: 0.7638 (m-30) cc_final: 0.7348 (m-30) REVERT: B 307 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: B 466 GLU cc_start: 0.7789 (tp30) cc_final: 0.7573 (mm-30) REVERT: B 488 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: B 529 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7608 (ttt90) REVERT: C 124 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7721 (mmp80) REVERT: C 382 ARG cc_start: 0.8506 (mtp180) cc_final: 0.8168 (mtp85) REVERT: C 488 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8373 (mm-30) outliers start: 31 outliers final: 10 residues processed: 203 average time/residue: 0.6156 time to fit residues: 135.1041 Evaluate side-chains 201 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 405 LYS Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 498 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [144, 35, 68, 95, 0, 36, 94, 75, 135, 37, 123] chunk 144 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 364 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.143337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.103976 restraints weight = 12832.409| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.85 r_work: 0.2904 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12684 Z= 0.128 Angle : 0.539 8.111 17214 Z= 0.270 Chirality : 0.042 0.190 2013 Planarity : 0.003 0.039 2190 Dihedral : 7.919 82.656 1884 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.99 % Allowed : 15.14 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.22), residues: 1497 helix: 2.35 (0.23), residues: 507 sheet: 0.73 (0.27), residues: 384 loop : -1.01 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 529 TYR 0.012 0.001 TYR C 274 PHE 0.009 0.001 PHE B 539 TRP 0.005 0.001 TRP C 71 HIS 0.004 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (12657) covalent geometry : angle 0.52412 / 0.27 (17148) SS BOND : bond 0.00159 / 0.10 ( 15) SS BOND : angle 1.05842 / 0.72 ( 30) hydrogen bonds : bond 0.03258 / 2.14 ( 432) hydrogen bonds : angle 4.36106 / 3.09 ( 1200) link_NAG-ASN : bond 0.00592 / 0.41 ( 12) link_NAG-ASN : angle 2.68084 / 1.65 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8814 (pp-130) REVERT: A 307 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: A 466 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7447 (tp30) REVERT: A 488 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8472 (mm-30) REVERT: B 124 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7332 (mmp80) REVERT: B 194 ASP cc_start: 0.7654 (m-30) cc_final: 0.7355 (m-30) REVERT: B 307 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7276 (tm-30) REVERT: B 488 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7921 (mm-30) REVERT: B 529 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7612 (ttt90) REVERT: C 124 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7743 (mmp80) REVERT: C 382 ARG cc_start: 0.8513 (mtp180) cc_final: 0.8189 (mtp85) REVERT: C 488 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8386 (mm-30) REVERT: C 529 ARG cc_start: 0.7987 (mtp-110) cc_final: 0.7647 (mtp85) outliers start: 28 outliers final: 11 residues processed: 199 average time/residue: 0.6261 time to fit residues: 134.7237 Evaluate side-chains 195 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 405 LYS Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 524 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [32, 144, 101, 132, 128, 68, 66, 39, 93, 48, 47] chunk 32 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 229 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.142021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.102500 restraints weight = 12870.229| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.86 r_work: 0.2876 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12684 Z= 0.160 Angle : 0.573 8.065 17214 Z= 0.286 Chirality : 0.043 0.158 2013 Planarity : 0.003 0.040 2190 Dihedral : 7.759 77.997 1884 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.27 % Allowed : 15.28 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.22), residues: 1497 helix: 2.34 (0.24), residues: 498 sheet: 0.50 (0.27), residues: 399 loop : -0.97 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 529 TYR 0.012 0.001 TYR B 459 PHE 0.007 0.001 PHE C 260 TRP 0.007 0.001 TRP C 71 HIS 0.003 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (12657) covalent geometry : angle 0.55765 / 0.28 (17148) SS BOND : bond 0.00190 / 0.11 ( 15) SS BOND : angle 1.11484 / 0.76 ( 30) hydrogen bonds : bond 0.03681 / 2.42 ( 432) hydrogen bonds : angle 4.46636 / 3.16 ( 1200) link_NAG-ASN : bond 0.00699 / 0.45 ( 12) link_NAG-ASN : angle 2.77543 / 1.69 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9220 (ptm) cc_final: 0.8820 (pp-130) REVERT: A 128 GLU cc_start: 0.8125 (pt0) cc_final: 0.7795 (pt0) REVERT: A 307 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: A 357 MET cc_start: 0.9154 (ptt) cc_final: 0.8550 (ttp) REVERT: A 466 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: A 488 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8461 (mm-30) REVERT: B 64 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8579 (ptm) REVERT: B 124 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7365 (mmp80) REVERT: B 307 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: B 488 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7917 (mm-30) REVERT: B 529 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7608 (ttt90) REVERT: C 382 ARG cc_start: 0.8514 (mtp180) cc_final: 0.8208 (mtp85) REVERT: C 488 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8397 (mm-30) outliers start: 32 outliers final: 14 residues processed: 198 average time/residue: 0.6259 time to fit residues: 133.9917 Evaluate side-chains 199 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 405 LYS Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 524 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [106, 78, 37, 122, 41, 121, 46, 102, 33, 111, 126] chunk 106 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 111 optimal weight: 0.3980 chunk 126 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.141719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.102192 restraints weight = 12915.205| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.85 r_work: 0.2866 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12684 Z= 0.162 Angle : 0.581 8.019 17214 Z= 0.290 Chirality : 0.043 0.177 2013 Planarity : 0.003 0.040 2190 Dihedral : 7.560 73.389 1884 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.92 % Allowed : 15.85 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.22), residues: 1497 helix: 2.37 (0.24), residues: 495 sheet: 0.48 (0.26), residues: 399 loop : -1.01 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 529 TYR 0.012 0.001 TYR B 459 PHE 0.008 0.001 PHE C 260 TRP 0.007 0.001 TRP C 71 HIS 0.004 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (12657) covalent geometry : angle 0.56503 / 0.29 (17148) SS BOND : bond 0.00200 / 0.12 ( 15) SS BOND : angle 1.12657 / 0.77 ( 30) hydrogen bonds : bond 0.03728 / 2.46 ( 432) hydrogen bonds : angle 4.50840 / 3.19 ( 1200) link_NAG-ASN : bond 0.00627 / 0.43 ( 12) link_NAG-ASN : angle 2.89135 / 1.74 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9224 (ptm) cc_final: 0.8812 (pp-130) REVERT: A 128 GLU cc_start: 0.8110 (pt0) cc_final: 0.7785 (pt0) REVERT: A 307 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: A 357 MET cc_start: 0.9170 (ptt) cc_final: 0.8582 (ttp) REVERT: A 466 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7496 (tp30) REVERT: A 488 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8447 (mm-30) REVERT: A 529 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7543 (tmt90) REVERT: B 64 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8611 (ptm) REVERT: B 124 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7402 (mmp80) REVERT: B 307 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: B 488 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7843 (mm-30) REVERT: B 529 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7654 (ttt90) REVERT: C 382 ARG cc_start: 0.8534 (mtp180) cc_final: 0.8220 (mtp85) REVERT: C 488 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8381 (mm-30) outliers start: 27 outliers final: 15 residues processed: 200 average time/residue: 0.6162 time to fit residues: 133.3323 Evaluate side-chains 201 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 405 LYS Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 524 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [73, 75, 84, 147, 17, 34, 123, 15, 88, 28, 89] chunk 73 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 147 optimal weight: 0.0040 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.142352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.103548 restraints weight = 12835.356| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.82 r_work: 0.2922 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12684 Z= 0.126 Angle : 0.555 7.974 17214 Z= 0.277 Chirality : 0.042 0.213 2013 Planarity : 0.003 0.041 2190 Dihedral : 7.292 69.094 1884 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.71 % Allowed : 16.49 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.22), residues: 1497 helix: 2.27 (0.23), residues: 504 sheet: 0.72 (0.27), residues: 384 loop : -0.99 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 529 TYR 0.011 0.001 TYR B 274 PHE 0.007 0.001 PHE C 260 TRP 0.005 0.001 TRP C 71 HIS 0.003 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (12657) covalent geometry : angle 0.53728 / 0.27 (17148) SS BOND : bond 0.00170 / 0.10 ( 15) SS BOND : angle 1.04273 / 0.74 ( 30) hydrogen bonds : bond 0.03315 / 2.18 ( 432) hydrogen bonds : angle 4.44378 / 3.13 ( 1200) link_NAG-ASN : bond 0.00835 / 0.50 ( 12) link_NAG-ASN : angle 3.00414 / 1.79 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9191 (ptm) cc_final: 0.8792 (pp-130) REVERT: A 128 GLU cc_start: 0.8080 (pt0) cc_final: 0.7743 (pt0) REVERT: A 307 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: A 466 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: A 488 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8402 (mm-30) REVERT: A 529 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7504 (tmt90) REVERT: B 64 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8631 (ptm) REVERT: B 124 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7361 (mmp80) REVERT: B 307 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: B 488 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7823 (mm-30) REVERT: B 529 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7628 (ttt90) REVERT: C 382 ARG cc_start: 0.8493 (mtp180) cc_final: 0.8192 (mtp85) REVERT: C 488 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8315 (mm-30) outliers start: 24 outliers final: 14 residues processed: 196 average time/residue: 0.6285 time to fit residues: 133.1761 Evaluate side-chains 201 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 405 LYS Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 524 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [148, 126, 95, 115, 87, 127, 64, 112, 27, 77, 113] chunk 148 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 77 optimal weight: 0.0980 chunk 113 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.143326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.104484 restraints weight = 12831.424| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.83 r_work: 0.2930 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12684 Z= 0.118 Angle : 0.555 7.800 17214 Z= 0.276 Chirality : 0.042 0.201 2013 Planarity : 0.003 0.041 2190 Dihedral : 6.990 63.061 1884 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.78 % Allowed : 16.35 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.22), residues: 1497 helix: 2.27 (0.23), residues: 504 sheet: 0.77 (0.27), residues: 384 loop : -0.99 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 529 TYR 0.015 0.001 TYR B 374 PHE 0.006 0.001 PHE B 260 TRP 0.005 0.001 TRP A 99 HIS 0.004 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (12657) covalent geometry : angle 0.53503 / 0.27 (17148) SS BOND : bond 0.00169 / 0.10 ( 15) SS BOND : angle 1.00392 / 0.71 ( 30) hydrogen bonds : bond 0.03154 / 2.07 ( 432) hydrogen bonds : angle 4.39925 / 3.10 ( 1200) link_NAG-ASN : bond 0.00870 / 0.51 ( 12) link_NAG-ASN : angle 3.21315 / 1.91 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8797 (pp-130) REVERT: A 292 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7153 (ttm170) REVERT: A 307 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: A 357 MET cc_start: 0.9127 (ptt) cc_final: 0.8508 (ttp) REVERT: A 466 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7477 (tp30) REVERT: A 488 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8416 (mm-30) REVERT: A 529 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7455 (tmt90) REVERT: B 64 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8620 (ptm) REVERT: B 124 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7324 (mmp80) REVERT: B 307 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: B 488 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7804 (mm-30) REVERT: C 117 ASP cc_start: 0.8953 (m-30) cc_final: 0.8662 (m-30) REVERT: C 382 ARG cc_start: 0.8463 (mtp180) cc_final: 0.8163 (mtp85) REVERT: C 529 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.7661 (mtp85) outliers start: 25 outliers final: 16 residues processed: 196 average time/residue: 0.6105 time to fit residues: 129.1966 Evaluate side-chains 199 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 405 LYS Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 524 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: [34, 73, 68, 123, 108, 29, 2, 55, 51, 39, 23] chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.146657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.106179 restraints weight = 12268.139| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.91 r_work: 0.2874 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12684 Z= 0.109 Angle : 0.545 7.461 17214 Z= 0.270 Chirality : 0.042 0.178 2013 Planarity : 0.003 0.040 2190 Dihedral : 6.589 58.485 1884 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.71 % Allowed : 16.92 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.22), residues: 1497 helix: 2.26 (0.23), residues: 501 sheet: 0.77 (0.27), residues: 384 loop : -0.96 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 529 TYR 0.015 0.001 TYR B 374 PHE 0.005 0.001 PHE C 260 TRP 0.005 0.001 TRP A 71 HIS 0.003 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (12657) covalent geometry : angle 0.52195 / 0.27 (17148) SS BOND : bond 0.00158 / 0.09 ( 15) SS BOND : angle 0.97823 / 0.70 ( 30) hydrogen bonds : bond 0.02979 / 1.96 ( 432) hydrogen bonds : angle 4.35687 / 3.07 ( 1200) link_NAG-ASN : bond 0.00823 / 0.49 ( 12) link_NAG-ASN : angle 3.34771 / 1.99 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4228.22 seconds wall clock time: 72 minutes 45.49 seconds (4365.49 seconds total)