Starting phenix.real_space_refine on Thu Mar 5 14:03:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wxb_21954/03_2026/6wxb_21954_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wxb_21954/03_2026/6wxb_21954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wxb_21954/03_2026/6wxb_21954_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wxb_21954/03_2026/6wxb_21954_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wxb_21954/03_2026/6wxb_21954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wxb_21954/03_2026/6wxb_21954.map" } resolution = 2.9 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= -0.001 sd= 0.298 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: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 7251 2.51 5 N 2025 2.21 5 O 2316 1.98 5 H 11049 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22698 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7499 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "B" Number of atoms: 7499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7499 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 7499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7499 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.24, per 1000 atoms: 0.14 Number of scatterers: 22698 At special positions: 0 Unit cell: (83.43, 85.49, 145.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 2316 8.00 N 2025 7.00 C 7251 6.00 H 11049 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 285 " " NAG A 602 " - " ASN A 165 " " NAG A 603 " - " ASN A 81 " " NAG B 601 " - " ASN B 285 " " NAG B 602 " - " ASN B 165 " " NAG B 603 " - " ASN B 81 " " NAG C 603 " - " ASN C 285 " " NAG C 604 " - " ASN C 165 " " NAG C 605 " - " ASN C 81 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 716.7 milliseconds 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 27.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.787A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 366 through 379 removed outlier: 4.344A pdb=" N GLY A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 404 through 455 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 487 through 490 removed outlier: 3.656A pdb=" N VAL A 490 " --> pdb=" O ASP A 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 487 through 490' Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.703A pdb=" N ASN A 497 " --> pdb=" O ASP A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 4.787A pdb=" N VAL B 78 " --> pdb=" O HIS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 366 through 379 removed outlier: 4.344A pdb=" N GLY B 379 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 404 through 455 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 487 through 490 removed outlier: 3.657A pdb=" N VAL B 490 " --> pdb=" O ASP B 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 487 through 490' Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.703A pdb=" N ASN B 497 " --> pdb=" O ASP B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 4.787A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 366 through 379 removed outlier: 4.344A pdb=" N GLY C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 404 through 455 Processing helix chain 'C' and resid 474 through 484 Processing helix chain 'C' and resid 487 through 490 removed outlier: 3.656A pdb=" N VAL C 490 " --> pdb=" O ASP C 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 487 through 490' Processing helix chain 'C' and resid 491 through 500 removed outlier: 3.702A pdb=" N ASN C 497 " --> pdb=" O ASP C 493 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 362 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.901A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.029A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.674A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU A 251 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 154 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TRP A 153 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 133 " --> pdb=" O TRP A 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 removed outlier: 4.976A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.133A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 362 through 365 Processing sheet with id=AB3, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AB4, first strand: chain 'B' and resid 40 through 41 Processing sheet with id=AB5, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 52 removed outlier: 5.901A pdb=" N ILE B 51 " --> pdb=" O ASP B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 58 through 61 Processing sheet with id=AB8, first strand: chain 'B' and resid 100 through 101 removed outlier: 5.029A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 100 through 101 removed outlier: 7.675A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU B 251 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 154 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TRP B 153 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 133 " --> pdb=" O TRP B 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 164 through 169 removed outlier: 4.976A pdb=" N ARG B 201 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 286 through 288 removed outlier: 4.134A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 362 through 365 Processing sheet with id=AC4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC5, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AC6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC7, first strand: chain 'C' and resid 51 through 52 removed outlier: 5.902A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AC9, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.030A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.674A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU C 251 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 154 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TRP C 153 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN C 133 " --> pdb=" O TRP C 153 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 164 through 169 removed outlier: 4.975A pdb=" N ARG C 201 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.133A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1440 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: 5.36 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11037 1.03 - 1.23: 96 1.23 - 1.43: 5006 1.43 - 1.63: 6718 1.63 - 1.83: 78 Bond restraints: 22935 Sorted by residual: bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.526 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" C1 NAG B 603 " pdb=" O5 NAG B 603 " ideal model delta sigma weight residual 1.406 1.526 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" C1 NAG C 605 " pdb=" O5 NAG C 605 " ideal model delta sigma weight residual 1.406 1.526 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C1 NAG C 604 " pdb=" O5 NAG C 604 " ideal model delta sigma weight residual 1.406 1.346 0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.347 0.059 2.00e-02 2.50e+03 8.84e+00 ... (remaining 22930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 40784 2.62 - 5.23: 373 5.23 - 7.85: 36 7.85 - 10.47: 3 10.47 - 13.08: 6 Bond angle restraints: 41202 Sorted by residual: angle pdb=" N THR B 388 " pdb=" CA THR B 388 " pdb=" C THR B 388 " ideal model delta sigma weight residual 110.80 101.42 9.38 2.13e+00 2.20e-01 1.94e+01 angle pdb=" N THR A 388 " pdb=" CA THR A 388 " pdb=" C THR A 388 " ideal model delta sigma weight residual 110.80 101.42 9.38 2.13e+00 2.20e-01 1.94e+01 angle pdb=" N THR C 388 " pdb=" CA THR C 388 " pdb=" C THR C 388 " ideal model delta sigma weight residual 110.80 101.45 9.35 2.13e+00 2.20e-01 1.93e+01 angle pdb=" C1 NAG B 603 " pdb=" O5 NAG B 603 " pdb=" C5 NAG B 603 " ideal model delta sigma weight residual 113.21 126.29 -13.08 3.00e+00 1.11e-01 1.90e+01 angle pdb=" C1 NAG C 605 " pdb=" O5 NAG C 605 " pdb=" C5 NAG C 605 " ideal model delta sigma weight residual 113.21 126.27 -13.06 3.00e+00 1.11e-01 1.90e+01 ... (remaining 41197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 10317 21.52 - 43.04: 546 43.04 - 64.56: 159 64.56 - 86.08: 36 86.08 - 107.60: 18 Dihedral angle restraints: 11076 sinusoidal: 6183 harmonic: 4893 Sorted by residual: dihedral pdb=" CA ARG A 141 " pdb=" C ARG A 141 " pdb=" N GLY A 142 " pdb=" CA GLY A 142 " ideal model delta harmonic sigma weight residual 180.00 144.84 35.16 0 5.00e+00 4.00e-02 4.95e+01 dihedral pdb=" CA ARG B 141 " pdb=" C ARG B 141 " pdb=" N GLY B 142 " pdb=" CA GLY B 142 " ideal model delta harmonic sigma weight residual 180.00 144.87 35.13 0 5.00e+00 4.00e-02 4.94e+01 dihedral pdb=" CA ARG C 141 " pdb=" C ARG C 141 " pdb=" N GLY C 142 " pdb=" CA GLY C 142 " ideal model delta harmonic sigma weight residual 180.00 144.92 35.08 0 5.00e+00 4.00e-02 4.92e+01 ... (remaining 11073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1545 0.067 - 0.134: 236 0.134 - 0.201: 22 0.201 - 0.268: 3 0.268 - 0.335: 6 Chirality restraints: 1812 Sorted by residual: chirality pdb=" C1 NAG B 602 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B 602 " pdb=" O5 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C1 NAG C 604 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C 604 " pdb=" O5 NAG C 604 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 1809 not shown) Planarity restraints: 3495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 168 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO B 169 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 169 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 169 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 81 " -0.012 2.00e-02 2.50e+03 1.33e-02 2.20e+00 pdb=" CG ASN C 81 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN C 81 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C 81 " 0.021 2.00e-02 2.50e+03 pdb=" C1 NAG C 605 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 168 " -0.025 5.00e-02 4.00e+02 3.70e-02 2.20e+00 pdb=" N PRO C 169 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 169 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 169 " -0.021 5.00e-02 4.00e+02 ... (remaining 3492 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 3085 2.26 - 2.85: 51881 2.85 - 3.43: 60045 3.43 - 4.02: 88158 4.02 - 4.60: 132800 Nonbonded interactions: 335969 Sorted by model distance: nonbonded pdb="HH12 ARG A 405 " pdb=" OE1 GLU B 403 " model vdw 1.677 2.450 nonbonded pdb=" OE1 GLU A 403 " pdb="HH12 ARG C 405 " model vdw 1.683 2.450 nonbonded pdb=" O CYS B 477 " pdb=" HG SER B 480 " model vdw 1.690 2.450 nonbonded pdb=" O CYS C 477 " pdb=" HG SER C 480 " model vdw 1.690 2.450 nonbonded pdb=" O CYS A 477 " pdb=" HG SER A 480 " model vdw 1.691 2.450 ... (remaining 335964 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' and (resid 9 through 601 or resid 603 through 604)) selection = (chain 'B' and (resid 9 through 601 or resid 603 through 604)) selection = (chain 'C' and (resid 9 through 601 or resid 603 through 604)) } 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: 1.060 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: 0.130 Extract box with map and model: 0.250 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.940 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 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 : 0.007 0.120 11907 Z= 0.296 Angle : 0.894 16.355 16173 Z= 0.431 Chirality : 0.051 0.335 1812 Planarity : 0.004 0.037 2094 Dihedral : 15.835 107.597 4599 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.71 % Allowed : 2.36 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.98 (0.18), residues: 1443 helix: -0.78 (0.23), residues: 333 sheet: -2.35 (0.26), residues: 255 loop : -2.44 (0.17), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 383 TYR 0.014 0.002 TYR A 105 PHE 0.017 0.002 PHE C 353 TRP 0.006 0.001 TRP B 222 HIS 0.006 0.002 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00677 (11886) covalent geometry : angle 0.84856 (16122) SS BOND : bond 0.00491 ( 12) SS BOND : angle 1.49422 ( 24) hydrogen bonds : bond 0.11988 ( 498) hydrogen bonds : angle 6.54601 ( 1440) link_NAG-ASN : bond 0.00731 ( 9) link_NAG-ASN : angle 6.81815 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 250 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8088 (ttmt) cc_final: 0.7879 (ttmm) REVERT: A 163 VAL cc_start: 0.9119 (t) cc_final: 0.8874 (p) REVERT: A 301 THR cc_start: 0.8308 (p) cc_final: 0.8061 (p) REVERT: A 368 LYS cc_start: 0.8006 (tttp) cc_final: 0.7628 (mppt) REVERT: A 383 ARG cc_start: 0.7320 (ptt-90) cc_final: 0.7015 (ptt180) REVERT: A 424 ASN cc_start: 0.7976 (m-40) cc_final: 0.7575 (m-40) REVERT: A 493 ASP cc_start: 0.8131 (m-30) cc_final: 0.7793 (m-30) REVERT: B 27 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7579 (ttpp) REVERT: B 101 ASP cc_start: 0.8295 (p0) cc_final: 0.8009 (p0) REVERT: B 247 SER cc_start: 0.8592 (t) cc_final: 0.8372 (p) REVERT: B 248 ASN cc_start: 0.7538 (t0) cc_final: 0.7101 (t0) REVERT: B 368 LYS cc_start: 0.7839 (tttp) cc_final: 0.7535 (mppt) REVERT: B 457 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6029 (mm-30) REVERT: B 493 ASP cc_start: 0.8194 (m-30) cc_final: 0.7964 (m-30) REVERT: C 248 ASN cc_start: 0.7627 (t0) cc_final: 0.7365 (t0) REVERT: C 291 ASP cc_start: 0.8217 (p0) cc_final: 0.7974 (p0) REVERT: C 301 THR cc_start: 0.8349 (p) cc_final: 0.8086 (p) REVERT: C 368 LYS cc_start: 0.7694 (tttp) cc_final: 0.7475 (mppt) REVERT: C 493 ASP cc_start: 0.8113 (m-30) cc_final: 0.7824 (m-30) outliers start: 9 outliers final: 3 residues processed: 259 average time/residue: 1.1256 time to fit residues: 317.9624 Evaluate side-chains 152 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 400 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 454 GLN B 498 ASN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN C 498 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.112838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.094055 restraints weight = 41198.879| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.06 r_work: 0.2937 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11907 Z= 0.161 Angle : 0.593 9.487 16173 Z= 0.300 Chirality : 0.045 0.206 1812 Planarity : 0.004 0.048 2094 Dihedral : 8.425 55.948 1887 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.34 % Allowed : 10.93 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.94 (0.20), residues: 1443 helix: 0.85 (0.25), residues: 333 sheet: -1.89 (0.29), residues: 255 loop : -2.06 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 452 TYR 0.011 0.001 TYR B 105 PHE 0.011 0.001 PHE A 353 TRP 0.007 0.001 TRP A 421 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00352 (11886) covalent geometry : angle 0.57492 (16122) SS BOND : bond 0.00487 ( 12) SS BOND : angle 1.00595 ( 24) hydrogen bonds : bond 0.03746 ( 498) hydrogen bonds : angle 5.24608 ( 1440) link_NAG-ASN : bond 0.00831 ( 9) link_NAG-ASN : angle 3.48282 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7822 (ttmm) REVERT: A 163 VAL cc_start: 0.9085 (t) cc_final: 0.8812 (p) REVERT: A 287 SER cc_start: 0.9217 (m) cc_final: 0.8738 (p) REVERT: A 323 VAL cc_start: 0.8591 (t) cc_final: 0.8351 (t) REVERT: A 368 LYS cc_start: 0.7729 (tttp) cc_final: 0.7222 (mppt) REVERT: A 493 ASP cc_start: 0.8151 (m-30) cc_final: 0.7947 (m-30) REVERT: B 27 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7595 (ttmm) REVERT: B 248 ASN cc_start: 0.7618 (t0) cc_final: 0.7263 (t0) REVERT: B 368 LYS cc_start: 0.7627 (tttp) cc_final: 0.7155 (mppt) REVERT: C 208 ARG cc_start: 0.7902 (ptm-80) cc_final: 0.7052 (ptp-170) REVERT: C 248 ASN cc_start: 0.7671 (t0) cc_final: 0.7391 (t0) REVERT: C 291 ASP cc_start: 0.8210 (p0) cc_final: 0.7997 (p0) REVERT: C 368 LYS cc_start: 0.7599 (tttp) cc_final: 0.7294 (mppt) outliers start: 17 outliers final: 6 residues processed: 173 average time/residue: 0.9766 time to fit residues: 187.0852 Evaluate side-chains 149 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 388 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.092451 restraints weight = 41836.188| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.04 r_work: 0.2933 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11907 Z= 0.167 Angle : 0.525 5.178 16173 Z= 0.272 Chirality : 0.043 0.191 1812 Planarity : 0.004 0.032 2094 Dihedral : 6.439 54.311 1878 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.49 % Allowed : 11.71 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.54 (0.21), residues: 1443 helix: 1.53 (0.26), residues: 333 sheet: -1.90 (0.28), residues: 282 loop : -1.84 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 57 TYR 0.010 0.001 TYR B 105 PHE 0.010 0.001 PHE C 353 TRP 0.006 0.001 TRP B 421 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00373 (11886) covalent geometry : angle 0.52073 (16122) SS BOND : bond 0.00468 ( 12) SS BOND : angle 0.88292 ( 24) hydrogen bonds : bond 0.03588 ( 498) hydrogen bonds : angle 4.95355 ( 1440) link_NAG-ASN : bond 0.00263 ( 9) link_NAG-ASN : angle 1.57871 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8089 (ttmt) cc_final: 0.7787 (ttmm) REVERT: A 163 VAL cc_start: 0.9062 (t) cc_final: 0.8801 (p) REVERT: A 323 VAL cc_start: 0.8692 (t) cc_final: 0.8467 (t) REVERT: A 368 LYS cc_start: 0.7810 (tttp) cc_final: 0.7295 (mppt) REVERT: B 27 LYS cc_start: 0.7946 (ttmt) cc_final: 0.7619 (ttmm) REVERT: B 368 LYS cc_start: 0.7628 (tttp) cc_final: 0.7184 (mppt) REVERT: C 208 ARG cc_start: 0.8033 (ptm-80) cc_final: 0.7287 (ptp-170) REVERT: C 291 ASP cc_start: 0.8261 (p0) cc_final: 0.7995 (p0) REVERT: C 398 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8301 (mt-10) outliers start: 19 outliers final: 9 residues processed: 157 average time/residue: 0.9104 time to fit residues: 159.9665 Evaluate side-chains 146 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 398 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 113 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 0.1980 chunk 127 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.091647 restraints weight = 42038.415| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.03 r_work: 0.2916 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 11907 Z= 0.171 Angle : 0.511 5.431 16173 Z= 0.265 Chirality : 0.043 0.179 1812 Planarity : 0.004 0.033 2094 Dihedral : 6.000 51.791 1878 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.42 % Allowed : 12.34 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.28 (0.21), residues: 1443 helix: 1.94 (0.26), residues: 333 sheet: -1.85 (0.27), residues: 282 loop : -1.73 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 452 TYR 0.009 0.001 TYR B 105 PHE 0.018 0.001 PHE C 353 TRP 0.006 0.001 TRP A 421 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00383 (11886) covalent geometry : angle 0.50683 (16122) SS BOND : bond 0.00492 ( 12) SS BOND : angle 0.97034 ( 24) hydrogen bonds : bond 0.03411 ( 498) hydrogen bonds : angle 4.86975 ( 1440) link_NAG-ASN : bond 0.00329 ( 9) link_NAG-ASN : angle 1.41221 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7757 (ttmm) REVERT: A 163 VAL cc_start: 0.9053 (t) cc_final: 0.8808 (p) REVERT: A 208 ARG cc_start: 0.8003 (ptm-80) cc_final: 0.7179 (ptp-170) REVERT: A 323 VAL cc_start: 0.8766 (t) cc_final: 0.8552 (t) REVERT: A 368 LYS cc_start: 0.7797 (tttp) cc_final: 0.7315 (mppt) REVERT: B 27 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7602 (ttmm) REVERT: B 368 LYS cc_start: 0.7622 (tttp) cc_final: 0.7191 (mppt) REVERT: C 208 ARG cc_start: 0.8070 (ptm-80) cc_final: 0.7345 (ptp-170) REVERT: C 248 ASN cc_start: 0.8150 (t0) cc_final: 0.7730 (t0) REVERT: C 291 ASP cc_start: 0.8262 (p0) cc_final: 0.7970 (p0) REVERT: C 368 LYS cc_start: 0.7552 (mtpp) cc_final: 0.7075 (mppt) outliers start: 18 outliers final: 12 residues processed: 156 average time/residue: 0.7704 time to fit residues: 136.8698 Evaluate side-chains 145 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 388 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 48 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.092784 restraints weight = 41539.443| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.01 r_work: 0.2897 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 11907 Z= 0.166 Angle : 0.496 5.791 16173 Z= 0.257 Chirality : 0.043 0.171 1812 Planarity : 0.003 0.033 2094 Dihedral : 5.704 50.454 1878 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.73 % Allowed : 12.50 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.09 (0.21), residues: 1443 helix: 2.27 (0.27), residues: 333 sheet: -1.77 (0.28), residues: 282 loop : -1.67 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 57 TYR 0.009 0.001 TYR C 491 PHE 0.013 0.001 PHE C 353 TRP 0.006 0.001 TRP A 421 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00370 (11886) covalent geometry : angle 0.49272 (16122) SS BOND : bond 0.00489 ( 12) SS BOND : angle 0.97781 ( 24) hydrogen bonds : bond 0.03350 ( 498) hydrogen bonds : angle 4.78160 ( 1440) link_NAG-ASN : bond 0.00271 ( 9) link_NAG-ASN : angle 1.22520 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7764 (ttmm) REVERT: A 163 VAL cc_start: 0.9049 (t) cc_final: 0.8814 (p) REVERT: A 208 ARG cc_start: 0.8038 (ptm-80) cc_final: 0.7234 (ptp-170) REVERT: A 323 VAL cc_start: 0.8794 (t) cc_final: 0.8589 (t) REVERT: A 368 LYS cc_start: 0.7790 (tttp) cc_final: 0.7329 (mppt) REVERT: A 398 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8542 (mt-10) REVERT: B 27 LYS cc_start: 0.7914 (ttmt) cc_final: 0.7554 (ttmm) REVERT: B 274 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8133 (mp) REVERT: B 280 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8256 (mm-30) REVERT: B 368 LYS cc_start: 0.7679 (tttp) cc_final: 0.7255 (mppt) REVERT: C 208 ARG cc_start: 0.8053 (ptm-80) cc_final: 0.7315 (ptp-170) REVERT: C 248 ASN cc_start: 0.8108 (t0) cc_final: 0.7634 (t0) REVERT: C 398 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8416 (mt-10) REVERT: C 406 ILE cc_start: 0.7921 (mm) cc_final: 0.7667 (mp) REVERT: C 449 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6741 (mm-30) outliers start: 22 outliers final: 16 residues processed: 153 average time/residue: 0.8558 time to fit residues: 147.4374 Evaluate side-chains 150 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 449 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 97 optimal weight: 0.0070 chunk 87 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.091394 restraints weight = 42364.620| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.03 r_work: 0.2919 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 11907 Z= 0.168 Angle : 0.494 5.978 16173 Z= 0.256 Chirality : 0.043 0.168 1812 Planarity : 0.003 0.035 2094 Dihedral : 5.600 49.868 1878 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.89 % Allowed : 12.81 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.01 (0.21), residues: 1443 helix: 2.34 (0.27), residues: 336 sheet: -1.73 (0.28), residues: 282 loop : -1.64 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 492 TYR 0.019 0.001 TYR B 195 PHE 0.011 0.001 PHE C 353 TRP 0.005 0.001 TRP A 421 HIS 0.004 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00378 (11886) covalent geometry : angle 0.49084 (16122) SS BOND : bond 0.00489 ( 12) SS BOND : angle 0.98830 ( 24) hydrogen bonds : bond 0.03324 ( 498) hydrogen bonds : angle 4.75010 ( 1440) link_NAG-ASN : bond 0.00271 ( 9) link_NAG-ASN : angle 1.18944 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7605 (ttmm) REVERT: A 128 THR cc_start: 0.8362 (t) cc_final: 0.8089 (p) REVERT: A 163 VAL cc_start: 0.9049 (t) cc_final: 0.8817 (p) REVERT: A 190 GLU cc_start: 0.7717 (tt0) cc_final: 0.7309 (tt0) REVERT: A 368 LYS cc_start: 0.7795 (tttp) cc_final: 0.7348 (mppt) REVERT: A 398 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8496 (mt-10) REVERT: B 27 LYS cc_start: 0.7913 (ttmt) cc_final: 0.7552 (ttmm) REVERT: B 264 LYS cc_start: 0.7256 (ptpp) cc_final: 0.7034 (ptpt) REVERT: B 274 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8179 (mp) REVERT: B 368 LYS cc_start: 0.7681 (tttp) cc_final: 0.7281 (mppt) REVERT: C 208 ARG cc_start: 0.8061 (ptm-80) cc_final: 0.7341 (ptp-170) REVERT: C 248 ASN cc_start: 0.8096 (t0) cc_final: 0.7568 (t0) REVERT: C 368 LYS cc_start: 0.7630 (mtpp) cc_final: 0.7098 (mppt) REVERT: C 406 ILE cc_start: 0.7904 (mm) cc_final: 0.7648 (mp) REVERT: C 449 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6655 (mm-30) outliers start: 24 outliers final: 16 residues processed: 158 average time/residue: 0.8196 time to fit residues: 146.1007 Evaluate side-chains 151 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 449 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 95 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.091378 restraints weight = 42343.005| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.04 r_work: 0.2922 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11907 Z= 0.164 Angle : 0.488 5.744 16173 Z= 0.253 Chirality : 0.043 0.164 1812 Planarity : 0.003 0.040 2094 Dihedral : 5.480 48.904 1878 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.57 % Allowed : 13.84 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.02 (0.21), residues: 1443 helix: 2.27 (0.27), residues: 342 sheet: -1.71 (0.28), residues: 282 loop : -1.65 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 492 TYR 0.016 0.001 TYR B 195 PHE 0.014 0.001 PHE C 353 TRP 0.005 0.001 TRP A 421 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00368 (11886) covalent geometry : angle 0.48488 (16122) SS BOND : bond 0.00479 ( 12) SS BOND : angle 0.98655 ( 24) hydrogen bonds : bond 0.03322 ( 498) hydrogen bonds : angle 4.73311 ( 1440) link_NAG-ASN : bond 0.00255 ( 9) link_NAG-ASN : angle 1.14014 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7625 (ttmm) REVERT: A 128 THR cc_start: 0.8364 (t) cc_final: 0.8091 (p) REVERT: A 190 GLU cc_start: 0.7704 (tt0) cc_final: 0.7323 (tt0) REVERT: A 368 LYS cc_start: 0.7797 (tttp) cc_final: 0.7350 (mppt) REVERT: A 398 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8506 (mt-10) REVERT: B 27 LYS cc_start: 0.7936 (ttmt) cc_final: 0.7586 (ttmm) REVERT: B 264 LYS cc_start: 0.7243 (ptpp) cc_final: 0.7016 (ptpt) REVERT: B 274 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8197 (mp) REVERT: B 368 LYS cc_start: 0.7684 (tttp) cc_final: 0.7286 (mppt) REVERT: C 208 ARG cc_start: 0.8079 (ptm-80) cc_final: 0.7357 (ptp-170) REVERT: C 248 ASN cc_start: 0.8064 (t0) cc_final: 0.7762 (t0) REVERT: C 368 LYS cc_start: 0.7635 (mtpp) cc_final: 0.7100 (mppt) REVERT: C 406 ILE cc_start: 0.7888 (mm) cc_final: 0.7645 (mp) REVERT: C 449 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6789 (mm-30) outliers start: 20 outliers final: 15 residues processed: 150 average time/residue: 0.8235 time to fit residues: 139.5792 Evaluate side-chains 151 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 449 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 118 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 124 optimal weight: 0.0030 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN C 376 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.093327 restraints weight = 41737.268| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.04 r_work: 0.2950 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11907 Z= 0.120 Angle : 0.458 5.620 16173 Z= 0.239 Chirality : 0.042 0.176 1812 Planarity : 0.003 0.034 2094 Dihedral : 5.082 44.116 1878 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.65 % Allowed : 13.60 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.21), residues: 1443 helix: 2.44 (0.27), residues: 342 sheet: -1.76 (0.28), residues: 288 loop : -1.55 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 492 TYR 0.013 0.001 TYR B 195 PHE 0.010 0.001 PHE C 353 TRP 0.005 0.001 TRP A 421 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00262 (11886) covalent geometry : angle 0.45509 (16122) SS BOND : bond 0.00374 ( 12) SS BOND : angle 0.97532 ( 24) hydrogen bonds : bond 0.03211 ( 498) hydrogen bonds : angle 4.59838 ( 1440) link_NAG-ASN : bond 0.00101 ( 9) link_NAG-ASN : angle 1.00828 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7649 (ttmm) REVERT: A 128 THR cc_start: 0.8333 (t) cc_final: 0.8083 (p) REVERT: A 190 GLU cc_start: 0.7706 (tt0) cc_final: 0.7326 (tt0) REVERT: A 248 ASN cc_start: 0.8269 (t0) cc_final: 0.8056 (t0) REVERT: A 274 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8322 (mp) REVERT: A 323 VAL cc_start: 0.8768 (t) cc_final: 0.8564 (m) REVERT: A 368 LYS cc_start: 0.7789 (tttp) cc_final: 0.7356 (mppt) REVERT: A 398 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8495 (mt-10) REVERT: A 406 ILE cc_start: 0.7755 (mm) cc_final: 0.7465 (mp) REVERT: B 27 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7593 (ttmm) REVERT: B 264 LYS cc_start: 0.7260 (ptpp) cc_final: 0.7018 (ptpt) REVERT: B 368 LYS cc_start: 0.7659 (tttp) cc_final: 0.7276 (mppt) REVERT: C 248 ASN cc_start: 0.8039 (t0) cc_final: 0.7718 (t0) REVERT: C 291 ASP cc_start: 0.8124 (p0) cc_final: 0.7876 (p0) REVERT: C 368 LYS cc_start: 0.7633 (mtpp) cc_final: 0.7100 (mppt) REVERT: C 406 ILE cc_start: 0.7898 (mm) cc_final: 0.7627 (mp) REVERT: C 449 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6761 (mm-30) outliers start: 21 outliers final: 14 residues processed: 159 average time/residue: 0.7549 time to fit residues: 137.5943 Evaluate side-chains 156 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 449 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 120 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.090967 restraints weight = 42399.855| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.03 r_work: 0.2913 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11907 Z= 0.190 Angle : 0.494 5.424 16173 Z= 0.258 Chirality : 0.043 0.161 1812 Planarity : 0.003 0.035 2094 Dihedral : 5.401 48.442 1878 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.49 % Allowed : 13.92 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.93 (0.21), residues: 1443 helix: 2.32 (0.27), residues: 342 sheet: -1.66 (0.28), residues: 291 loop : -1.57 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 492 TYR 0.016 0.001 TYR B 195 PHE 0.014 0.001 PHE C 353 TRP 0.006 0.001 TRP A 421 HIS 0.003 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00430 (11886) covalent geometry : angle 0.49128 (16122) SS BOND : bond 0.00546 ( 12) SS BOND : angle 0.98915 ( 24) hydrogen bonds : bond 0.03329 ( 498) hydrogen bonds : angle 4.71092 ( 1440) link_NAG-ASN : bond 0.00316 ( 9) link_NAG-ASN : angle 1.16040 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7620 (ttmm) REVERT: A 128 THR cc_start: 0.8387 (t) cc_final: 0.8111 (p) REVERT: A 189 GLN cc_start: 0.7497 (tm-30) cc_final: 0.7269 (tm-30) REVERT: A 190 GLU cc_start: 0.7718 (tt0) cc_final: 0.7379 (tt0) REVERT: A 274 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8338 (mp) REVERT: A 368 LYS cc_start: 0.7793 (tttp) cc_final: 0.7378 (mppt) REVERT: A 406 ILE cc_start: 0.7795 (mm) cc_final: 0.7516 (mp) REVERT: B 27 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7574 (ttmm) REVERT: B 264 LYS cc_start: 0.7279 (ptpp) cc_final: 0.6998 (ptpt) REVERT: B 368 LYS cc_start: 0.7650 (tttp) cc_final: 0.7272 (mppt) REVERT: C 208 ARG cc_start: 0.8124 (ptm-80) cc_final: 0.7385 (ptp-170) REVERT: C 248 ASN cc_start: 0.8108 (t0) cc_final: 0.7746 (t0) REVERT: C 368 LYS cc_start: 0.7643 (mtpp) cc_final: 0.7104 (mppt) REVERT: C 406 ILE cc_start: 0.7917 (mm) cc_final: 0.7653 (mp) outliers start: 19 outliers final: 12 residues processed: 150 average time/residue: 0.8291 time to fit residues: 140.6072 Evaluate side-chains 145 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 388 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 GLN ** B 216 ASN ** 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 = 0.3267 r_free = 0.3267 target = 0.111519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.092388 restraints weight = 42142.078| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.04 r_work: 0.2934 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11907 Z= 0.135 Angle : 0.467 4.735 16173 Z= 0.243 Chirality : 0.042 0.167 1812 Planarity : 0.003 0.035 2094 Dihedral : 5.127 45.275 1878 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.10 % Allowed : 14.47 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.85 (0.21), residues: 1443 helix: 2.44 (0.27), residues: 342 sheet: -1.65 (0.28), residues: 291 loop : -1.53 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 492 TYR 0.013 0.001 TYR B 195 PHE 0.011 0.001 PHE C 353 TRP 0.005 0.001 TRP A 421 HIS 0.004 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00301 (11886) covalent geometry : angle 0.46415 (16122) SS BOND : bond 0.00409 ( 12) SS BOND : angle 0.98092 ( 24) hydrogen bonds : bond 0.03233 ( 498) hydrogen bonds : angle 4.63673 ( 1440) link_NAG-ASN : bond 0.00159 ( 9) link_NAG-ASN : angle 1.05389 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7990 (ttmt) cc_final: 0.7663 (ttmm) REVERT: A 128 THR cc_start: 0.8373 (t) cc_final: 0.8116 (p) REVERT: A 189 GLN cc_start: 0.7495 (tm-30) cc_final: 0.7233 (tm-30) REVERT: A 190 GLU cc_start: 0.7699 (tt0) cc_final: 0.7372 (tt0) REVERT: A 248 ASN cc_start: 0.8285 (t0) cc_final: 0.8076 (t0) REVERT: A 274 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8344 (mp) REVERT: A 368 LYS cc_start: 0.7810 (tttp) cc_final: 0.7397 (mppt) REVERT: A 406 ILE cc_start: 0.7782 (mm) cc_final: 0.7498 (mp) REVERT: B 27 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7561 (ttmm) REVERT: B 264 LYS cc_start: 0.7290 (ptpp) cc_final: 0.7005 (ptpt) REVERT: B 368 LYS cc_start: 0.7622 (tttp) cc_final: 0.7240 (mppt) REVERT: C 248 ASN cc_start: 0.8106 (t0) cc_final: 0.7751 (t0) REVERT: C 368 LYS cc_start: 0.7651 (mtpp) cc_final: 0.7089 (mppt) REVERT: C 406 ILE cc_start: 0.7918 (mm) cc_final: 0.7650 (mp) outliers start: 14 outliers final: 10 residues processed: 147 average time/residue: 0.7117 time to fit residues: 120.8937 Evaluate side-chains 145 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 205 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 94 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 115 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.092357 restraints weight = 42143.766| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.03 r_work: 0.2903 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11907 Z= 0.139 Angle : 0.467 4.515 16173 Z= 0.244 Chirality : 0.042 0.162 1812 Planarity : 0.003 0.035 2094 Dihedral : 5.049 44.730 1878 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.02 % Allowed : 14.70 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1443 helix: 2.46 (0.27), residues: 342 sheet: -1.62 (0.28), residues: 291 loop : -1.52 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 492 TYR 0.014 0.001 TYR B 195 PHE 0.011 0.001 PHE C 353 TRP 0.005 0.001 TRP A 421 HIS 0.004 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00311 (11886) covalent geometry : angle 0.46438 (16122) SS BOND : bond 0.00397 ( 12) SS BOND : angle 0.95819 ( 24) hydrogen bonds : bond 0.03216 ( 498) hydrogen bonds : angle 4.62460 ( 1440) link_NAG-ASN : bond 0.00163 ( 9) link_NAG-ASN : angle 1.04424 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6035.93 seconds wall clock time: 103 minutes 1.41 seconds (6181.41 seconds total)