Starting phenix.real_space_refine on Tue Jun 10 08:42:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yg8_39238/06_2025/8yg8_39238.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yg8_39238/06_2025/8yg8_39238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yg8_39238/06_2025/8yg8_39238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yg8_39238/06_2025/8yg8_39238.map" model { file = "/net/cci-nas-00/data/ceres_data/8yg8_39238/06_2025/8yg8_39238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yg8_39238/06_2025/8yg8_39238.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 87 5.16 5 C 7085 2.51 5 N 1966 2.21 5 O 2276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11414 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3730 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain: "B" Number of atoms: 3730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3730 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain: "C" Number of atoms: 3730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3730 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 7.54, per 1000 atoms: 0.66 Number of scatterers: 11414 At special positions: 0 Unit cell: (92.16, 111.36, 155.52, 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 87 16.00 O 2276 8.00 N 1966 7.00 C 7085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS B 372 " distance=2.04 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 267 " distance=2.04 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS C 24 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 402 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS C 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 262 " - pdb=" SG CYS B 267 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 402 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 164 " distance=2.02 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 177 " - pdb=" SG CYS C 184 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 262 " - pdb=" SG CYS C 267 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 402 " 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " NAG D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " NAG-ASN " NAG A 501 " - " ASN A 197 " " NAG A 502 " - " ASN A 384 " " NAG A 503 " - " ASN A 426 " " NAG C 501 " - " ASN B 384 " " NAG C 502 " - " ASN C 197 " " NAG C 503 " - " ASN C 384 " " NAG C 504 " - " ASN C 426 " " NAG D 1 " - " ASN A 354 " " NAG E 1 " - " ASN B 354 " " NAG F 1 " - " ASN C 354 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 22 sheets defined 24.5% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 298 through 342 Processing helix chain 'A' and resid 347 through 353 Processing helix chain 'A' and resid 439 through 456 removed outlier: 5.398A pdb=" N SER A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASN A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.710A pdb=" N ASP A 467 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE A 468 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 487 removed outlier: 4.280A pdb=" N GLU A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 475 " --> pdb=" O MET A 471 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.542A pdb=" N ASP B 131 " --> pdb=" O ASP B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 removed outlier: 4.039A pdb=" N ASN B 194 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 342 Processing helix chain 'B' and resid 347 through 353 Processing helix chain 'B' and resid 439 through 456 removed outlier: 5.381A pdb=" N SER B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ASN B 448 " --> pdb=" O GLN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 467 removed outlier: 3.653A pdb=" N ASP B 467 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 487 removed outlier: 4.391A pdb=" N ALA B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 475 " --> pdb=" O MET B 471 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 298 through 342 removed outlier: 3.681A pdb=" N LEU C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 353 Processing helix chain 'C' and resid 439 through 456 removed outlier: 5.431A pdb=" N SER C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASN C 448 " --> pdb=" O GLN C 444 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR C 456 " --> pdb=" O THR C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 467 removed outlier: 4.050A pdb=" N ASP C 467 " --> pdb=" O SER C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 472 removed outlier: 3.663A pdb=" N ALA C 472 " --> pdb=" O THR C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 487 Processing sheet with id=AA1, first strand: chain 'B' and resid 357 through 361 removed outlier: 5.915A pdb=" N LYS A 34 " --> pdb=" O LEU C 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 252 through 254 removed outlier: 4.637A pdb=" N ALA A 227 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 266 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 263 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 268 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN A 261 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 94 removed outlier: 3.559A pdb=" N GLY A 70 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 72 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS A 158 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 361 Processing sheet with id=AA7, first strand: chain 'A' and resid 382 through 383 Processing sheet with id=AA8, first strand: chain 'A' and resid 410 through 411 removed outlier: 3.501A pdb=" N THR C 360 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 252 through 254 removed outlier: 4.662A pdb=" N ALA B 227 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 266 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 263 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 268 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AB2, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.706A pdb=" N TYR B 71 " --> pdb=" O LYS B 93 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS B 93 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN B 73 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B 91 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.535A pdb=" N TYR B 72 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 76 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 157 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS B 156 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 120 " --> pdb=" O CYS B 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 111 through 113 removed outlier: 3.882A pdb=" N VAL B 139 " --> pdb=" O CYS B 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 173 through 176 removed outlier: 3.816A pdb=" N GLU B 176 " --> pdb=" O GLN B 185 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 185 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 386 through 389 Processing sheet with id=AB7, first strand: chain 'B' and resid 411 through 412 removed outlier: 6.863A pdb=" N LEU B 411 " --> pdb=" O LYS C 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 252 through 254 removed outlier: 3.519A pdb=" N LEU C 247 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA C 227 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE C 268 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN C 261 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AC1, first strand: chain 'C' and resid 87 through 95 removed outlier: 4.433A pdb=" N LYS C 69 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LYS C 160 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE C 118 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 111 through 113 Processing sheet with id=AC3, first strand: chain 'C' and resid 173 through 177 Processing sheet with id=AC4, first strand: chain 'C' and resid 386 through 389 419 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 3.25 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: 3795 1.34 - 1.46: 2667 1.46 - 1.59: 5042 1.59 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 11636 Sorted by residual: bond pdb=" C1 NAG A 502 " pdb=" O5 NAG A 502 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.17e+00 bond pdb=" N HIS B 285 " pdb=" CA HIS B 285 " ideal model delta sigma weight residual 1.453 1.478 -0.025 1.37e-02 5.33e+03 3.38e+00 bond pdb=" C1 NAG E 3 " pdb=" O5 NAG E 3 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" C1 NAG F 3 " pdb=" O5 NAG F 3 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.65e+00 bond pdb=" C1 NAG C 504 " pdb=" O5 NAG C 504 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.45e+00 ... (remaining 11631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 15484 2.03 - 4.06: 233 4.06 - 6.10: 19 6.10 - 8.13: 1 8.13 - 10.16: 2 Bond angle restraints: 15739 Sorted by residual: angle pdb=" C MET C 484 " pdb=" N PHE C 485 " pdb=" CA PHE C 485 " ideal model delta sigma weight residual 121.58 114.85 6.73 1.95e+00 2.63e-01 1.19e+01 angle pdb=" CB MET A 370 " pdb=" CG MET A 370 " pdb=" SD MET A 370 " ideal model delta sigma weight residual 112.70 102.54 10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" N ASN A 132 " pdb=" CA ASN A 132 " pdb=" C ASN A 132 " ideal model delta sigma weight residual 114.56 110.41 4.15 1.27e+00 6.20e-01 1.07e+01 angle pdb=" C GLY C 438 " pdb=" N TRP C 439 " pdb=" CA TRP C 439 " ideal model delta sigma weight residual 121.54 126.87 -5.33 1.91e+00 2.74e-01 7.79e+00 angle pdb=" C GLY A 438 " pdb=" N TRP A 439 " pdb=" CA TRP A 439 " ideal model delta sigma weight residual 121.54 126.77 -5.23 1.91e+00 2.74e-01 7.50e+00 ... (remaining 15734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.16: 6757 22.16 - 44.32: 420 44.32 - 66.49: 67 66.49 - 88.65: 14 88.65 - 110.81: 32 Dihedral angle restraints: 7290 sinusoidal: 3210 harmonic: 4080 Sorted by residual: dihedral pdb=" CB CYS B 24 " pdb=" SG CYS B 24 " pdb=" SG CYS C 372 " pdb=" CB CYS C 372 " ideal model delta sinusoidal sigma weight residual 93.00 12.23 80.77 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS A 24 " pdb=" SG CYS A 24 " pdb=" SG CYS B 372 " pdb=" CB CYS B 372 " ideal model delta sinusoidal sigma weight residual 93.00 23.22 69.78 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 402 " pdb=" CB CYS A 402 " ideal model delta sinusoidal sigma weight residual -86.00 -136.55 50.55 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 7287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1446 0.051 - 0.103: 241 0.103 - 0.154: 79 0.154 - 0.206: 4 0.206 - 0.257: 2 Chirality restraints: 1772 Sorted by residual: chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 197 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 354 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 354 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 1769 not shown) Planarity restraints: 2027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 383 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.37e+00 pdb=" C TYR A 383 " 0.050 2.00e-02 2.50e+03 pdb=" O TYR A 383 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN A 384 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 192 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C GLU B 192 " 0.024 2.00e-02 2.50e+03 pdb=" O GLU B 192 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY B 193 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 108 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C ARG B 108 " 0.022 2.00e-02 2.50e+03 pdb=" O ARG B 108 " -0.008 2.00e-02 2.50e+03 pdb=" N GLN B 109 " -0.007 2.00e-02 2.50e+03 ... (remaining 2024 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 744 2.73 - 3.27: 11307 3.27 - 3.82: 17797 3.82 - 4.36: 19986 4.36 - 4.90: 35379 Nonbonded interactions: 85213 Sorted by model distance: nonbonded pdb=" OG1 THR B 181 " pdb=" OE1 GLU B 183 " model vdw 2.190 3.040 nonbonded pdb=" OG SER A 440 " pdb=" OE2 GLU C 346 " model vdw 2.202 3.040 nonbonded pdb=" OE2 GLU B 346 " pdb=" OG SER C 440 " model vdw 2.206 3.040 nonbonded pdb=" OE2 GLU A 346 " pdb=" OG SER B 440 " model vdw 2.238 3.040 nonbonded pdb=" O ALA A 26 " pdb=" OH TYR C 429 " model vdw 2.267 3.040 ... (remaining 85208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 23 through 487) selection = chain 'B' selection = (chain 'C' and resid 23 through 487) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.610 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.990 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 : 0.003 0.045 11674 Z= 0.165 Angle : 0.603 10.160 15829 Z= 0.319 Chirality : 0.044 0.257 1772 Planarity : 0.002 0.031 2017 Dihedral : 16.021 110.809 4587 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.49 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.22), residues: 1389 helix: 2.62 (0.31), residues: 294 sheet: 0.17 (0.29), residues: 304 loop : -2.02 (0.19), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 121 HIS 0.009 0.001 HIS A 152 PHE 0.019 0.001 PHE B 485 TYR 0.016 0.001 TYR A 172 ARG 0.002 0.000 ARG A 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00667 ( 10) link_NAG-ASN : angle 2.79537 ( 30) link_BETA1-4 : bond 0.00629 ( 6) link_BETA1-4 : angle 2.24978 ( 18) hydrogen bonds : bond 0.20052 ( 411) hydrogen bonds : angle 7.67445 ( 1158) SS BOND : bond 0.00455 ( 21) SS BOND : angle 1.07221 ( 42) covalent geometry : bond 0.00334 (11636) covalent geometry : angle 0.58445 (15739) Misc. bond : bond 0.00110 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.337 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 72 average time/residue: 1.5745 time to fit residues: 121.9068 Evaluate side-chains 58 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 484 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 41 optimal weight: 0.0070 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** C 286 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 = 0.3400 r_free = 0.3400 target = 0.051094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038279 restraints weight = 64332.654| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.52 r_work: 0.2884 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11674 Z= 0.155 Angle : 0.638 7.432 15829 Z= 0.325 Chirality : 0.045 0.247 1772 Planarity : 0.003 0.036 2017 Dihedral : 13.439 95.690 1836 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.92 % Favored : 92.01 % Rotamer: Outliers : 0.32 % Allowed : 6.49 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1389 helix: 2.57 (0.31), residues: 297 sheet: 0.05 (0.26), residues: 346 loop : -2.08 (0.19), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 121 HIS 0.010 0.001 HIS A 285 PHE 0.036 0.002 PHE C 485 TYR 0.016 0.001 TYR A 172 ARG 0.004 0.000 ARG B 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 10) link_NAG-ASN : angle 2.56557 ( 30) link_BETA1-4 : bond 0.00568 ( 6) link_BETA1-4 : angle 2.58409 ( 18) hydrogen bonds : bond 0.06226 ( 411) hydrogen bonds : angle 5.95681 ( 1158) SS BOND : bond 0.00384 ( 21) SS BOND : angle 1.06208 ( 42) covalent geometry : bond 0.00341 (11636) covalent geometry : angle 0.62193 (15739) Misc. bond : bond 0.00081 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 310 MET cc_start: 0.9069 (mmm) cc_final: 0.8836 (mmp) outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 1.3633 time to fit residues: 89.0383 Evaluate side-chains 60 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain B residue 458 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 1 optimal weight: 0.0470 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN C 132 ASN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.050834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.037987 restraints weight = 64663.931| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.56 r_work: 0.2869 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11674 Z= 0.153 Angle : 0.617 7.831 15829 Z= 0.312 Chirality : 0.044 0.276 1772 Planarity : 0.003 0.033 2017 Dihedral : 11.425 87.806 1833 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.70 % Favored : 92.22 % Rotamer: Outliers : 1.11 % Allowed : 7.84 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.22), residues: 1389 helix: 2.57 (0.31), residues: 298 sheet: 0.07 (0.27), residues: 326 loop : -2.05 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 121 HIS 0.006 0.001 HIS A 285 PHE 0.032 0.001 PHE C 485 TYR 0.012 0.001 TYR A 172 ARG 0.001 0.000 ARG A 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 10) link_NAG-ASN : angle 2.47647 ( 30) link_BETA1-4 : bond 0.00657 ( 6) link_BETA1-4 : angle 2.85779 ( 18) hydrogen bonds : bond 0.06085 ( 411) hydrogen bonds : angle 5.58437 ( 1158) SS BOND : bond 0.00359 ( 21) SS BOND : angle 0.99425 ( 42) covalent geometry : bond 0.00340 (11636) covalent geometry : angle 0.59920 (15739) Misc. bond : bond 0.00077 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9048 (mp0) cc_final: 0.8766 (pm20) REVERT: B 370 MET cc_start: 0.8797 (ttm) cc_final: 0.8554 (ttm) outliers start: 14 outliers final: 4 residues processed: 67 average time/residue: 1.3120 time to fit residues: 96.1691 Evaluate side-chains 61 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain C residue 262 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 0.0050 chunk 23 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.051570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.038739 restraints weight = 64172.054| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 4.56 r_work: 0.2905 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 11674 Z= 0.116 Angle : 0.617 9.786 15829 Z= 0.307 Chirality : 0.044 0.279 1772 Planarity : 0.002 0.030 2017 Dihedral : 9.979 80.724 1833 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.49 % Favored : 92.44 % Rotamer: Outliers : 0.71 % Allowed : 10.06 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1389 helix: 2.56 (0.31), residues: 304 sheet: 0.13 (0.27), residues: 332 loop : -2.04 (0.19), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 121 HIS 0.003 0.001 HIS B 487 PHE 0.029 0.001 PHE C 485 TYR 0.010 0.001 TYR B 383 ARG 0.002 0.000 ARG C 163 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 10) link_NAG-ASN : angle 2.33785 ( 30) link_BETA1-4 : bond 0.00876 ( 6) link_BETA1-4 : angle 2.99728 ( 18) hydrogen bonds : bond 0.05509 ( 411) hydrogen bonds : angle 5.35932 ( 1158) SS BOND : bond 0.00310 ( 21) SS BOND : angle 1.47485 ( 42) covalent geometry : bond 0.00247 (11636) covalent geometry : angle 0.59680 (15739) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9013 (mp0) cc_final: 0.8696 (pm20) REVERT: B 370 MET cc_start: 0.8739 (ttm) cc_final: 0.8476 (ttm) outliers start: 9 outliers final: 4 residues processed: 62 average time/residue: 1.4283 time to fit residues: 96.3523 Evaluate side-chains 59 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 262 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 115 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 85 optimal weight: 0.0570 chunk 65 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 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 = 0.3402 r_free = 0.3402 target = 0.051144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.038347 restraints weight = 64009.722| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.54 r_work: 0.2886 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11674 Z= 0.137 Angle : 0.627 8.648 15829 Z= 0.308 Chirality : 0.044 0.298 1772 Planarity : 0.002 0.030 2017 Dihedral : 8.735 70.845 1833 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.85 % Favored : 92.08 % Rotamer: Outliers : 1.11 % Allowed : 10.69 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1389 helix: 2.58 (0.31), residues: 304 sheet: 0.20 (0.28), residues: 308 loop : -2.02 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 121 HIS 0.003 0.001 HIS B 487 PHE 0.028 0.001 PHE C 485 TYR 0.011 0.001 TYR B 383 ARG 0.001 0.000 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 10) link_NAG-ASN : angle 2.25454 ( 30) link_BETA1-4 : bond 0.00838 ( 6) link_BETA1-4 : angle 3.13196 ( 18) hydrogen bonds : bond 0.05592 ( 411) hydrogen bonds : angle 5.25437 ( 1158) SS BOND : bond 0.00310 ( 21) SS BOND : angle 1.33445 ( 42) covalent geometry : bond 0.00303 (11636) covalent geometry : angle 0.60765 (15739) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: A 370 MET cc_start: 0.8785 (tpp) cc_final: 0.8578 (tpt) REVERT: A 473 GLU cc_start: 0.9005 (mp0) cc_final: 0.8697 (pm20) REVERT: B 370 MET cc_start: 0.8742 (ttm) cc_final: 0.8482 (ttm) outliers start: 14 outliers final: 6 residues processed: 65 average time/residue: 1.5080 time to fit residues: 106.7493 Evaluate side-chains 62 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 262 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 110 optimal weight: 0.2980 chunk 111 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 109 optimal weight: 0.4980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.052028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.039226 restraints weight = 64591.601| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 4.61 r_work: 0.2917 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11674 Z= 0.110 Angle : 0.605 8.686 15829 Z= 0.297 Chirality : 0.044 0.287 1772 Planarity : 0.002 0.029 2017 Dihedral : 7.172 59.258 1833 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.06 % Favored : 92.87 % Rotamer: Outliers : 0.87 % Allowed : 11.80 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.22), residues: 1389 helix: 2.69 (0.32), residues: 304 sheet: 0.27 (0.28), residues: 322 loop : -1.96 (0.19), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 121 HIS 0.004 0.001 HIS B 487 PHE 0.028 0.001 PHE C 485 TYR 0.009 0.001 TYR A 71 ARG 0.001 0.000 ARG B 266 Details of bonding type rmsd link_NAG-ASN : bond 0.00694 ( 10) link_NAG-ASN : angle 2.18223 ( 30) link_BETA1-4 : bond 0.01021 ( 6) link_BETA1-4 : angle 3.28124 ( 18) hydrogen bonds : bond 0.05025 ( 411) hydrogen bonds : angle 5.05045 ( 1158) SS BOND : bond 0.00348 ( 21) SS BOND : angle 1.04659 ( 42) covalent geometry : bond 0.00231 (11636) covalent geometry : angle 0.58622 (15739) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 370 MET cc_start: 0.8803 (tpp) cc_final: 0.8584 (tpt) REVERT: A 473 GLU cc_start: 0.8977 (mp0) cc_final: 0.8643 (pm20) REVERT: B 370 MET cc_start: 0.8728 (ttm) cc_final: 0.8463 (ttm) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 1.4315 time to fit residues: 103.9822 Evaluate side-chains 62 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 262 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 123 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 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 = 0.3401 r_free = 0.3401 target = 0.051213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038299 restraints weight = 64193.940| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.56 r_work: 0.2880 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11674 Z= 0.153 Angle : 0.647 9.542 15829 Z= 0.315 Chirality : 0.044 0.266 1772 Planarity : 0.002 0.029 2017 Dihedral : 6.510 55.399 1833 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.85 % Favored : 92.08 % Rotamer: Outliers : 0.79 % Allowed : 12.83 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.22), residues: 1389 helix: 2.64 (0.31), residues: 304 sheet: 0.26 (0.28), residues: 308 loop : -1.98 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 121 HIS 0.004 0.001 HIS C 335 PHE 0.027 0.001 PHE C 485 TYR 0.012 0.001 TYR A 172 ARG 0.003 0.000 ARG B 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 10) link_NAG-ASN : angle 2.18486 ( 30) link_BETA1-4 : bond 0.01005 ( 6) link_BETA1-4 : angle 3.43752 ( 18) hydrogen bonds : bond 0.05500 ( 411) hydrogen bonds : angle 5.10963 ( 1158) SS BOND : bond 0.00320 ( 21) SS BOND : angle 1.22090 ( 42) covalent geometry : bond 0.00348 (11636) covalent geometry : angle 0.62789 (15739) Misc. bond : bond 0.00090 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8962 (mp0) cc_final: 0.8640 (pm20) REVERT: B 370 MET cc_start: 0.8753 (ttm) cc_final: 0.8475 (ttm) outliers start: 10 outliers final: 9 residues processed: 64 average time/residue: 1.3466 time to fit residues: 93.6099 Evaluate side-chains 65 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 262 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 74 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 132 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.051983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.039066 restraints weight = 63491.987| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 4.58 r_work: 0.2846 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11674 Z= 0.113 Angle : 0.627 10.507 15829 Z= 0.305 Chirality : 0.043 0.264 1772 Planarity : 0.002 0.029 2017 Dihedral : 5.909 53.831 1833 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.20 % Favored : 92.73 % Rotamer: Outliers : 0.71 % Allowed : 13.70 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1389 helix: 2.67 (0.32), residues: 304 sheet: 0.30 (0.28), residues: 322 loop : -1.94 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 121 HIS 0.004 0.001 HIS B 487 PHE 0.026 0.001 PHE C 485 TYR 0.009 0.001 TYR A 71 ARG 0.001 0.000 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 10) link_NAG-ASN : angle 2.14878 ( 30) link_BETA1-4 : bond 0.01137 ( 6) link_BETA1-4 : angle 3.45340 ( 18) hydrogen bonds : bond 0.05122 ( 411) hydrogen bonds : angle 4.98621 ( 1158) SS BOND : bond 0.00302 ( 21) SS BOND : angle 0.98371 ( 42) covalent geometry : bond 0.00243 (11636) covalent geometry : angle 0.60814 (15739) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8949 (mp0) cc_final: 0.8599 (pm20) REVERT: B 370 MET cc_start: 0.8754 (ttm) cc_final: 0.8459 (ttm) outliers start: 9 outliers final: 6 residues processed: 64 average time/residue: 1.3901 time to fit residues: 96.7367 Evaluate side-chains 63 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 262 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 122 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.051472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.038546 restraints weight = 64129.236| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.58 r_work: 0.2825 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11674 Z= 0.137 Angle : 0.654 11.219 15829 Z= 0.316 Chirality : 0.043 0.272 1772 Planarity : 0.002 0.029 2017 Dihedral : 5.644 53.933 1833 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.78 % Favored : 92.15 % Rotamer: Outliers : 0.87 % Allowed : 13.70 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1389 helix: 2.66 (0.32), residues: 304 sheet: 0.37 (0.28), residues: 303 loop : -1.99 (0.19), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 121 HIS 0.003 0.001 HIS B 487 PHE 0.025 0.001 PHE C 485 TYR 0.010 0.001 TYR B 383 ARG 0.001 0.000 ARG B 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 10) link_NAG-ASN : angle 2.15911 ( 30) link_BETA1-4 : bond 0.01096 ( 6) link_BETA1-4 : angle 3.49029 ( 18) hydrogen bonds : bond 0.05331 ( 411) hydrogen bonds : angle 5.02385 ( 1158) SS BOND : bond 0.00309 ( 21) SS BOND : angle 1.11386 ( 42) covalent geometry : bond 0.00308 (11636) covalent geometry : angle 0.63567 (15739) Misc. bond : bond 0.00085 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 370 MET cc_start: 0.8866 (tpt) cc_final: 0.8595 (tpt) REVERT: A 473 GLU cc_start: 0.8946 (mp0) cc_final: 0.8621 (pm20) REVERT: B 370 MET cc_start: 0.8807 (ttm) cc_final: 0.8517 (ttm) outliers start: 11 outliers final: 6 residues processed: 65 average time/residue: 1.3494 time to fit residues: 96.0597 Evaluate side-chains 62 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 262 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 83 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** A 25 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 = 0.3385 r_free = 0.3385 target = 0.050713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.037795 restraints weight = 63827.183| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 4.53 r_work: 0.2859 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11674 Z= 0.167 Angle : 0.683 12.591 15829 Z= 0.333 Chirality : 0.044 0.284 1772 Planarity : 0.003 0.030 2017 Dihedral : 5.552 55.409 1833 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.28 % Favored : 91.65 % Rotamer: Outliers : 0.63 % Allowed : 14.01 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.22), residues: 1389 helix: 2.45 (0.31), residues: 304 sheet: 0.37 (0.28), residues: 301 loop : -2.04 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 121 HIS 0.003 0.001 HIS C 285 PHE 0.026 0.001 PHE C 485 TYR 0.014 0.001 TYR A 172 ARG 0.002 0.000 ARG B 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 10) link_NAG-ASN : angle 2.27189 ( 30) link_BETA1-4 : bond 0.01082 ( 6) link_BETA1-4 : angle 3.57543 ( 18) hydrogen bonds : bond 0.05951 ( 411) hydrogen bonds : angle 5.16665 ( 1158) SS BOND : bond 0.00386 ( 21) SS BOND : angle 1.26661 ( 42) covalent geometry : bond 0.00381 (11636) covalent geometry : angle 0.66368 (15739) Misc. bond : bond 0.00108 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: A 370 MET cc_start: 0.8862 (tpt) cc_final: 0.8607 (tpt) REVERT: A 473 GLU cc_start: 0.8982 (mp0) cc_final: 0.8620 (pm20) REVERT: B 370 MET cc_start: 0.8768 (ttm) cc_final: 0.8504 (ttm) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 1.5262 time to fit residues: 103.9092 Evaluate side-chains 61 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 262 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 77 optimal weight: 3.9990 chunk 136 optimal weight: 0.1980 chunk 73 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 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 = 0.3379 r_free = 0.3379 target = 0.050558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.037717 restraints weight = 63838.593| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 4.46 r_work: 0.2800 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11674 Z= 0.171 Angle : 0.692 12.257 15829 Z= 0.336 Chirality : 0.044 0.274 1772 Planarity : 0.003 0.030 2017 Dihedral : 5.477 55.513 1833 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.42 % Favored : 91.50 % Rotamer: Outliers : 0.55 % Allowed : 14.57 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.22), residues: 1389 helix: 2.37 (0.31), residues: 304 sheet: 0.32 (0.28), residues: 301 loop : -2.07 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 121 HIS 0.003 0.001 HIS B 487 PHE 0.027 0.001 PHE C 485 TYR 0.015 0.001 TYR A 172 ARG 0.002 0.000 ARG B 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 10) link_NAG-ASN : angle 2.32287 ( 30) link_BETA1-4 : bond 0.01139 ( 6) link_BETA1-4 : angle 3.65370 ( 18) hydrogen bonds : bond 0.06067 ( 411) hydrogen bonds : angle 5.17194 ( 1158) SS BOND : bond 0.00353 ( 21) SS BOND : angle 1.37623 ( 42) covalent geometry : bond 0.00389 (11636) covalent geometry : angle 0.67119 (15739) Misc. bond : bond 0.00116 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8783.07 seconds wall clock time: 154 minutes 57.33 seconds (9297.33 seconds total)