Starting phenix.real_space_refine on Wed May 14 06:43:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yg8_39238/05_2025/8yg8_39238.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yg8_39238/05_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_39238/05_2025/8yg8_39238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yg8_39238/05_2025/8yg8_39238.map" model { file = "/net/cci-nas-00/data/ceres_data/8yg8_39238/05_2025/8yg8_39238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yg8_39238/05_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-5687/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: 7.59, 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: 2.96 Conformation dependent library (CDL) restraints added in 1.7 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: 1.41 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: 3.67 Time building geometry restraints manager: 3.45 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: 3.250 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: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.210 Find NCS groups from input model: 0.590 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.150 ------------------------------------------------------------------------------- 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 : 1.344 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 72 average time/residue: 1.5110 time to fit residues: 117.2781 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 : 1.215 ------------------------------------------------------------------------------- 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 = 64332.649| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.52 r_work: 0.2881 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 : 1.401 Fit side-chains revert: symmetry clash REVERT: A 310 MET cc_start: 0.9071 (mmm) cc_final: 0.8846 (mmp) outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 1.4756 time to fit residues: 96.0323 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 : 1.310 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.7980 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- 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** C 324 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.050891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.038041 restraints weight = 64632.486| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.56 r_work: 0.2872 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11674 Z= 0.150 Angle : 0.615 7.749 15829 Z= 0.310 Chirality : 0.044 0.287 1772 Planarity : 0.003 0.033 2017 Dihedral : 11.463 88.024 1833 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % 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: -0.66 (0.22), residues: 1389 helix: 2.58 (0.31), residues: 298 sheet: 0.08 (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 0.013 0.001 TYR A 172 ARG 0.002 0.000 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 10) link_NAG-ASN : angle 2.44442 ( 30) link_BETA1-4 : bond 0.00632 ( 6) link_BETA1-4 : angle 2.85070 ( 18) hydrogen bonds : bond 0.06055 ( 411) hydrogen bonds : angle 5.58400 ( 1158) SS BOND : bond 0.00357 ( 21) SS BOND : angle 0.99150 ( 42) covalent geometry : bond 0.00331 (11636) covalent geometry : angle 0.59727 (15739) Misc. bond : bond 0.00074 ( 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 : 1.300 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9053 (mp0) cc_final: 0.8778 (pm20) REVERT: B 370 MET cc_start: 0.8773 (ttm) cc_final: 0.8522 (ttm) REVERT: C 370 MET cc_start: 0.9092 (ttm) cc_final: 0.8868 (ttt) outliers start: 14 outliers final: 4 residues processed: 67 average time/residue: 1.3014 time to fit residues: 95.5117 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 : 1.381 ------------------------------------------------------------------------------- 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: 0.7980 chunk 23 optimal weight: 0.9980 chunk 67 optimal weight: 0.0050 chunk 117 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.051401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.038573 restraints weight = 64194.749| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.55 r_work: 0.2898 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11674 Z= 0.120 Angle : 0.620 9.916 15829 Z= 0.309 Chirality : 0.044 0.269 1772 Planarity : 0.002 0.031 2017 Dihedral : 10.169 81.386 1833 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.49 % Favored : 92.44 % Rotamer: Outliers : 0.63 % Allowed : 9.98 % Favored : 89.39 % 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: -0.63 (0.22), residues: 1389 helix: 2.55 (0.31), residues: 304 sheet: 0.10 (0.27), residues: 332 loop : -2.06 (0.19), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 121 HIS 0.004 0.001 HIS A 285 PHE 0.028 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 0.00566 ( 10) link_NAG-ASN : angle 2.38324 ( 30) link_BETA1-4 : bond 0.00806 ( 6) link_BETA1-4 : angle 2.96123 ( 18) hydrogen bonds : bond 0.05613 ( 411) hydrogen bonds : angle 5.39048 ( 1158) SS BOND : bond 0.00330 ( 21) SS BOND : angle 1.41389 ( 42) covalent geometry : bond 0.00258 (11636) covalent geometry : angle 0.60085 (15739) Misc. bond : bond 0.00050 ( 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 64 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9023 (mp0) cc_final: 0.8702 (pm20) REVERT: B 370 MET cc_start: 0.8712 (ttm) cc_final: 0.8434 (ttm) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 1.3587 time to fit residues: 91.7589 Evaluate side-chains 60 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 453 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: 2.9990 chunk 27 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.050865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.038060 restraints weight = 63951.165| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.53 r_work: 0.2878 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11674 Z= 0.146 Angle : 0.632 8.527 15829 Z= 0.312 Chirality : 0.044 0.301 1772 Planarity : 0.003 0.030 2017 Dihedral : 8.738 70.291 1833 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.78 % Favored : 92.15 % Rotamer: Outliers : 1.03 % Allowed : 11.16 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.63 (0.22), residues: 1389 helix: 2.55 (0.31), residues: 304 sheet: 0.23 (0.28), residues: 306 loop : -2.05 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 121 HIS 0.003 0.001 HIS A 245 PHE 0.028 0.001 PHE C 485 TYR 0.011 0.001 TYR B 383 ARG 0.001 0.000 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 10) link_NAG-ASN : angle 2.28475 ( 30) link_BETA1-4 : bond 0.00854 ( 6) link_BETA1-4 : angle 3.17902 ( 18) hydrogen bonds : bond 0.05775 ( 411) hydrogen bonds : angle 5.29212 ( 1158) SS BOND : bond 0.00316 ( 21) SS BOND : angle 1.34637 ( 42) covalent geometry : bond 0.00325 (11636) covalent geometry : angle 0.61222 (15739) Misc. bond : bond 0.00085 ( 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 70 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 1.418 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9004 (mp0) cc_final: 0.8697 (pm20) REVERT: B 370 MET cc_start: 0.8749 (ttm) cc_final: 0.8490 (ttm) outliers start: 13 outliers final: 4 residues processed: 65 average time/residue: 1.3636 time to fit residues: 96.4214 Evaluate side-chains 60 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** ** 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 = 0.3348 r_free = 0.3348 target = 0.049546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.036706 restraints weight = 65110.606| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 4.48 r_work: 0.2820 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11674 Z= 0.239 Angle : 0.714 9.565 15829 Z= 0.355 Chirality : 0.046 0.299 1772 Planarity : 0.003 0.033 2017 Dihedral : 7.654 59.026 1833 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.07 % Favored : 90.86 % Rotamer: Outliers : 1.11 % Allowed : 12.51 % 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: -0.89 (0.21), residues: 1389 helix: 2.23 (0.31), residues: 303 sheet: 0.06 (0.28), residues: 305 loop : -2.17 (0.18), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 121 HIS 0.004 0.001 HIS C 285 PHE 0.029 0.002 PHE C 485 TYR 0.017 0.002 TYR A 172 ARG 0.004 0.000 ARG B 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 10) link_NAG-ASN : angle 2.44755 ( 30) link_BETA1-4 : bond 0.00942 ( 6) link_BETA1-4 : angle 3.62838 ( 18) hydrogen bonds : bond 0.06896 ( 411) hydrogen bonds : angle 5.51377 ( 1158) SS BOND : bond 0.00414 ( 21) SS BOND : angle 1.69262 ( 42) covalent geometry : bond 0.00548 (11636) covalent geometry : angle 0.69188 (15739) Misc. bond : bond 0.00154 ( 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 69 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9056 (mp0) cc_final: 0.8704 (pm20) REVERT: B 370 MET cc_start: 0.8846 (ttm) cc_final: 0.8600 (ttm) REVERT: B 484 MET cc_start: 0.1948 (mtt) cc_final: 0.1676 (mtt) outliers start: 14 outliers final: 5 residues processed: 63 average time/residue: 1.3197 time to fit residues: 90.7004 Evaluate side-chains 60 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 262 CYS Chi-restraints excluded: chain C residue 338 ILE 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: 9.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** ** A 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 = 0.3337 r_free = 0.3337 target = 0.049195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.036317 restraints weight = 65446.411| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.50 r_work: 0.2806 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11674 Z= 0.249 Angle : 0.725 9.954 15829 Z= 0.359 Chirality : 0.046 0.283 1772 Planarity : 0.003 0.032 2017 Dihedral : 6.895 59.143 1833 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.14 % Favored : 90.78 % Rotamer: Outliers : 1.35 % Allowed : 13.30 % 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: -1.04 (0.21), residues: 1389 helix: 2.06 (0.31), residues: 303 sheet: -0.10 (0.27), residues: 312 loop : -2.21 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 121 HIS 0.005 0.001 HIS A 285 PHE 0.028 0.002 PHE C 485 TYR 0.015 0.002 TYR A 172 ARG 0.005 0.000 ARG B 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 10) link_NAG-ASN : angle 2.50948 ( 30) link_BETA1-4 : bond 0.01073 ( 6) link_BETA1-4 : angle 3.89162 ( 18) hydrogen bonds : bond 0.07169 ( 411) hydrogen bonds : angle 5.57000 ( 1158) SS BOND : bond 0.00395 ( 21) SS BOND : angle 1.65928 ( 42) covalent geometry : bond 0.00568 (11636) covalent geometry : angle 0.70172 (15739) Misc. bond : bond 0.00169 ( 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 73 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9074 (mp0) cc_final: 0.8776 (pm20) outliers start: 17 outliers final: 8 residues processed: 69 average time/residue: 1.3271 time to fit residues: 99.9894 Evaluate side-chains 63 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain B residue 212 ILE 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 Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 338 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 ** A 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 = 0.3372 r_free = 0.3372 target = 0.050415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.037557 restraints weight = 63593.714| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.49 r_work: 0.2855 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11674 Z= 0.132 Angle : 0.655 9.672 15829 Z= 0.322 Chirality : 0.044 0.252 1772 Planarity : 0.003 0.031 2017 Dihedral : 6.272 58.567 1833 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.85 % Favored : 92.08 % Rotamer: Outliers : 1.19 % Allowed : 14.01 % Favored : 84.80 % 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: -0.84 (0.22), residues: 1389 helix: 2.32 (0.31), residues: 303 sheet: 0.01 (0.27), residues: 321 loop : -2.15 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 121 HIS 0.005 0.001 HIS B 487 PHE 0.027 0.001 PHE C 485 TYR 0.013 0.001 TYR A 172 ARG 0.004 0.000 ARG B 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 10) link_NAG-ASN : angle 2.32338 ( 30) link_BETA1-4 : bond 0.01144 ( 6) link_BETA1-4 : angle 3.71236 ( 18) hydrogen bonds : bond 0.06310 ( 411) hydrogen bonds : angle 5.32816 ( 1158) SS BOND : bond 0.00376 ( 21) SS BOND : angle 1.20493 ( 42) covalent geometry : bond 0.00283 (11636) covalent geometry : angle 0.63393 (15739) Misc. bond : bond 0.00088 ( 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 74 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9034 (mp0) cc_final: 0.8700 (pm20) REVERT: C 487 HIS cc_start: 0.8928 (OUTLIER) cc_final: 0.8535 (p-80) outliers start: 15 outliers final: 5 residues processed: 71 average time/residue: 1.3577 time to fit residues: 105.2359 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 : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 487 HIS 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: 4.9990 chunk 38 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 109 optimal weight: 0.0070 chunk 118 optimal weight: 0.0050 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.3616 ------------------------------------------------------------------------------- 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 ** A 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 = 0.3367 r_free = 0.3367 target = 0.050240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.037465 restraints weight = 63473.379| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 4.43 r_work: 0.2854 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11674 Z= 0.159 Angle : 0.688 11.835 15829 Z= 0.334 Chirality : 0.044 0.271 1772 Planarity : 0.003 0.030 2017 Dihedral : 5.980 56.565 1833 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.57 % Favored : 91.36 % Rotamer: Outliers : 1.03 % Allowed : 14.81 % Favored : 84.16 % 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: -0.82 (0.22), residues: 1389 helix: 2.36 (0.31), residues: 303 sheet: 0.15 (0.28), residues: 301 loop : -2.16 (0.19), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 121 HIS 0.004 0.001 HIS B 487 PHE 0.028 0.001 PHE C 485 TYR 0.012 0.001 TYR B 383 ARG 0.001 0.000 ARG B 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 10) link_NAG-ASN : angle 2.37306 ( 30) link_BETA1-4 : bond 0.01136 ( 6) link_BETA1-4 : angle 3.72773 ( 18) hydrogen bonds : bond 0.06237 ( 411) hydrogen bonds : angle 5.31130 ( 1158) SS BOND : bond 0.00368 ( 21) SS BOND : angle 1.31792 ( 42) covalent geometry : bond 0.00359 (11636) covalent geometry : angle 0.66645 (15739) Misc. bond : bond 0.00102 ( 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 70 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9023 (mp0) cc_final: 0.8710 (pm20) REVERT: C 475 GLU cc_start: 0.8559 (mp0) cc_final: 0.8308 (mp0) REVERT: C 487 HIS cc_start: 0.8937 (OUTLIER) cc_final: 0.8508 (p-80) outliers start: 13 outliers final: 6 residues processed: 68 average time/residue: 1.4127 time to fit residues: 104.4521 Evaluate side-chains 63 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 458 PHE Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 262 CYS Chi-restraints excluded: chain C residue 487 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 132 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 ** A 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 = 0.3366 r_free = 0.3366 target = 0.050272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.037523 restraints weight = 63006.859| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 4.44 r_work: 0.2854 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11674 Z= 0.162 Angle : 0.695 12.006 15829 Z= 0.338 Chirality : 0.044 0.275 1772 Planarity : 0.003 0.030 2017 Dihedral : 5.801 56.140 1833 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.42 % Favored : 91.50 % Rotamer: Outliers : 0.79 % Allowed : 15.20 % Favored : 84.01 % 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: -0.84 (0.21), residues: 1389 helix: 2.29 (0.31), residues: 303 sheet: 0.14 (0.28), residues: 301 loop : -2.15 (0.19), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 121 HIS 0.004 0.001 HIS B 487 PHE 0.027 0.001 PHE C 485 TYR 0.013 0.001 TYR C 68 ARG 0.002 0.000 ARG B 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 10) link_NAG-ASN : angle 2.38996 ( 30) link_BETA1-4 : bond 0.01138 ( 6) link_BETA1-4 : angle 3.72321 ( 18) hydrogen bonds : bond 0.06201 ( 411) hydrogen bonds : angle 5.33525 ( 1158) SS BOND : bond 0.00366 ( 21) SS BOND : angle 1.44061 ( 42) covalent geometry : bond 0.00366 (11636) covalent geometry : angle 0.67372 (15739) Misc. bond : bond 0.00105 ( 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 66 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9023 (mp0) cc_final: 0.8680 (pm20) REVERT: C 475 GLU cc_start: 0.8597 (mp0) cc_final: 0.8361 (mp0) REVERT: C 487 HIS cc_start: 0.8941 (OUTLIER) cc_final: 0.8519 (p-80) outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 1.4250 time to fit residues: 97.6315 Evaluate side-chains 63 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 262 CYS Chi-restraints excluded: chain C residue 487 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 77 optimal weight: 4.9990 chunk 136 optimal weight: 0.0670 chunk 73 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- 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 ** 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 = 0.3342 r_free = 0.3342 target = 0.049436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.036618 restraints weight = 64963.941| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 4.42 r_work: 0.2821 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11674 Z= 0.238 Angle : 0.750 11.569 15829 Z= 0.365 Chirality : 0.046 0.292 1772 Planarity : 0.003 0.031 2017 Dihedral : 5.989 59.812 1833 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 1.03 % Allowed : 15.12 % Favored : 83.85 % 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: -1.00 (0.21), residues: 1389 helix: 2.12 (0.31), residues: 303 sheet: 0.01 (0.28), residues: 299 loop : -2.22 (0.19), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 121 HIS 0.004 0.001 HIS C 285 PHE 0.028 0.002 PHE C 485 TYR 0.015 0.002 TYR A 172 ARG 0.002 0.000 ARG B 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 10) link_NAG-ASN : angle 2.58792 ( 30) link_BETA1-4 : bond 0.01090 ( 6) link_BETA1-4 : angle 3.90682 ( 18) hydrogen bonds : bond 0.06820 ( 411) hydrogen bonds : angle 5.49036 ( 1158) SS BOND : bond 0.00414 ( 21) SS BOND : angle 1.68580 ( 42) covalent geometry : bond 0.00547 (11636) covalent geometry : angle 0.72625 (15739) Misc. bond : bond 0.00152 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6822.89 seconds wall clock time: 119 minutes 1.13 seconds (7141.13 seconds total)