Starting phenix.real_space_refine on Wed Sep 17 21:30:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yg8_39238/09_2025/8yg8_39238.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yg8_39238/09_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_39238/09_2025/8yg8_39238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yg8_39238/09_2025/8yg8_39238.map" model { file = "/net/cci-nas-00/data/ceres_data/8yg8_39238/09_2025/8yg8_39238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yg8_39238/09_2025/8yg8_39238.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.00, per 1000 atoms: 0.26 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: 1.01 Conformation dependent library (CDL) restraints added in 541.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.44 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: 1.81 Time building geometry restraints manager: 1.35 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: 3.200 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.990 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 130 TYR 0.016 0.001 TYR A 172 PHE 0.019 0.001 PHE B 485 TRP 0.013 0.001 TRP A 121 HIS 0.009 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00334 (11636) covalent geometry : angle 0.58445 (15739) SS BOND : bond 0.00455 ( 21) SS BOND : angle 1.07221 ( 42) hydrogen bonds : bond 0.20052 ( 411) hydrogen bonds : angle 7.67445 ( 1158) Misc. bond : bond 0.00110 ( 1) link_BETA1-4 : bond 0.00629 ( 6) link_BETA1-4 : angle 2.24978 ( 18) link_NAG-ASN : bond 0.00667 ( 10) link_NAG-ASN : angle 2.79537 ( 30) *********************** 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 : 0.353 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 72 average time/residue: 0.7765 time to fit residues: 59.7987 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 : 0.503 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 63 ASN C 286 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.051645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.038836 restraints weight = 64553.160| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 4.53 r_work: 0.2905 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11674 Z= 0.129 Angle : 0.625 7.327 15829 Z= 0.318 Chirality : 0.045 0.247 1772 Planarity : 0.003 0.035 2017 Dihedral : 13.288 95.716 1836 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.70 % Favored : 92.22 % Rotamer: Outliers : 0.48 % Allowed : 6.49 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.22), residues: 1389 helix: 2.67 (0.31), residues: 297 sheet: 0.05 (0.26), residues: 348 loop : -2.01 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 130 TYR 0.014 0.001 TYR A 172 PHE 0.036 0.001 PHE C 485 TRP 0.025 0.001 TRP A 121 HIS 0.012 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00273 (11636) covalent geometry : angle 0.60879 (15739) SS BOND : bond 0.00375 ( 21) SS BOND : angle 0.95999 ( 42) hydrogen bonds : bond 0.05995 ( 411) hydrogen bonds : angle 5.90367 ( 1158) Misc. bond : bond 0.00068 ( 1) link_BETA1-4 : bond 0.00573 ( 6) link_BETA1-4 : angle 2.57770 ( 18) link_NAG-ASN : bond 0.00624 ( 10) link_NAG-ASN : angle 2.57380 ( 30) *********************** 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 65 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 370 MET cc_start: 0.9116 (tpp) cc_final: 0.8860 (tpt) outliers start: 6 outliers final: 3 residues processed: 63 average time/residue: 0.7006 time to fit residues: 47.5348 Evaluate side-chains 61 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 35 optimal weight: 0.0270 chunk 41 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 125 optimal weight: 0.0770 overall best weight: 1.5600 ------------------------------------------------------------------------------- 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 132 ASN C 286 ASN C 324 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.050831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.037725 restraints weight = 65454.065| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 4.66 r_work: 0.2856 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11674 Z= 0.167 Angle : 0.626 8.113 15829 Z= 0.318 Chirality : 0.045 0.305 1772 Planarity : 0.003 0.032 2017 Dihedral : 11.159 86.276 1833 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.99 % Favored : 91.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.22), residues: 1389 helix: 2.54 (0.31), residues: 298 sheet: 0.07 (0.27), residues: 322 loop : -2.07 (0.19), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 275 TYR 0.017 0.001 TYR A 172 PHE 0.033 0.002 PHE C 485 TRP 0.015 0.001 TRP A 121 HIS 0.006 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00372 (11636) covalent geometry : angle 0.60825 (15739) SS BOND : bond 0.00383 ( 21) SS BOND : angle 1.09711 ( 42) hydrogen bonds : bond 0.06217 ( 411) hydrogen bonds : angle 5.55006 ( 1158) Misc. bond : bond 0.00087 ( 1) link_BETA1-4 : bond 0.00666 ( 6) link_BETA1-4 : angle 2.92371 ( 18) link_NAG-ASN : bond 0.00567 ( 10) link_NAG-ASN : angle 2.44005 ( 30) *********************** 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 74 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9046 (mp0) cc_final: 0.8749 (pm20) outliers start: 14 outliers final: 3 residues processed: 67 average time/residue: 0.6332 time to fit residues: 46.0209 Evaluate side-chains 61 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain B residue 420 TRP 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 55 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.0070 overall best weight: 1.3604 ------------------------------------------------------------------------------- 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 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.050791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.037995 restraints weight = 65087.569| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.55 r_work: 0.2873 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 11674 Z= 0.154 Angle : 0.638 10.178 15829 Z= 0.318 Chirality : 0.044 0.283 1772 Planarity : 0.003 0.031 2017 Dihedral : 9.902 77.904 1833 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.70 % Favored : 92.22 % Rotamer: Outliers : 0.79 % Allowed : 9.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.21), residues: 1389 helix: 2.39 (0.31), residues: 305 sheet: 0.16 (0.28), residues: 306 loop : -2.08 (0.19), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 163 TYR 0.012 0.001 TYR B 383 PHE 0.028 0.001 PHE C 485 TRP 0.018 0.001 TRP A 121 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00346 (11636) covalent geometry : angle 0.61691 (15739) SS BOND : bond 0.00351 ( 21) SS BOND : angle 1.64987 ( 42) hydrogen bonds : bond 0.06050 ( 411) hydrogen bonds : angle 5.43467 ( 1158) Misc. bond : bond 0.00045 ( 1) link_BETA1-4 : bond 0.00825 ( 6) link_BETA1-4 : angle 3.07499 ( 18) link_NAG-ASN : bond 0.00518 ( 10) link_NAG-ASN : angle 2.40455 ( 30) *********************** 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 68 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9039 (mp0) cc_final: 0.8735 (pm20) REVERT: C 370 MET cc_start: 0.9087 (ttm) cc_final: 0.8864 (ttt) outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 0.6523 time to fit residues: 45.7409 Evaluate side-chains 62 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 108 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.050652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.037796 restraints weight = 64773.169| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 4.56 r_work: 0.2869 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1581 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= 0.148 Angle : 0.635 8.962 15829 Z= 0.315 Chirality : 0.044 0.286 1772 Planarity : 0.002 0.031 2017 Dihedral : 8.817 69.767 1833 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.92 % Favored : 92.01 % Rotamer: Outliers : 0.87 % Allowed : 10.61 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.22), residues: 1389 helix: 2.45 (0.31), residues: 304 sheet: 0.18 (0.28), residues: 306 loop : -2.07 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 135 TYR 0.011 0.001 TYR B 383 PHE 0.027 0.001 PHE C 485 TRP 0.016 0.001 TRP A 121 HIS 0.003 0.001 HIS B 487 Details of bonding type rmsd covalent geometry : bond 0.00331 (11636) covalent geometry : angle 0.61414 (15739) SS BOND : bond 0.00381 ( 21) SS BOND : angle 1.44848 ( 42) hydrogen bonds : bond 0.05962 ( 411) hydrogen bonds : angle 5.35063 ( 1158) Misc. bond : bond 0.00087 ( 1) link_BETA1-4 : bond 0.00901 ( 6) link_BETA1-4 : angle 3.22788 ( 18) link_NAG-ASN : bond 0.00520 ( 10) link_NAG-ASN : angle 2.37815 ( 30) *********************** 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 69 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 370 MET cc_start: 0.8867 (tpp) cc_final: 0.8542 (tpt) REVERT: A 473 GLU cc_start: 0.9045 (mp0) cc_final: 0.8707 (pm20) REVERT: B 370 MET cc_start: 0.8713 (ttm) cc_final: 0.8503 (ttm) outliers start: 11 outliers final: 5 residues processed: 64 average time/residue: 0.7354 time to fit residues: 50.7667 Evaluate side-chains 62 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS 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 14 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 35 optimal weight: 0.0980 chunk 128 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.051244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.038389 restraints weight = 63184.599| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.54 r_work: 0.2885 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11674 Z= 0.126 Angle : 0.621 8.864 15829 Z= 0.306 Chirality : 0.044 0.295 1772 Planarity : 0.002 0.030 2017 Dihedral : 7.490 59.595 1833 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.34 % Favored : 92.58 % Rotamer: Outliers : 1.11 % Allowed : 12.19 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.22), residues: 1389 helix: 2.53 (0.31), residues: 304 sheet: 0.15 (0.27), residues: 322 loop : -2.04 (0.19), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 288 TYR 0.010 0.001 TYR B 383 PHE 0.027 0.001 PHE C 485 TRP 0.018 0.001 TRP A 121 HIS 0.004 0.001 HIS B 487 Details of bonding type rmsd covalent geometry : bond 0.00275 (11636) covalent geometry : angle 0.60107 (15739) SS BOND : bond 0.00307 ( 21) SS BOND : angle 1.20047 ( 42) hydrogen bonds : bond 0.05625 ( 411) hydrogen bonds : angle 5.18897 ( 1158) Misc. bond : bond 0.00071 ( 1) link_BETA1-4 : bond 0.00987 ( 6) link_BETA1-4 : angle 3.34462 ( 18) link_NAG-ASN : bond 0.00653 ( 10) link_NAG-ASN : angle 2.25394 ( 30) *********************** 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 72 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 370 MET cc_start: 0.8817 (tpp) cc_final: 0.8560 (tpt) REVERT: A 473 GLU cc_start: 0.8985 (mp0) cc_final: 0.8677 (pm20) REVERT: B 370 MET cc_start: 0.8758 (ttm) cc_final: 0.8549 (ttm) outliers start: 14 outliers final: 7 residues processed: 67 average time/residue: 0.6867 time to fit residues: 49.8862 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 : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS 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 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 86 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.050486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.037572 restraints weight = 64280.680| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.55 r_work: 0.2852 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11674 Z= 0.171 Angle : 0.665 9.570 15829 Z= 0.326 Chirality : 0.044 0.289 1772 Planarity : 0.003 0.030 2017 Dihedral : 6.694 56.540 1833 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.28 % Favored : 91.65 % Rotamer: Outliers : 0.87 % Allowed : 13.30 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.22), residues: 1389 helix: 2.41 (0.31), residues: 304 sheet: 0.20 (0.28), residues: 307 loop : -2.08 (0.19), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 288 TYR 0.012 0.001 TYR A 172 PHE 0.028 0.001 PHE C 485 TRP 0.018 0.001 TRP A 121 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00388 (11636) covalent geometry : angle 0.64461 (15739) SS BOND : bond 0.00353 ( 21) SS BOND : angle 1.39096 ( 42) hydrogen bonds : bond 0.06032 ( 411) hydrogen bonds : angle 5.23935 ( 1158) Misc. bond : bond 0.00103 ( 1) link_BETA1-4 : bond 0.01001 ( 6) link_BETA1-4 : angle 3.55246 ( 18) link_NAG-ASN : bond 0.00518 ( 10) link_NAG-ASN : angle 2.27333 ( 30) *********************** 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 69 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 370 MET cc_start: 0.8769 (tpp) cc_final: 0.8511 (tpt) REVERT: A 473 GLU cc_start: 0.9007 (mp0) cc_final: 0.8662 (pm20) REVERT: B 370 MET cc_start: 0.8732 (ttm) cc_final: 0.8487 (ttm) REVERT: B 484 MET cc_start: 0.1797 (mtt) cc_final: 0.1580 (mtt) REVERT: C 475 GLU cc_start: 0.8536 (mp0) cc_final: 0.8206 (mp0) outliers start: 11 outliers final: 6 residues processed: 64 average time/residue: 0.6975 time to fit residues: 48.3395 Evaluate side-chains 64 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 364 ASP 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 119 optimal weight: 0.6980 chunk 113 optimal weight: 0.0370 chunk 131 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 118 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.051776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.038895 restraints weight = 63213.244| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 4.54 r_work: 0.2839 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11674 Z= 0.111 Angle : 0.625 10.328 15829 Z= 0.306 Chirality : 0.043 0.273 1772 Planarity : 0.002 0.029 2017 Dihedral : 5.906 53.645 1833 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.49 % Favored : 92.44 % Rotamer: Outliers : 1.03 % Allowed : 13.46 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.22), residues: 1389 helix: 2.62 (0.31), residues: 304 sheet: 0.22 (0.27), residues: 322 loop : -2.00 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.010 0.001 TYR A 71 PHE 0.025 0.001 PHE C 485 TRP 0.021 0.001 TRP A 121 HIS 0.004 0.001 HIS B 487 Details of bonding type rmsd covalent geometry : bond 0.00233 (11636) covalent geometry : angle 0.60564 (15739) SS BOND : bond 0.00327 ( 21) SS BOND : angle 0.99364 ( 42) hydrogen bonds : bond 0.05266 ( 411) hydrogen bonds : angle 5.01879 ( 1158) Misc. bond : bond 0.00054 ( 1) link_BETA1-4 : bond 0.01181 ( 6) link_BETA1-4 : angle 3.51882 ( 18) link_NAG-ASN : bond 0.00629 ( 10) link_NAG-ASN : angle 2.18147 ( 30) *********************** 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 71 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8961 (mp0) cc_final: 0.8643 (pm20) REVERT: B 370 MET cc_start: 0.8769 (ttm) cc_final: 0.8516 (ttm) REVERT: C 475 GLU cc_start: 0.8554 (mp0) cc_final: 0.8236 (mp0) outliers start: 13 outliers final: 4 residues processed: 69 average time/residue: 0.6540 time to fit residues: 49.0133 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 : 0.473 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 25 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 109 optimal weight: 0.0170 chunk 104 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 9 optimal weight: 0.0370 chunk 114 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.052169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.039306 restraints weight = 63167.344| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 4.56 r_work: 0.2855 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11674 Z= 0.110 Angle : 0.629 11.048 15829 Z= 0.306 Chirality : 0.043 0.240 1772 Planarity : 0.002 0.028 2017 Dihedral : 5.453 52.285 1833 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.20 % Favored : 92.73 % Rotamer: Outliers : 0.71 % Allowed : 14.17 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.22), residues: 1389 helix: 2.71 (0.32), residues: 304 sheet: 0.32 (0.28), residues: 312 loop : -2.00 (0.19), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 266 TYR 0.009 0.001 TYR A 71 PHE 0.025 0.001 PHE C 485 TRP 0.019 0.001 TRP A 121 HIS 0.004 0.001 HIS B 487 Details of bonding type rmsd covalent geometry : bond 0.00234 (11636) covalent geometry : angle 0.61027 (15739) SS BOND : bond 0.00343 ( 21) SS BOND : angle 1.05716 ( 42) hydrogen bonds : bond 0.04930 ( 411) hydrogen bonds : angle 4.98414 ( 1158) Misc. bond : bond 0.00054 ( 1) link_BETA1-4 : bond 0.01151 ( 6) link_BETA1-4 : angle 3.46624 ( 18) link_NAG-ASN : bond 0.00561 ( 10) link_NAG-ASN : angle 2.13017 ( 30) *********************** 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 66 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8924 (mp0) cc_final: 0.8555 (pm20) REVERT: B 211 MET cc_start: 0.6928 (ppp) cc_final: 0.6647 (pmm) REVERT: B 213 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7623 (pt) REVERT: B 370 MET cc_start: 0.8763 (ttm) cc_final: 0.8508 (ttm) REVERT: C 475 GLU cc_start: 0.8607 (mp0) cc_final: 0.8290 (mp0) outliers start: 9 outliers final: 3 residues processed: 64 average time/residue: 0.6961 time to fit residues: 47.9975 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 : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 LEU 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 57 optimal weight: 8.9990 chunk 118 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 ** 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 = 0.3348 r_free = 0.3348 target = 0.049514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.036687 restraints weight = 63287.367| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 4.49 r_work: 0.2824 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 11674 Z= 0.248 Angle : 0.772 12.997 15829 Z= 0.378 Chirality : 0.046 0.329 1772 Planarity : 0.003 0.031 2017 Dihedral : 5.918 57.198 1833 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.22 % Favored : 90.71 % Rotamer: Outliers : 0.63 % Allowed : 14.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.21), residues: 1389 helix: 2.27 (0.31), residues: 303 sheet: 0.19 (0.27), residues: 308 loop : -2.16 (0.19), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 288 TYR 0.018 0.002 TYR A 172 PHE 0.028 0.002 PHE C 485 TRP 0.020 0.001 TRP A 121 HIS 0.008 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00572 (11636) covalent geometry : angle 0.75034 (15739) SS BOND : bond 0.00434 ( 21) SS BOND : angle 1.86784 ( 42) hydrogen bonds : bond 0.06809 ( 411) hydrogen bonds : angle 5.42278 ( 1158) Misc. bond : bond 0.00161 ( 1) link_BETA1-4 : bond 0.01013 ( 6) link_BETA1-4 : angle 3.70826 ( 18) link_NAG-ASN : bond 0.00492 ( 10) link_NAG-ASN : angle 2.43200 ( 30) ********************** 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 : 0.485 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9037 (mp0) cc_final: 0.8728 (pm20) REVERT: B 370 MET cc_start: 0.8809 (ttm) cc_final: 0.8566 (ttm) outliers start: 8 outliers final: 3 residues processed: 64 average time/residue: 0.6771 time to fit residues: 46.9950 Evaluate side-chains 58 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 129 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 chunk 108 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.051142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.038316 restraints weight = 62488.040| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.50 r_work: 0.2881 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 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 : 0.003 0.057 11674 Z= 0.125 Angle : 0.676 12.151 15829 Z= 0.330 Chirality : 0.044 0.268 1772 Planarity : 0.002 0.029 2017 Dihedral : 5.425 55.037 1833 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.98 % Favored : 92.94 % Rotamer: Outliers : 0.32 % Allowed : 15.28 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.22), residues: 1389 helix: 2.40 (0.31), residues: 304 sheet: 0.19 (0.27), residues: 317 loop : -2.09 (0.19), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 135 TYR 0.013 0.001 TYR C 68 PHE 0.026 0.001 PHE C 485 TRP 0.022 0.001 TRP A 121 HIS 0.005 0.001 HIS B 487 Details of bonding type rmsd covalent geometry : bond 0.00268 (11636) covalent geometry : angle 0.65613 (15739) SS BOND : bond 0.00387 ( 21) SS BOND : angle 1.26784 ( 42) hydrogen bonds : bond 0.05869 ( 411) hydrogen bonds : angle 5.20629 ( 1158) Misc. bond : bond 0.00059 ( 1) link_BETA1-4 : bond 0.01203 ( 6) link_BETA1-4 : angle 3.60795 ( 18) link_NAG-ASN : bond 0.00624 ( 10) link_NAG-ASN : angle 2.27947 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3624.39 seconds wall clock time: 62 minutes 43.39 seconds (3763.39 seconds total)