Starting phenix.real_space_refine on Sat Jan 18 00:17:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yg8_39238/01_2025/8yg8_39238.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yg8_39238/01_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_39238/01_2025/8yg8_39238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yg8_39238/01_2025/8yg8_39238.map" model { file = "/net/cci-nas-00/data/ceres_data/8yg8_39238/01_2025/8yg8_39238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yg8_39238/01_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-5571/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: 7.24, per 1000 atoms: 0.63 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: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 22 sheets defined 24.5% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 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: 3.55 Time building geometry restraints manager: 3.18 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 26.920 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.720 ------------------------------------------------------------------------------- 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 11636 Z= 0.215 Angle : 0.584 10.160 15739 Z= 0.315 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 *********************** 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 : 1.319 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 72 average time/residue: 1.5962 time to fit residues: 123.5531 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 : 1.358 ------------------------------------------------------------------------------- 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: 9.9990 chunk 70 optimal weight: 0.4980 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: 1.2802 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.051121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.038308 restraints weight = 64366.257| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.52 r_work: 0.2882 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11636 Z= 0.221 Angle : 0.617 7.177 15739 Z= 0.321 Chirality : 0.045 0.274 1772 Planarity : 0.003 0.036 2017 Dihedral : 13.424 95.820 1836 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.85 % Favored : 92.08 % 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: -0.65 (0.22), residues: 1389 helix: 2.59 (0.31), residues: 297 sheet: 0.07 (0.26), residues: 346 loop : -2.08 (0.19), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 121 HIS 0.010 0.001 HIS A 285 PHE 0.035 0.002 PHE C 485 TYR 0.015 0.001 TYR A 172 ARG 0.004 0.000 ARG B 130 *********************** 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 : 1.352 Fit side-chains revert: symmetry clash REVERT: A 310 MET cc_start: 0.9070 (mmm) cc_final: 0.8844 (mmp) REVERT: A 370 MET cc_start: 0.9083 (tpp) cc_final: 0.8832 (tpt) outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 1.6077 time to fit residues: 104.5065 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 : 1.282 ------------------------------------------------------------------------------- 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: 2.9990 chunk 62 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.049455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.036580 restraints weight = 64452.117| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 4.47 r_work: 0.2820 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11636 Z= 0.369 Angle : 0.681 7.509 15739 Z= 0.351 Chirality : 0.046 0.291 1772 Planarity : 0.003 0.033 2017 Dihedral : 11.514 85.912 1833 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.78 % Favored : 91.14 % Rotamer: Outliers : 1.27 % Allowed : 8.71 % Favored : 90.02 % 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: -0.96 (0.21), residues: 1389 helix: 2.24 (0.31), residues: 297 sheet: -0.07 (0.27), residues: 322 loop : -2.21 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 121 HIS 0.008 0.001 HIS A 285 PHE 0.035 0.002 PHE C 485 TYR 0.018 0.002 TYR A 172 ARG 0.002 0.000 ARG A 266 *********************** 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: 16 poor density : 57 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8944 (mmp) REVERT: A 473 GLU cc_start: 0.9045 (mp0) cc_final: 0.8771 (pm20) REVERT: B 370 MET cc_start: 0.8814 (ttm) cc_final: 0.8601 (ttm) outliers start: 16 outliers final: 3 residues processed: 66 average time/residue: 1.3499 time to fit residues: 97.4113 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 : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain C residue 262 CYS Chi-restraints excluded: chain C residue 338 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 111 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.050168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.037187 restraints weight = 64159.294| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.55 r_work: 0.2838 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 11636 Z= 0.247 Angle : 0.634 12.101 15739 Z= 0.324 Chirality : 0.045 0.279 1772 Planarity : 0.003 0.031 2017 Dihedral : 10.320 79.690 1833 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.28 % Favored : 91.65 % Rotamer: Outliers : 0.95 % Allowed : 10.53 % 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 (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: -0.93 (0.21), residues: 1389 helix: 2.18 (0.31), residues: 303 sheet: -0.04 (0.26), residues: 328 loop : -2.20 (0.19), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 121 HIS 0.004 0.001 HIS A 285 PHE 0.029 0.001 PHE C 485 TYR 0.013 0.001 TYR B 383 ARG 0.002 0.000 ARG B 135 *********************** 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 69 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9132 (mmm) cc_final: 0.8912 (mmp) REVERT: A 473 GLU cc_start: 0.9043 (mp0) cc_final: 0.8776 (pm20) REVERT: B 484 MET cc_start: 0.2225 (mtt) cc_final: 0.1960 (mtt) REVERT: C 370 MET cc_start: 0.9100 (ttm) cc_final: 0.8875 (ttt) outliers start: 12 outliers final: 5 residues processed: 64 average time/residue: 1.4513 time to fit residues: 101.0807 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 : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 262 CYS Chi-restraints excluded: chain C residue 310 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 115 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 100 optimal weight: 0.0040 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.050641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.037699 restraints weight = 63565.371| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.57 r_work: 0.2852 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11636 Z= 0.197 Angle : 0.610 9.858 15739 Z= 0.310 Chirality : 0.044 0.284 1772 Planarity : 0.003 0.031 2017 Dihedral : 9.088 72.123 1833 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.92 % Favored : 92.01 % Rotamer: Outliers : 1.03 % Allowed : 12.11 % Favored : 86.86 % 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: -0.78 (0.22), residues: 1389 helix: 2.27 (0.31), residues: 306 sheet: 0.07 (0.27), residues: 320 loop : -2.10 (0.19), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 121 HIS 0.004 0.001 HIS B 487 PHE 0.029 0.001 PHE C 485 TYR 0.012 0.001 TYR B 383 ARG 0.002 0.000 ARG B 135 *********************** 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 72 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9129 (mmm) cc_final: 0.8922 (mmp) REVERT: A 370 MET cc_start: 0.8856 (tpp) cc_final: 0.8543 (tpt) REVERT: A 473 GLU cc_start: 0.9045 (mp0) cc_final: 0.8701 (pm20) REVERT: B 370 MET cc_start: 0.8697 (ttm) cc_final: 0.8455 (ttm) outliers start: 13 outliers final: 3 residues processed: 68 average time/residue: 1.4150 time to fit residues: 104.5580 Evaluate side-chains 59 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS 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: 0.9980 chunk 68 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** 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 = 0.3372 r_free = 0.3372 target = 0.050374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.037583 restraints weight = 63774.759| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.48 r_work: 0.2794 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11636 Z= 0.223 Angle : 0.627 9.747 15739 Z= 0.313 Chirality : 0.044 0.279 1772 Planarity : 0.003 0.030 2017 Dihedral : 7.799 61.032 1833 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.14 % Favored : 91.79 % Rotamer: Outliers : 1.11 % Allowed : 13.38 % 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 (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: -0.77 (0.22), residues: 1389 helix: 2.31 (0.31), residues: 306 sheet: 0.11 (0.28), residues: 307 loop : -2.09 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 121 HIS 0.004 0.001 HIS B 487 PHE 0.029 0.001 PHE C 485 TYR 0.011 0.001 TYR B 383 ARG 0.002 0.000 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8960 (mmp) REVERT: A 370 MET cc_start: 0.8820 (tpp) cc_final: 0.8551 (tpt) REVERT: A 473 GLU cc_start: 0.8993 (mp0) cc_final: 0.8712 (pm20) REVERT: B 370 MET cc_start: 0.8790 (ttm) cc_final: 0.8538 (ttm) outliers start: 14 outliers final: 4 residues processed: 65 average time/residue: 1.3360 time to fit residues: 95.0152 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 : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain B residue 212 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 123 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** C 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.049386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.036516 restraints weight = 64856.447| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 4.49 r_work: 0.2818 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 11636 Z= 0.331 Angle : 0.679 9.325 15739 Z= 0.343 Chirality : 0.046 0.312 1772 Planarity : 0.003 0.031 2017 Dihedral : 6.915 59.227 1833 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.36 % Favored : 90.57 % Rotamer: Outliers : 1.50 % Allowed : 13.94 % Favored : 84.56 % 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: -0.97 (0.21), residues: 1389 helix: 2.11 (0.31), residues: 304 sheet: -0.01 (0.27), residues: 305 loop : -2.19 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 121 HIS 0.004 0.001 HIS C 285 PHE 0.029 0.002 PHE C 485 TYR 0.014 0.002 TYR B 383 ARG 0.004 0.000 ARG B 288 *********************** 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 75 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8912 (mmp) REVERT: A 370 MET cc_start: 0.8746 (tpp) cc_final: 0.8467 (tpt) REVERT: A 473 GLU cc_start: 0.9063 (mp0) cc_final: 0.8716 (pm20) outliers start: 19 outliers final: 6 residues processed: 66 average time/residue: 1.3166 time to fit residues: 95.0556 Evaluate side-chains 62 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 132 optimal weight: 0.0770 chunk 108 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.051006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.038201 restraints weight = 62930.897| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 4.52 r_work: 0.2876 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11636 Z= 0.167 Angle : 0.612 10.126 15739 Z= 0.306 Chirality : 0.044 0.271 1772 Planarity : 0.002 0.030 2017 Dihedral : 6.044 55.301 1833 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 1.27 % Allowed : 14.57 % 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: -0.76 (0.22), residues: 1389 helix: 2.36 (0.31), residues: 306 sheet: -0.03 (0.27), residues: 333 loop : -2.09 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 121 HIS 0.005 0.001 HIS B 487 PHE 0.026 0.001 PHE C 485 TYR 0.010 0.001 TYR A 71 ARG 0.005 0.000 ARG B 206 *********************** 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 73 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8887 (mmp) REVERT: A 473 GLU cc_start: 0.8996 (mp0) cc_final: 0.8690 (pm20) REVERT: B 370 MET cc_start: 0.8675 (ttm) cc_final: 0.8454 (ttm) outliers start: 16 outliers final: 4 residues processed: 71 average time/residue: 1.3756 time to fit residues: 106.4219 Evaluate side-chains 61 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 164 CYS Chi-restraints excluded: chain C residue 262 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 122 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 118 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** 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 = 0.3343 r_free = 0.3343 target = 0.049435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.036710 restraints weight = 63851.015| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 4.42 r_work: 0.2825 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11636 Z= 0.342 Angle : 0.709 11.622 15739 Z= 0.352 Chirality : 0.045 0.287 1772 Planarity : 0.004 0.107 2017 Dihedral : 6.132 57.544 1833 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.29 % Favored : 90.64 % Rotamer: Outliers : 0.87 % Allowed : 15.52 % Favored : 83.61 % 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: -0.93 (0.21), residues: 1389 helix: 2.12 (0.31), residues: 305 sheet: 0.14 (0.28), residues: 299 loop : -2.20 (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 C 155 PHE 0.029 0.002 PHE C 485 TYR 0.014 0.002 TYR B 383 ARG 0.019 0.000 ARG B 288 *********************** 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 68 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8965 (mmp) REVERT: A 473 GLU cc_start: 0.9020 (mp0) cc_final: 0.8669 (pm20) REVERT: B 288 ARG cc_start: 0.8825 (mmm160) cc_final: 0.8452 (tpp-160) REVERT: B 370 MET cc_start: 0.8777 (ttm) cc_final: 0.8551 (ttm) outliers start: 11 outliers final: 6 residues processed: 62 average time/residue: 1.5567 time to fit residues: 104.7036 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 : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 453 MET 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 83 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.049738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.036835 restraints weight = 64422.626| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 4.50 r_work: 0.2831 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11636 Z= 0.291 Angle : 0.691 12.000 15739 Z= 0.341 Chirality : 0.045 0.281 1772 Planarity : 0.003 0.080 2017 Dihedral : 6.006 58.754 1833 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.35 % Favored : 91.58 % Rotamer: Outliers : 0.71 % Allowed : 16.07 % Favored : 83.21 % 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: -0.95 (0.21), residues: 1389 helix: 2.07 (0.31), residues: 305 sheet: 0.12 (0.28), residues: 301 loop : -2.20 (0.19), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 121 HIS 0.005 0.001 HIS C 285 PHE 0.027 0.001 PHE C 485 TYR 0.013 0.001 TYR B 383 ARG 0.016 0.000 ARG B 288 ********************** 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: 9 poor density : 56 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8908 (mmp) REVERT: A 473 GLU cc_start: 0.9023 (mp0) cc_final: 0.8713 (pm20) REVERT: B 288 ARG cc_start: 0.8840 (mmm160) cc_final: 0.8476 (tpp-160) REVERT: C 487 HIS cc_start: 0.8939 (t-90) cc_final: 0.8500 (p-80) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 1.5189 time to fit residues: 103.5155 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 : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain B residue 186 VAL 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 Chi-restraints excluded: chain C residue 310 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 77 optimal weight: 3.9990 chunk 136 optimal weight: 0.0000 chunk 73 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 85 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.050939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.038172 restraints weight = 62351.231| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.46 r_work: 0.2879 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11636 Z= 0.173 Angle : 0.647 12.731 15739 Z= 0.319 Chirality : 0.044 0.276 1772 Planarity : 0.003 0.075 2017 Dihedral : 5.460 54.688 1833 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.87 % Allowed : 15.84 % Favored : 83.29 % 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: -0.80 (0.22), residues: 1389 helix: 2.27 (0.31), residues: 306 sheet: 0.06 (0.28), residues: 313 loop : -2.09 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 121 HIS 0.005 0.001 HIS B 487 PHE 0.027 0.001 PHE C 485 TYR 0.010 0.001 TYR A 71 ARG 0.016 0.000 ARG B 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7072.53 seconds wall clock time: 128 minutes 9.02 seconds (7689.02 seconds total)