Starting phenix.real_space_refine on Wed Sep 25 23:14:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yg8_39238/09_2024/8yg8_39238.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yg8_39238/09_2024/8yg8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yg8_39238/09_2024/8yg8_39238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yg8_39238/09_2024/8yg8_39238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yg8_39238/09_2024/8yg8_39238.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yg8_39238/09_2024/8yg8_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-5461/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: 7.57, per 1000 atoms: 0.66 Number of scatterers: 11414 At special positions: 0 Unit cell: (92.16, 111.36, 155.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2276 8.00 N 1966 7.00 C 7085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS B 372 " distance=2.04 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 267 " distance=2.04 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS C 24 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 402 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS C 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 262 " - pdb=" SG CYS B 267 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 402 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 164 " distance=2.02 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 177 " - pdb=" SG CYS C 184 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 262 " - pdb=" SG CYS C 267 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 402 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " NAG D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " NAG-ASN " NAG A 501 " - " ASN A 197 " " NAG A 502 " - " ASN A 384 " " NAG A 503 " - " ASN A 426 " " NAG C 501 " - " ASN B 384 " " NAG C 502 " - " ASN C 197 " " NAG C 503 " - " ASN C 384 " " NAG C 504 " - " ASN C 426 " " NAG D 1 " - " ASN A 354 " " NAG E 1 " - " ASN B 354 " " NAG F 1 " - " ASN C 354 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.5 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: 1.32 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: 3.97 Time building geometry restraints manager: 3.24 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: 2.830 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: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.850 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.020 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.380 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 72 average time/residue: 1.6094 time to fit residues: 124.9532 Evaluate side-chains 58 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: A 310 MET cc_start: 0.8943 (mmm) cc_final: 0.8690 (mmp) outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 1.5234 time to fit residues: 98.9705 Evaluate side-chains 61 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 69 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 34 optimal weight: 0.0000 chunk 125 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN C 132 ASN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11636 Z= 0.179 Angle : 0.585 7.827 15739 Z= 0.300 Chirality : 0.044 0.271 1772 Planarity : 0.003 0.033 2017 Dihedral : 11.337 88.164 1833 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.13 % Favored : 92.80 % Rotamer: Outliers : 0.79 % Allowed : 8.55 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1389 helix: 2.66 (0.31), residues: 298 sheet: 0.08 (0.27), residues: 328 loop : -2.00 (0.19), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 121 HIS 0.007 0.001 HIS A 285 PHE 0.035 0.001 PHE C 485 TYR 0.011 0.001 TYR B 383 ARG 0.001 0.000 ARG B 108 *********************** 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 70 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9013 (mmm) cc_final: 0.8791 (mmp) REVERT: A 473 GLU cc_start: 0.8872 (mp0) cc_final: 0.8540 (pm20) REVERT: B 310 MET cc_start: 0.9227 (mmp) cc_final: 0.9026 (mmm) REVERT: B 370 MET cc_start: 0.8309 (ttm) cc_final: 0.8024 (ttm) outliers start: 10 outliers final: 3 residues processed: 66 average time/residue: 1.3351 time to fit residues: 96.6224 Evaluate side-chains 61 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain C residue 262 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 11636 Z= 0.473 Angle : 0.752 11.794 15739 Z= 0.383 Chirality : 0.048 0.305 1772 Planarity : 0.004 0.039 2017 Dihedral : 10.372 76.304 1833 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.29 % Favored : 90.64 % Rotamer: Outliers : 1.27 % Allowed : 9.98 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.21), residues: 1389 helix: 1.99 (0.31), residues: 303 sheet: -0.16 (0.26), residues: 328 loop : -2.27 (0.19), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 121 HIS 0.006 0.002 HIS A 245 PHE 0.032 0.002 PHE C 485 TYR 0.019 0.002 TYR A 172 ARG 0.005 0.001 ARG C 163 *********************** 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 72 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 310 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8742 (mmp) REVERT: A 473 GLU cc_start: 0.8936 (mp0) cc_final: 0.8661 (pm20) REVERT: B 484 MET cc_start: 0.1546 (mtt) cc_final: 0.1327 (mtt) outliers start: 16 outliers final: 5 residues processed: 66 average time/residue: 1.2803 time to fit residues: 92.5574 Evaluate side-chains 60 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 338 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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** B 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11636 Z= 0.177 Angle : 0.610 8.756 15739 Z= 0.311 Chirality : 0.044 0.290 1772 Planarity : 0.003 0.031 2017 Dihedral : 8.858 69.900 1833 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.27 % Favored : 92.66 % Rotamer: Outliers : 1.11 % Allowed : 11.96 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1389 helix: 2.26 (0.31), residues: 304 sheet: 0.12 (0.27), residues: 316 loop : -2.15 (0.19), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 121 HIS 0.005 0.001 HIS A 285 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 71 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: A 310 MET cc_start: 0.8992 (mmm) cc_final: 0.8756 (mmp) REVERT: A 473 GLU cc_start: 0.8901 (mp0) cc_final: 0.8545 (pm20) REVERT: B 370 MET cc_start: 0.8238 (ttm) cc_final: 0.7980 (ttm) REVERT: C 370 MET cc_start: 0.8663 (ttm) cc_final: 0.8456 (ttt) outliers start: 14 outliers final: 6 residues processed: 66 average time/residue: 1.3826 time to fit residues: 99.1922 Evaluate side-chains 60 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 110 optimal weight: 0.0570 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 128 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 : 0.002 0.037 11636 Z= 0.162 Angle : 0.597 9.253 15739 Z= 0.301 Chirality : 0.044 0.303 1772 Planarity : 0.002 0.030 2017 Dihedral : 7.224 58.392 1833 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.42 % Favored : 92.51 % Rotamer: Outliers : 0.95 % Allowed : 13.06 % Favored : 85.99 % 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: 2.53 (0.31), residues: 304 sheet: 0.15 (0.28), residues: 308 loop : -2.03 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 121 HIS 0.004 0.001 HIS B 487 PHE 0.030 0.001 PHE C 485 TYR 0.009 0.001 TYR B 383 ARG 0.001 0.000 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 310 MET cc_start: 0.9002 (mmm) cc_final: 0.8772 (mmp) REVERT: A 473 GLU cc_start: 0.8859 (mp0) cc_final: 0.8525 (pm20) REVERT: B 370 MET cc_start: 0.8235 (ttm) cc_final: 0.7953 (ttm) REVERT: C 475 GLU cc_start: 0.8614 (mp0) cc_final: 0.8270 (mp0) outliers start: 12 outliers final: 5 residues processed: 67 average time/residue: 1.3062 time to fit residues: 95.4607 Evaluate side-chains 61 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 81 optimal weight: 0.0470 chunk 61 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS C 285 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11636 Z= 0.162 Angle : 0.595 9.634 15739 Z= 0.298 Chirality : 0.044 0.274 1772 Planarity : 0.002 0.029 2017 Dihedral : 6.417 54.379 1833 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 0.95 % Allowed : 14.25 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1389 helix: 2.62 (0.32), residues: 304 sheet: 0.11 (0.27), residues: 323 loop : -2.03 (0.19), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 121 HIS 0.003 0.001 HIS B 487 PHE 0.027 0.001 PHE C 485 TYR 0.009 0.001 TYR A 71 ARG 0.001 0.000 ARG A 206 *********************** 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 68 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 310 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8802 (mmp) REVERT: A 473 GLU cc_start: 0.8841 (mp0) cc_final: 0.8483 (pm20) REVERT: B 370 MET cc_start: 0.8204 (ttm) cc_final: 0.7901 (ttm) REVERT: C 370 MET cc_start: 0.8648 (ttm) cc_final: 0.8429 (ttt) outliers start: 12 outliers final: 4 residues processed: 65 average time/residue: 1.3106 time to fit residues: 92.7993 Evaluate side-chains 60 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 25 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 12 optimal weight: 0.0570 chunk 104 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 11636 Z= 0.155 Angle : 0.602 10.833 15739 Z= 0.298 Chirality : 0.043 0.275 1772 Planarity : 0.002 0.028 2017 Dihedral : 5.810 53.215 1833 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.42 % Favored : 92.51 % Rotamer: Outliers : 1.11 % Allowed : 14.57 % Favored : 84.32 % 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: -0.57 (0.22), residues: 1389 helix: 2.67 (0.32), residues: 304 sheet: 0.10 (0.28), residues: 319 loop : -2.00 (0.19), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 121 HIS 0.006 0.001 HIS C 285 PHE 0.027 0.001 PHE C 485 TYR 0.009 0.001 TYR A 172 ARG 0.003 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 70 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8832 (mp0) cc_final: 0.8482 (pm20) REVERT: B 370 MET cc_start: 0.8239 (ttm) cc_final: 0.7927 (ttm) outliers start: 14 outliers final: 5 residues processed: 68 average time/residue: 1.2458 time to fit residues: 92.4825 Evaluate side-chains 59 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 THR 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 127 optimal weight: 0.1980 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 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 23 HIS A 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11636 Z= 0.239 Angle : 0.651 11.119 15739 Z= 0.322 Chirality : 0.044 0.287 1772 Planarity : 0.003 0.091 2017 Dihedral : 5.696 54.812 1833 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.50 % Favored : 91.43 % Rotamer: Outliers : 0.71 % Allowed : 14.96 % Favored : 84.32 % 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: 2.54 (0.32), residues: 304 sheet: 0.19 (0.28), residues: 311 loop : -2.08 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 121 HIS 0.006 0.001 HIS C 285 PHE 0.027 0.001 PHE C 485 TYR 0.014 0.001 TYR A 172 ARG 0.023 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 64 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8860 (mp0) cc_final: 0.8494 (pm20) REVERT: B 288 ARG cc_start: 0.8648 (mmm160) cc_final: 0.8434 (mmm160) REVERT: B 370 MET cc_start: 0.8261 (ttm) cc_final: 0.7953 (ttm) REVERT: C 370 MET cc_start: 0.8674 (ttm) cc_final: 0.8468 (ttt) outliers start: 9 outliers final: 5 residues processed: 63 average time/residue: 1.3658 time to fit residues: 93.6953 Evaluate side-chains 60 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 0.0970 chunk 67 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1976 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= 0.170 Angle : 0.645 12.648 15739 Z= 0.315 Chirality : 0.043 0.269 1772 Planarity : 0.003 0.074 2017 Dihedral : 5.349 53.637 1833 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.42 % Favored : 92.51 % Rotamer: Outliers : 0.55 % Allowed : 15.28 % 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: -0.61 (0.22), residues: 1389 helix: 2.60 (0.32), residues: 304 sheet: 0.13 (0.27), residues: 327 loop : -2.05 (0.19), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 121 HIS 0.006 0.001 HIS C 285 PHE 0.026 0.001 PHE C 485 TYR 0.009 0.001 TYR B 383 ARG 0.017 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 63 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 473 GLU cc_start: 0.8825 (mp0) cc_final: 0.8471 (pm20) REVERT: B 288 ARG cc_start: 0.8688 (mmm160) cc_final: 0.8123 (tpm170) REVERT: B 370 MET cc_start: 0.8211 (ttm) cc_final: 0.7889 (ttm) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 1.4095 time to fit residues: 94.7287 Evaluate side-chains 61 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.051432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.038546 restraints weight = 63432.351| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.54 r_work: 0.2825 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11636 Z= 0.195 Angle : 0.648 12.392 15739 Z= 0.318 Chirality : 0.044 0.269 1772 Planarity : 0.003 0.072 2017 Dihedral : 5.239 53.623 1833 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.06 % Favored : 91.86 % Rotamer: Outliers : 0.63 % Allowed : 15.60 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1389 helix: 2.56 (0.32), residues: 304 sheet: 0.11 (0.28), residues: 313 loop : -2.06 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 121 HIS 0.006 0.001 HIS C 285 PHE 0.026 0.001 PHE C 485 TYR 0.010 0.001 TYR B 383 ARG 0.017 0.000 ARG B 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2985.03 seconds wall clock time: 54 minutes 17.58 seconds (3257.58 seconds total)