Starting phenix.real_space_refine on Thu Jul 2 14:50:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsl_18635/07_2026/8qsl_18635_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsl_18635/07_2026/8qsl_18635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qsl_18635/07_2026/8qsl_18635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsl_18635/07_2026/8qsl_18635.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsl_18635/07_2026/8qsl_18635_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsl_18635/07_2026/8qsl_18635_neut.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.018 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 48 5.16 5 C 5702 2.51 5 N 1310 2.21 5 O 1444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8506 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 23, 'TRANS': 499} Chain breaks: 1 Chain: "C" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 23, 'TRANS': 499} Chain breaks: 1 Chain: "A" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'NAG': 1, 'PGT': 1, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'NAG': 1, 'PGT': 1, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.68, per 1000 atoms: 0.20 Number of scatterers: 8506 At special positions: 0 Unit cell: (122.265, 80.465, 87.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 2 15.00 O 1444 8.00 N 1310 7.00 C 5702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 153 " 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=2, symmetry=0 Links applied NAG-ASN " NAG A 604 " - " ASN A 140 " " NAG C 604 " - " ASN C 140 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 302.8 milliseconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 81.8% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 removed outlier: 3.834A pdb=" N ALA A 20 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 57 removed outlier: 3.797A pdb=" N CYS A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 70 through 98 removed outlier: 3.981A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 101 through 118 Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.887A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 153 through 183 removed outlier: 4.402A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.874A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 220 removed outlier: 3.796A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 248 removed outlier: 3.610A pdb=" N ALA A 227 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 4.166A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 removed outlier: 3.972A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A 265 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 4.059A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 347 removed outlier: 3.671A pdb=" N VAL A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix removed outlier: 4.014A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 367 through 395 removed outlier: 4.880A pdb=" N ASP A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Proline residue: A 382 - end of helix removed outlier: 4.648A pdb=" N ASP A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix removed outlier: 3.917A pdb=" N HIS A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 431 removed outlier: 3.789A pdb=" N ARG A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 480 removed outlier: 4.596A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 511 Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 531 through 560 removed outlier: 4.049A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 29 removed outlier: 4.071A pdb=" N ALA C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 57 removed outlier: 3.771A pdb=" N CYS C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 70 through 98 removed outlier: 3.987A pdb=" N SER C 89 " --> pdb=" O THR C 85 " (cutoff:3.500A) Proline residue: C 90 - end of helix Processing helix chain 'C' and resid 101 through 125 removed outlier: 4.200A pdb=" N ALA C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) Proline residue: C 121 - end of helix Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 153 through 183 removed outlier: 4.360A pdb=" N THR C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) Proline residue: C 177 - end of helix removed outlier: 3.873A pdb=" N VAL C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 220 removed outlier: 3.797A pdb=" N ALA C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 248 removed outlier: 3.630A pdb=" N ALA C 227 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C 228 " --> pdb=" O THR C 224 " (cutoff:3.500A) Proline residue: C 229 - end of helix removed outlier: 4.164A pdb=" N SER C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL C 246 " --> pdb=" O CYS C 242 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 273 removed outlier: 3.893A pdb=" N MET C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 265 " --> pdb=" O PHE C 261 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 removed outlier: 4.060A pdb=" N GLY C 304 " --> pdb=" O LYS C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 347 removed outlier: 3.705A pdb=" N VAL C 312 " --> pdb=" O THR C 308 " (cutoff:3.500A) Proline residue: C 323 - end of helix Proline residue: C 330 - end of helix removed outlier: 4.012A pdb=" N VAL C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 367 through 395 removed outlier: 4.824A pdb=" N ASP C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA C 374 " --> pdb=" O THR C 370 " (cutoff:3.500A) Proline residue: C 382 - end of helix removed outlier: 4.653A pdb=" N ASP C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Proline residue: C 390 - end of helix removed outlier: 3.918A pdb=" N HIS C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 431 removed outlier: 3.821A pdb=" N ARG C 404 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 453 Processing helix chain 'C' and resid 454 through 480 removed outlier: 4.608A pdb=" N ILE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 480 " --> pdb=" O ALA C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 511 Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 531 through 560 removed outlier: 4.084A pdb=" N TYR C 535 " --> pdb=" O TYR C 531 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AA2, first strand: chain 'C' and resid 435 through 436 594 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1316 1.32 - 1.44: 2295 1.44 - 1.57: 5057 1.57 - 1.69: 4 1.69 - 1.81: 70 Bond restraints: 8742 Sorted by residual: bond pdb=" N GLY A 16 " pdb=" CA GLY A 16 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.36e+00 bond pdb=" N GLY C 16 " pdb=" CA GLY C 16 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.13e+00 bond pdb=" CB GLN C 182 " pdb=" CG GLN C 182 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.00e+00 bond pdb=" CB GLN A 182 " pdb=" CG GLN A 182 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.74e-01 bond pdb=" CB LYS A 513 " pdb=" CG LYS A 513 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.26e-01 ... (remaining 8737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 11577 1.68 - 3.37: 290 3.37 - 5.05: 48 5.05 - 6.74: 16 6.74 - 8.42: 1 Bond angle restraints: 11932 Sorted by residual: angle pdb=" N SER A 255 " pdb=" CA SER A 255 " pdb=" C SER A 255 " ideal model delta sigma weight residual 113.43 108.80 4.63 1.26e+00 6.30e-01 1.35e+01 angle pdb=" N SER C 255 " pdb=" CA SER C 255 " pdb=" C SER C 255 " ideal model delta sigma weight residual 113.43 109.15 4.28 1.26e+00 6.30e-01 1.15e+01 angle pdb=" C VAL A 322 " pdb=" CA VAL A 322 " pdb=" CB VAL A 322 " ideal model delta sigma weight residual 113.70 110.57 3.13 9.50e-01 1.11e+00 1.08e+01 angle pdb=" OG1 THR C 359 " pdb=" CB THR C 359 " pdb=" CG2 THR C 359 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.93e+00 angle pdb=" OG1 THR C 358 " pdb=" CB THR C 358 " pdb=" CG2 THR C 358 " ideal model delta sigma weight residual 109.30 103.33 5.97 2.00e+00 2.50e-01 8.90e+00 ... (remaining 11927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 5058 18.02 - 36.05: 491 36.05 - 54.07: 120 54.07 - 72.10: 30 72.10 - 90.12: 5 Dihedral angle restraints: 5704 sinusoidal: 2712 harmonic: 2992 Sorted by residual: dihedral pdb=" CA GLY C 396 " pdb=" C GLY C 396 " pdb=" N LEU C 397 " pdb=" CA LEU C 397 " ideal model delta harmonic sigma weight residual -180.00 -157.22 -22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLY A 396 " pdb=" C GLY A 396 " pdb=" N LEU A 397 " pdb=" CA LEU A 397 " ideal model delta harmonic sigma weight residual -180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA LEU A 397 " pdb=" C LEU A 397 " pdb=" N LEU A 398 " pdb=" CA LEU A 398 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 5701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1029 0.034 - 0.067: 260 0.067 - 0.101: 88 0.101 - 0.135: 15 0.135 - 0.169: 6 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CB THR C 358 " pdb=" CA THR C 358 " pdb=" OG1 THR C 358 " pdb=" CG2 THR C 358 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CB THR C 359 " pdb=" CA THR C 359 " pdb=" OG1 THR C 359 " pdb=" CG2 THR C 359 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CB THR A 359 " pdb=" CA THR A 359 " pdb=" OG1 THR A 359 " pdb=" CG2 THR A 359 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 1395 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 452 " 0.019 2.00e-02 2.50e+03 1.49e-02 5.57e+00 pdb=" CG TRP C 452 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 452 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 452 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 452 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 452 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 452 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 452 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 452 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 452 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 452 " 0.017 2.00e-02 2.50e+03 1.31e-02 4.30e+00 pdb=" CG TRP A 452 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 452 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 452 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 452 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 452 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 452 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 452 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 452 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 452 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 356 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C ASN A 356 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN A 356 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 357 " 0.010 2.00e-02 2.50e+03 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 96 2.55 - 3.14: 7830 3.14 - 3.73: 13398 3.73 - 4.31: 17834 4.31 - 4.90: 29454 Nonbonded interactions: 68612 Sorted by model distance: nonbonded pdb=" O ALA A 227 " pdb=" OG1 THR A 230 " model vdw 1.968 3.040 nonbonded pdb=" O ALA C 227 " pdb=" OG1 THR C 230 " model vdw 1.973 3.040 nonbonded pdb=" O GLN C 218 " pdb=" NE2 GLN C 218 " model vdw 2.037 3.120 nonbonded pdb=" OG SER A 346 " pdb=" OE1 GLN A 454 " model vdw 2.063 3.040 nonbonded pdb=" OG SER C 346 " pdb=" OE1 GLN C 454 " model vdw 2.067 3.040 ... (remaining 68607 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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: 0.950 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.220 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:8.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.013 0.871 8750 Z= 1.297 Angle : 0.671 8.420 11946 Z= 0.350 Chirality : 0.036 0.169 1398 Planarity : 0.004 0.032 1410 Dihedral : 15.066 90.122 3776 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.12 % Allowed : 25.85 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.27), residues: 1038 helix: 2.28 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -2.92 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 102 TYR 0.006 0.001 TYR C 86 PHE 0.017 0.001 PHE A 194 TRP 0.040 0.002 TRP C 452 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 ( 8742) covalent geometry : angle 0.67087 / 0.35 (11932) SS BOND : bond 0.00188 / 0.11 ( 4) SS BOND : angle 0.41924 / 0.24 ( 8) hydrogen bonds : bond 0.14117 / 10.16 ( 594) hydrogen bonds : angle 5.43517 / 4.02 ( 1749) Misc. bond : bond 0.85041 / 50.43 ( 2) link_NAG-ASN : bond 0.00194 / 0.12 ( 2) link_NAG-ASN : angle 1.41883 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 ASP cc_start: 0.7764 (t0) cc_final: 0.7512 (t0) REVERT: C 373 ASP cc_start: 0.7789 (t0) cc_final: 0.7505 (t0) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.3557 time to fit residues: 74.5589 Evaluate side-chains 156 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 345 GLN A 356 ASN A 454 GLN C 218 GLN C 345 GLN C 454 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.137787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.109438 restraints weight = 16985.302| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.46 r_work: 0.3612 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8750 Z= 0.160 Angle : 0.751 8.357 11946 Z= 0.360 Chirality : 0.041 0.195 1398 Planarity : 0.005 0.034 1410 Dihedral : 10.253 59.956 2076 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.41 % Allowed : 23.17 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.27), residues: 1038 helix: 2.16 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -2.44 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 426 TYR 0.014 0.001 TYR C 226 PHE 0.022 0.001 PHE A 194 TRP 0.017 0.001 TRP C 452 HIS 0.002 0.001 HIS C 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 8742) covalent geometry : angle 0.74889 / 0.36 (11932) SS BOND : bond 0.00088 / 0.05 ( 4) SS BOND : angle 0.47505 / 0.29 ( 8) hydrogen bonds : bond 0.05186 / 3.57 ( 594) hydrogen bonds : angle 4.59943 / 3.38 ( 1749) Misc. bond : bond 0.00363 / 0.22 ( 2) link_NAG-ASN : bond 0.00211 / 0.12 ( 2) link_NAG-ASN : angle 2.52863 / 1.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8278 (m-80) cc_final: 0.8056 (t80) REVERT: A 452 TRP cc_start: 0.8162 (m100) cc_final: 0.7941 (m100) REVERT: A 453 TRP cc_start: 0.8196 (m100) cc_final: 0.7991 (m100) REVERT: C 62 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8169 (mm) REVERT: C 226 TYR cc_start: 0.8568 (m-80) cc_final: 0.7579 (m-80) REVERT: C 260 MET cc_start: 0.8185 (mmm) cc_final: 0.7918 (mmm) REVERT: C 528 ASN cc_start: 0.6769 (t0) cc_final: 0.6506 (m-40) outliers start: 28 outliers final: 6 residues processed: 203 average time/residue: 0.3036 time to fit residues: 69.1356 Evaluate side-chains 160 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 504 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 78 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 GLN A 218 GLN C 218 GLN C 428 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.139151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.109227 restraints weight = 16751.032| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.49 r_work: 0.3612 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8750 Z= 0.154 Angle : 0.792 9.449 11946 Z= 0.364 Chirality : 0.042 0.358 1398 Planarity : 0.005 0.057 1410 Dihedral : 10.219 59.665 2076 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.55 % Favored : 93.26 % Rotamer: Outliers : 4.88 % Allowed : 23.66 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.27), residues: 1038 helix: 2.00 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -2.51 (0.43), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.007 0.001 TYR C 86 PHE 0.024 0.001 PHE C 550 TRP 0.015 0.001 TRP C 453 HIS 0.002 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 8742) covalent geometry : angle 0.77867 / 0.36 (11932) SS BOND : bond 0.00061 / 0.03 ( 4) SS BOND : angle 0.44758 / 0.26 ( 8) hydrogen bonds : bond 0.04886 / 3.34 ( 594) hydrogen bonds : angle 4.45434 / 3.28 ( 1749) Misc. bond : bond 0.00039 / 0.02 ( 2) link_NAG-ASN : bond 0.01908 / 1.15 ( 2) link_NAG-ASN : angle 6.62890 / 3.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8356 (m-80) cc_final: 0.8029 (t80) REVERT: A 351 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7051 (pp) REVERT: A 435 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7569 (pp) REVERT: C 226 TYR cc_start: 0.8648 (m-80) cc_final: 0.7562 (m-80) REVERT: C 260 MET cc_start: 0.8190 (mmm) cc_final: 0.7855 (mmm) outliers start: 40 outliers final: 16 residues processed: 204 average time/residue: 0.2942 time to fit residues: 67.0585 Evaluate side-chains 174 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 549 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 84 optimal weight: 0.0050 chunk 39 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 0.0870 overall best weight: 0.7576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 454 GLN C 454 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.137866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.109403 restraints weight = 17318.937| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.46 r_work: 0.3616 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8750 Z= 0.154 Angle : 0.802 12.134 11946 Z= 0.363 Chirality : 0.043 0.327 1398 Planarity : 0.004 0.054 1410 Dihedral : 10.141 59.468 2076 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.73 % Allowed : 24.02 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.27), residues: 1038 helix: 1.91 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -2.49 (0.43), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 129 TYR 0.017 0.001 TYR C 557 PHE 0.020 0.001 PHE A 536 TRP 0.015 0.001 TRP A 453 HIS 0.004 0.001 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 8742) covalent geometry : angle 0.79469 / 0.36 (11932) SS BOND : bond 0.00131 / 0.07 ( 4) SS BOND : angle 0.29478 / 0.18 ( 8) hydrogen bonds : bond 0.04730 / 3.25 ( 594) hydrogen bonds : angle 4.43384 / 3.25 ( 1749) Misc. bond : bond 0.00012 / 0.01 ( 2) link_NAG-ASN : bond 0.00989 / 0.60 ( 2) link_NAG-ASN : angle 4.81134 / 2.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8266 (tm-30) cc_final: 0.8026 (tm-30) REVERT: A 222 PHE cc_start: 0.8408 (m-80) cc_final: 0.8073 (t80) REVERT: A 351 ILE cc_start: 0.7167 (OUTLIER) cc_final: 0.6715 (pp) REVERT: A 435 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7618 (pp) REVERT: C 44 GLU cc_start: 0.8640 (tp30) cc_final: 0.8433 (tp30) REVERT: C 47 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8071 (tm-30) REVERT: C 154 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8291 (t) REVERT: C 218 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8019 (tp-100) REVERT: C 222 PHE cc_start: 0.8419 (m-80) cc_final: 0.7704 (m-80) REVERT: C 226 TYR cc_start: 0.8676 (m-80) cc_final: 0.7423 (m-80) REVERT: C 260 MET cc_start: 0.8185 (mmm) cc_final: 0.7805 (mmm) REVERT: C 297 ASP cc_start: 0.6298 (OUTLIER) cc_final: 0.6073 (p0) outliers start: 47 outliers final: 19 residues processed: 218 average time/residue: 0.3004 time to fit residues: 73.4404 Evaluate side-chains 177 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 549 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 GLN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN C 454 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.138030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.109786 restraints weight = 17055.526| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.41 r_work: 0.3610 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8750 Z= 0.152 Angle : 0.804 11.440 11946 Z= 0.365 Chirality : 0.044 0.392 1398 Planarity : 0.004 0.046 1410 Dihedral : 9.983 59.260 2076 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 6.46 % Allowed : 24.39 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.27), residues: 1038 helix: 1.83 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -2.51 (0.43), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 129 TYR 0.007 0.001 TYR A 535 PHE 0.018 0.001 PHE C 550 TRP 0.018 0.001 TRP A 453 HIS 0.006 0.001 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 8742) covalent geometry : angle 0.80017 / 0.36 (11932) SS BOND : bond 0.00107 / 0.06 ( 4) SS BOND : angle 0.27439 / 0.16 ( 8) hydrogen bonds : bond 0.04702 / 3.22 ( 594) hydrogen bonds : angle 4.46825 / 3.29 ( 1749) Misc. bond : bond 0.00008 / 0.00 ( 2) link_NAG-ASN : bond 0.00578 / 0.35 ( 2) link_NAG-ASN : angle 3.81475 / 2.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7866 (tm-30) REVERT: A 222 PHE cc_start: 0.8396 (m-80) cc_final: 0.8074 (t80) REVERT: A 244 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7492 (tp40) REVERT: A 297 ASP cc_start: 0.6395 (OUTLIER) cc_final: 0.6049 (p0) REVERT: A 351 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.6910 (pp) REVERT: A 435 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7653 (pp) REVERT: C 47 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8176 (tm-30) REVERT: C 154 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8339 (t) REVERT: C 215 TYR cc_start: 0.7825 (t80) cc_final: 0.7621 (t80) REVERT: C 218 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8265 (mm-40) REVERT: C 244 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7545 (tp40) REVERT: C 260 MET cc_start: 0.8189 (mmm) cc_final: 0.7785 (mmm) REVERT: C 452 TRP cc_start: 0.8196 (m100) cc_final: 0.7916 (m100) REVERT: C 484 MET cc_start: 0.8575 (ptp) cc_final: 0.8214 (mpt) outliers start: 53 outliers final: 22 residues processed: 201 average time/residue: 0.3378 time to fit residues: 75.1821 Evaluate side-chains 181 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 504 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 1 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 0.0570 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 GLN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.138773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.110797 restraints weight = 17140.000| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 3.44 r_work: 0.3631 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8750 Z= 0.147 Angle : 0.836 12.285 11946 Z= 0.371 Chirality : 0.045 0.365 1398 Planarity : 0.004 0.043 1410 Dihedral : 9.840 58.377 2076 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 5.00 % Allowed : 27.80 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.28), residues: 1038 helix: 1.84 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -2.50 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 426 TYR 0.009 0.001 TYR C 226 PHE 0.020 0.001 PHE C 536 TRP 0.016 0.001 TRP A 452 HIS 0.008 0.001 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 8742) covalent geometry : angle 0.83334 / 0.37 (11932) SS BOND : bond 0.00062 / 0.04 ( 4) SS BOND : angle 0.23603 / 0.14 ( 8) hydrogen bonds : bond 0.04478 / 3.07 ( 594) hydrogen bonds : angle 4.45136 / 3.26 ( 1749) Misc. bond : bond 0.00014 / 0.01 ( 2) link_NAG-ASN : bond 0.00553 / 0.33 ( 2) link_NAG-ASN : angle 3.39781 / 1.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9092 (tt) cc_final: 0.8749 (tt) REVERT: A 47 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7861 (tm-30) REVERT: A 222 PHE cc_start: 0.8411 (m-80) cc_final: 0.8116 (t80) REVERT: A 244 GLN cc_start: 0.8038 (tp-100) cc_final: 0.7499 (tp40) REVERT: A 266 TYR cc_start: 0.8784 (m-10) cc_final: 0.8500 (m-10) REVERT: A 297 ASP cc_start: 0.6264 (OUTLIER) cc_final: 0.5904 (p0) REVERT: A 307 PHE cc_start: 0.6256 (m-10) cc_final: 0.5505 (m-80) REVERT: A 351 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6724 (pp) REVERT: A 435 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7690 (pp) REVERT: A 484 MET cc_start: 0.8349 (ptp) cc_final: 0.8066 (mpt) REVERT: C 44 GLU cc_start: 0.8640 (tp30) cc_final: 0.8437 (tp30) REVERT: C 47 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7739 (tm-30) REVERT: C 154 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8371 (t) REVERT: C 222 PHE cc_start: 0.8427 (m-80) cc_final: 0.8003 (t80) REVERT: C 244 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7728 (tp40) REVERT: C 260 MET cc_start: 0.8273 (mmm) cc_final: 0.7887 (mmm) REVERT: C 297 ASP cc_start: 0.6268 (OUTLIER) cc_final: 0.5934 (p0) REVERT: C 307 PHE cc_start: 0.6182 (m-10) cc_final: 0.5511 (m-80) REVERT: C 345 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7522 (tp-100) REVERT: C 452 TRP cc_start: 0.8227 (m100) cc_final: 0.7990 (m100) REVERT: C 484 MET cc_start: 0.8460 (ptp) cc_final: 0.8153 (mpt) outliers start: 41 outliers final: 17 residues processed: 200 average time/residue: 0.3278 time to fit residues: 72.8903 Evaluate side-chains 177 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 504 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 93 optimal weight: 0.0670 chunk 88 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 ASN A 345 GLN A 454 GLN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.139212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.111455 restraints weight = 17262.875| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.44 r_work: 0.3636 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8750 Z= 0.152 Angle : 0.843 12.695 11946 Z= 0.376 Chirality : 0.045 0.380 1398 Planarity : 0.004 0.046 1410 Dihedral : 9.711 59.914 2076 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 5.00 % Allowed : 28.29 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.28), residues: 1038 helix: 1.85 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -2.53 (0.43), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 129 TYR 0.007 0.001 TYR C 52 PHE 0.018 0.001 PHE C 536 TRP 0.023 0.001 TRP C 368 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 8742) covalent geometry : angle 0.84006 / 0.38 (11932) SS BOND : bond 0.00056 / 0.03 ( 4) SS BOND : angle 0.23658 / 0.14 ( 8) hydrogen bonds : bond 0.04495 / 3.07 ( 594) hydrogen bonds : angle 4.48987 / 3.28 ( 1749) Misc. bond : bond 0.00024 / 0.01 ( 2) link_NAG-ASN : bond 0.00449 / 0.27 ( 2) link_NAG-ASN : angle 3.20639 / 1.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 222 PHE cc_start: 0.8401 (m-80) cc_final: 0.8147 (t80) REVERT: A 244 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7551 (tp40) REVERT: A 266 TYR cc_start: 0.8809 (m-10) cc_final: 0.8516 (m-10) REVERT: A 297 ASP cc_start: 0.6381 (OUTLIER) cc_final: 0.5959 (p0) REVERT: A 307 PHE cc_start: 0.6326 (m-10) cc_final: 0.5433 (m-80) REVERT: A 351 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6756 (pp) REVERT: A 484 MET cc_start: 0.8346 (ptp) cc_final: 0.8119 (mpt) REVERT: C 44 GLU cc_start: 0.8712 (tp30) cc_final: 0.8488 (tp30) REVERT: C 47 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7848 (tm-30) REVERT: C 222 PHE cc_start: 0.8483 (m-80) cc_final: 0.8054 (t80) REVERT: C 244 GLN cc_start: 0.8132 (tp-100) cc_final: 0.7614 (tp40) REVERT: C 260 MET cc_start: 0.8269 (mmm) cc_final: 0.7880 (mmm) REVERT: C 297 ASP cc_start: 0.6121 (OUTLIER) cc_final: 0.5742 (p0) REVERT: C 307 PHE cc_start: 0.6278 (m-10) cc_final: 0.5617 (m-80) REVERT: C 345 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7510 (tp-100) REVERT: C 452 TRP cc_start: 0.8293 (m100) cc_final: 0.8054 (m100) REVERT: C 484 MET cc_start: 0.8429 (ptp) cc_final: 0.8134 (mpt) outliers start: 41 outliers final: 25 residues processed: 195 average time/residue: 0.3428 time to fit residues: 74.0030 Evaluate side-chains 182 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 549 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 0.0970 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN C 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.139795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.111923 restraints weight = 17170.019| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.42 r_work: 0.3657 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 8750 Z= 0.150 Angle : 0.850 13.036 11946 Z= 0.378 Chirality : 0.044 0.373 1398 Planarity : 0.004 0.044 1410 Dihedral : 9.578 59.743 2076 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.39 % Allowed : 29.88 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.28), residues: 1038 helix: 1.83 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -2.50 (0.43), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 350 TYR 0.008 0.001 TYR C 557 PHE 0.016 0.001 PHE C 536 TRP 0.024 0.002 TRP A 452 HIS 0.004 0.001 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 8742) covalent geometry : angle 0.84760 / 0.38 (11932) SS BOND : bond 0.00036 / 0.02 ( 4) SS BOND : angle 0.27972 / 0.19 ( 8) hydrogen bonds : bond 0.04430 / 3.04 ( 594) hydrogen bonds : angle 4.46831 / 3.29 ( 1749) Misc. bond : bond 0.00018 / 0.01 ( 2) link_NAG-ASN : bond 0.00444 / 0.27 ( 2) link_NAG-ASN : angle 3.08869 / 1.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8715 (tp30) cc_final: 0.8483 (tp30) REVERT: A 47 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7749 (tm-30) REVERT: A 215 TYR cc_start: 0.7783 (t80) cc_final: 0.7571 (t80) REVERT: A 222 PHE cc_start: 0.8359 (m-80) cc_final: 0.8095 (t80) REVERT: A 244 GLN cc_start: 0.8122 (tp-100) cc_final: 0.7743 (tp40) REVERT: A 266 TYR cc_start: 0.8784 (m-10) cc_final: 0.8493 (m-10) REVERT: A 297 ASP cc_start: 0.6172 (OUTLIER) cc_final: 0.5718 (p0) REVERT: A 307 PHE cc_start: 0.6417 (m-10) cc_final: 0.5606 (m-80) REVERT: A 371 MET cc_start: 0.7702 (ttm) cc_final: 0.7328 (ttm) REVERT: A 484 MET cc_start: 0.8323 (ptp) cc_final: 0.8084 (mpt) REVERT: C 47 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7905 (tm-30) REVERT: C 222 PHE cc_start: 0.8458 (m-80) cc_final: 0.8124 (t80) REVERT: C 244 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7820 (tp40) REVERT: C 260 MET cc_start: 0.8284 (mmm) cc_final: 0.7903 (mmm) REVERT: C 297 ASP cc_start: 0.6130 (OUTLIER) cc_final: 0.5686 (p0) REVERT: C 307 PHE cc_start: 0.6244 (m-10) cc_final: 0.5603 (m-80) REVERT: C 427 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8593 (mm) REVERT: C 452 TRP cc_start: 0.8256 (m100) cc_final: 0.8043 (m100) REVERT: C 484 MET cc_start: 0.8378 (ptp) cc_final: 0.8104 (mpt) outliers start: 36 outliers final: 21 residues processed: 199 average time/residue: 0.3231 time to fit residues: 71.5742 Evaluate side-chains 177 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 504 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.139278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.111240 restraints weight = 17195.339| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.41 r_work: 0.3649 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8750 Z= 0.157 Angle : 0.878 13.149 11946 Z= 0.394 Chirality : 0.045 0.391 1398 Planarity : 0.004 0.049 1410 Dihedral : 9.421 59.842 2076 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.29 % Allowed : 31.22 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.28), residues: 1038 helix: 1.79 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -2.56 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 350 TYR 0.007 0.001 TYR C 557 PHE 0.015 0.001 PHE C 536 TRP 0.028 0.002 TRP A 452 HIS 0.003 0.001 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 8742) covalent geometry : angle 0.87581 / 0.39 (11932) SS BOND : bond 0.00045 / 0.03 ( 4) SS BOND : angle 0.23776 / 0.14 ( 8) hydrogen bonds : bond 0.04484 / 3.04 ( 594) hydrogen bonds : angle 4.56343 / 3.35 ( 1749) Misc. bond : bond 0.00030 / 0.02 ( 2) link_NAG-ASN : bond 0.00404 / 0.25 ( 2) link_NAG-ASN : angle 3.01371 / 1.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 215 TYR cc_start: 0.7816 (t80) cc_final: 0.7591 (t80) REVERT: A 222 PHE cc_start: 0.8378 (m-80) cc_final: 0.8152 (t80) REVERT: A 244 GLN cc_start: 0.8164 (tp-100) cc_final: 0.7661 (tp40) REVERT: A 266 TYR cc_start: 0.8775 (m-10) cc_final: 0.8489 (m-10) REVERT: A 297 ASP cc_start: 0.6102 (OUTLIER) cc_final: 0.5647 (p0) REVERT: A 307 PHE cc_start: 0.6476 (m-10) cc_final: 0.5799 (m-80) REVERT: A 371 MET cc_start: 0.7705 (ttm) cc_final: 0.7403 (ttm) REVERT: A 484 MET cc_start: 0.8319 (ptp) cc_final: 0.8104 (mpt) REVERT: C 44 GLU cc_start: 0.8775 (tp30) cc_final: 0.8572 (tp30) REVERT: C 47 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7984 (tm-30) REVERT: C 244 GLN cc_start: 0.8148 (tp-100) cc_final: 0.7662 (tp40) REVERT: C 260 MET cc_start: 0.8244 (mmm) cc_final: 0.7873 (mmm) REVERT: C 297 ASP cc_start: 0.6204 (OUTLIER) cc_final: 0.5649 (p0) REVERT: C 307 PHE cc_start: 0.6434 (m-10) cc_final: 0.5711 (m-80) REVERT: C 427 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8591 (mm) REVERT: C 452 TRP cc_start: 0.8319 (m100) cc_final: 0.8098 (m100) REVERT: C 484 MET cc_start: 0.8408 (ptp) cc_final: 0.8135 (mpt) outliers start: 27 outliers final: 21 residues processed: 188 average time/residue: 0.3338 time to fit residues: 69.6757 Evaluate side-chains 176 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 504 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 75 optimal weight: 0.0040 chunk 39 optimal weight: 6.9990 chunk 73 optimal weight: 0.0470 chunk 2 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN C 454 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.140238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.112679 restraints weight = 17095.448| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.38 r_work: 0.3662 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8750 Z= 0.155 Angle : 0.903 13.826 11946 Z= 0.406 Chirality : 0.046 0.394 1398 Planarity : 0.004 0.048 1410 Dihedral : 9.288 58.440 2076 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.54 % Allowed : 31.34 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.27), residues: 1038 helix: 1.73 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -2.55 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 393 TYR 0.005 0.001 TYR C 557 PHE 0.014 0.001 PHE C 550 TRP 0.032 0.002 TRP A 452 HIS 0.014 0.001 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 8742) covalent geometry : angle 0.90066 / 0.41 (11932) SS BOND : bond 0.00028 / 0.02 ( 4) SS BOND : angle 0.23380 / 0.14 ( 8) hydrogen bonds : bond 0.04506 / 3.06 ( 594) hydrogen bonds : angle 4.54410 / 3.34 ( 1749) Misc. bond : bond 0.00018 / 0.01 ( 2) link_NAG-ASN : bond 0.00424 / 0.26 ( 2) link_NAG-ASN : angle 2.99213 / 1.61 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7855 (tm-30) REVERT: A 215 TYR cc_start: 0.7787 (t80) cc_final: 0.7573 (t80) REVERT: A 222 PHE cc_start: 0.8415 (m-80) cc_final: 0.8189 (t80) REVERT: A 244 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7644 (tp40) REVERT: A 266 TYR cc_start: 0.8795 (m-10) cc_final: 0.8499 (m-10) REVERT: A 297 ASP cc_start: 0.6187 (OUTLIER) cc_final: 0.5648 (p0) REVERT: A 307 PHE cc_start: 0.6678 (m-10) cc_final: 0.5790 (m-80) REVERT: A 340 THR cc_start: 0.8637 (m) cc_final: 0.8415 (m) REVERT: A 371 MET cc_start: 0.7593 (ttm) cc_final: 0.7292 (ttm) REVERT: A 484 MET cc_start: 0.8277 (ptp) cc_final: 0.8016 (mpt) REVERT: C 44 GLU cc_start: 0.8715 (tp30) cc_final: 0.8501 (tp30) REVERT: C 47 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7881 (tm-30) REVERT: C 244 GLN cc_start: 0.8149 (tp40) cc_final: 0.7666 (tp40) REVERT: C 260 MET cc_start: 0.8246 (mmm) cc_final: 0.7870 (mmm) REVERT: C 297 ASP cc_start: 0.6192 (OUTLIER) cc_final: 0.5682 (p0) REVERT: C 307 PHE cc_start: 0.6425 (m-10) cc_final: 0.5696 (m-80) REVERT: C 427 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8537 (mm) REVERT: C 452 TRP cc_start: 0.8333 (m100) cc_final: 0.8088 (m100) REVERT: C 484 MET cc_start: 0.8382 (ptp) cc_final: 0.8094 (mpt) outliers start: 29 outliers final: 18 residues processed: 188 average time/residue: 0.3354 time to fit residues: 69.9385 Evaluate side-chains 183 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 335 TYR Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 504 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 356 ASN A 454 GLN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.137900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.109727 restraints weight = 17182.184| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.40 r_work: 0.3625 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 8750 Z= 0.173 Angle : 0.915 14.442 11946 Z= 0.417 Chirality : 0.046 0.389 1398 Planarity : 0.004 0.044 1410 Dihedral : 9.185 59.001 2076 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.41 % Allowed : 32.56 % Favored : 64.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.28), residues: 1038 helix: 1.74 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -2.62 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 393 TYR 0.007 0.001 TYR A 113 PHE 0.014 0.001 PHE C 550 TRP 0.038 0.002 TRP A 452 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 8742) covalent geometry : angle 0.91349 / 0.42 (11932) SS BOND : bond 0.00073 / 0.05 ( 4) SS BOND : angle 0.26798 / 0.16 ( 8) hydrogen bonds : bond 0.04764 / 3.21 ( 594) hydrogen bonds : angle 4.62009 / 3.39 ( 1749) Misc. bond : bond 0.00031 / 0.02 ( 2) link_NAG-ASN : bond 0.00328 / 0.20 ( 2) link_NAG-ASN : angle 2.87419 / 1.56 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.59 seconds wall clock time: 45 minutes 59.52 seconds (2759.52 seconds total)