Starting phenix.real_space_refine on Sat Aug 23 01:57:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsl_18635/08_2025/8qsl_18635_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsl_18635/08_2025/8qsl_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qsl_18635/08_2025/8qsl_18635_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsl_18635/08_2025/8qsl_18635_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qsl_18635/08_2025/8qsl_18635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsl_18635/08_2025/8qsl_18635.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 1.97, per 1000 atoms: 0.23 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: 0.70 Conformation dependent library (CDL) restraints added in 226.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.15 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: 0.95 Time building geometry restraints manager: 0.83 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 - 30.78: 5472 30.78 - 61.56: 246 61.56 - 92.34: 14 92.34 - 123.12: 0 123.12 - 153.90: 2 Dihedral angle restraints: 5734 sinusoidal: 2742 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=" C3 PGT A 608 " pdb=" C1 PGT A 608 " pdb=" C2 PGT A 608 " pdb=" O3P PGT A 608 " ideal model delta sinusoidal sigma weight residual -66.13 87.77 -153.90 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 5731 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: 0.720 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.660 Find NCS groups from input model: 0.120 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 15.580 153.903 3806 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 aren 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 covalent geometry : bond 0.00362 ( 8742) covalent geometry : angle 0.67087 (11932) SS BOND : bond 0.00188 ( 4) SS BOND : angle 0.41924 ( 8) hydrogen bonds : bond 0.14117 ( 594) hydrogen bonds : angle 5.43517 ( 1749) Misc. bond : bond 0.85041 ( 2) link_NAG-ASN : bond 0.00194 ( 2) link_NAG-ASN : angle 1.41883 ( 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 : 0.313 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: 0.3034 time to fit residues: 63.8046 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 : 0.271 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 345 GLN A 356 ASN A 454 GLN C 218 GLN C 345 GLN C 356 ASN C 454 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.138091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.108972 restraints weight = 16981.577| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.50 r_work: 0.3612 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1564 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= 0.164 Angle : 0.767 8.562 11946 Z= 0.366 Chirality : 0.041 0.208 1398 Planarity : 0.005 0.038 1410 Dihedral : 11.582 149.480 2106 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.66 % Allowed : 22.80 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.27), residues: 1038 helix: 2.13 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -2.46 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 426 TYR 0.015 0.001 TYR C 226 PHE 0.023 0.002 PHE A 194 TRP 0.017 0.001 TRP C 452 HIS 0.002 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8742) covalent geometry : angle 0.76529 (11932) SS BOND : bond 0.00078 ( 4) SS BOND : angle 0.46894 ( 8) hydrogen bonds : bond 0.05095 ( 594) hydrogen bonds : angle 4.59878 ( 1749) Misc. bond : bond 0.00330 ( 2) link_NAG-ASN : bond 0.00075 ( 2) link_NAG-ASN : angle 2.56580 ( 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 222 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8217 (tm-30) REVERT: A 222 PHE cc_start: 0.8274 (m-80) cc_final: 0.8069 (t80) REVERT: A 453 TRP cc_start: 0.8246 (m100) cc_final: 0.8044 (m100) REVERT: C 47 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8251 (tm-30) REVERT: C 62 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8164 (mm) REVERT: C 260 MET cc_start: 0.8186 (mmm) cc_final: 0.7921 (mmm) REVERT: C 528 ASN cc_start: 0.6768 (t0) cc_final: 0.6514 (m-40) outliers start: 30 outliers final: 6 residues processed: 203 average time/residue: 0.2515 time to fit residues: 57.2071 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 : 0.223 ------------------------------------------------------------------------------- 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: 0.8980 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 218 GLN A 356 ASN C 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.138828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.108919 restraints weight = 16739.277| |-----------------------------------------------------------------------------| r_work (start): 0.3743 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: 0.7787 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8750 Z= 0.156 Angle : 0.791 9.468 11946 Z= 0.364 Chirality : 0.042 0.373 1398 Planarity : 0.005 0.060 1410 Dihedral : 11.449 147.284 2106 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 5.00 % Allowed : 23.17 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.27), residues: 1038 helix: 1.98 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -2.54 (0.43), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 129 TYR 0.029 0.001 TYR C 226 PHE 0.020 0.001 PHE A 550 TRP 0.015 0.001 TRP C 453 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8742) covalent geometry : angle 0.77850 (11932) SS BOND : bond 0.00102 ( 4) SS BOND : angle 0.46292 ( 8) hydrogen bonds : bond 0.04896 ( 594) hydrogen bonds : angle 4.46913 ( 1749) Misc. bond : bond 0.00086 ( 2) link_NAG-ASN : bond 0.00984 ( 2) link_NAG-ASN : angle 6.30960 ( 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: 41 poor density : 187 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8009 (tm-30) REVERT: A 222 PHE cc_start: 0.8354 (m-80) cc_final: 0.8039 (t80) REVERT: A 351 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7022 (pp) REVERT: A 435 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7575 (pp) REVERT: C 47 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8091 (tm-30) REVERT: C 260 MET cc_start: 0.8201 (mmm) cc_final: 0.7864 (mmm) outliers start: 41 outliers final: 16 residues processed: 204 average time/residue: 0.2724 time to fit residues: 61.8481 Evaluate side-chains 176 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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: 0.8980 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.136784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.108204 restraints weight = 17306.846| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 3.45 r_work: 0.3596 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8750 Z= 0.163 Angle : 0.811 11.020 11946 Z= 0.370 Chirality : 0.046 0.390 1398 Planarity : 0.004 0.052 1410 Dihedral : 11.372 145.361 2106 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.37 % Allowed : 24.63 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.27), residues: 1038 helix: 1.86 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -2.59 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 129 TYR 0.029 0.001 TYR C 226 PHE 0.027 0.002 PHE C 550 TRP 0.017 0.002 TRP A 452 HIS 0.005 0.001 HIS C 559 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8742) covalent geometry : angle 0.80714 (11932) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.32567 ( 8) hydrogen bonds : bond 0.04869 ( 594) hydrogen bonds : angle 4.50638 ( 1749) Misc. bond : bond 0.00011 ( 2) link_NAG-ASN : bond 0.00678 ( 2) link_NAG-ASN : angle 3.89251 ( 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 218 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8676 (tp30) cc_final: 0.8467 (tp30) REVERT: A 47 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 222 PHE cc_start: 0.8380 (m-80) cc_final: 0.8051 (t80) REVERT: A 351 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6754 (pp) REVERT: A 435 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7604 (pp) REVERT: C 44 GLU cc_start: 0.8661 (tp30) cc_final: 0.8434 (tp30) REVERT: C 47 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8062 (tm-30) REVERT: C 154 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8317 (t) REVERT: C 218 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8035 (tp-100) REVERT: C 260 MET cc_start: 0.8205 (mmm) cc_final: 0.7826 (mmm) REVERT: C 297 ASP cc_start: 0.6203 (OUTLIER) cc_final: 0.6003 (p0) outliers start: 44 outliers final: 20 residues processed: 206 average time/residue: 0.2770 time to fit residues: 63.5637 Evaluate side-chains 174 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 221 SER 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 40 optimal weight: 0.0970 chunk 76 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 454 GLN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.138362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.110483 restraints weight = 16959.774| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.39 r_work: 0.3624 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8750 Z= 0.150 Angle : 0.790 11.750 11946 Z= 0.360 Chirality : 0.044 0.370 1398 Planarity : 0.004 0.051 1410 Dihedral : 11.182 143.849 2106 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 5.73 % Allowed : 25.00 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.27), residues: 1038 helix: 1.84 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -2.54 (0.43), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 129 TYR 0.006 0.001 TYR A 535 PHE 0.018 0.001 PHE A 536 TRP 0.016 0.001 TRP A 453 HIS 0.006 0.001 HIS C 559 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8742) covalent geometry : angle 0.78770 (11932) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.29146 ( 8) hydrogen bonds : bond 0.04664 ( 594) hydrogen bonds : angle 4.46038 ( 1749) Misc. bond : bond 0.00010 ( 2) link_NAG-ASN : bond 0.00488 ( 2) link_NAG-ASN : angle 3.15117 ( 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 226 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8613 (tp30) cc_final: 0.8311 (tp30) REVERT: A 47 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7984 (tm-30) REVERT: A 218 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8241 (mm-40) REVERT: A 222 PHE cc_start: 0.8412 (m-80) cc_final: 0.8110 (t80) REVERT: A 244 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7659 (tp40) REVERT: A 297 ASP cc_start: 0.6367 (OUTLIER) cc_final: 0.6079 (p0) REVERT: A 351 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6607 (pp) REVERT: A 435 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7684 (pp) REVERT: C 47 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8113 (tm-30) REVERT: C 154 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8331 (t) REVERT: C 244 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7724 (tp40) REVERT: C 260 MET cc_start: 0.8190 (mmm) cc_final: 0.7793 (mmm) REVERT: C 484 MET cc_start: 0.8559 (ptp) cc_final: 0.8203 (mpt) outliers start: 47 outliers final: 23 residues processed: 210 average time/residue: 0.2778 time to fit residues: 64.7789 Evaluate side-chains 174 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 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 154 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 221 SER 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 395 HIS Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 551 LEU 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: 0.9990 chunk 1 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 0.0870 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.138160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.110385 restraints weight = 17025.238| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.39 r_work: 0.3619 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8750 Z= 0.154 Angle : 0.832 12.335 11946 Z= 0.373 Chirality : 0.046 0.387 1398 Planarity : 0.004 0.048 1410 Dihedral : 11.059 142.536 2106 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.63 % Allowed : 27.93 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.28), residues: 1038 helix: 1.78 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -2.52 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 129 TYR 0.008 0.001 TYR C 226 PHE 0.020 0.001 PHE C 536 TRP 0.014 0.001 TRP C 452 HIS 0.008 0.001 HIS C 559 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8742) covalent geometry : angle 0.83024 (11932) SS BOND : bond 0.00075 ( 4) SS BOND : angle 0.25825 ( 8) hydrogen bonds : bond 0.04625 ( 594) hydrogen bonds : angle 4.51975 ( 1749) Misc. bond : bond 0.00019 ( 2) link_NAG-ASN : bond 0.00414 ( 2) link_NAG-ASN : angle 2.83732 ( 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 209 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8644 (tp30) cc_final: 0.8340 (tp30) REVERT: A 47 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 82 MET cc_start: 0.9129 (tpp) cc_final: 0.8907 (mmp) REVERT: A 218 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8268 (mm-40) REVERT: A 222 PHE cc_start: 0.8444 (m-80) cc_final: 0.8135 (t80) REVERT: A 244 GLN cc_start: 0.8043 (tp-100) cc_final: 0.7518 (tp40) REVERT: A 266 TYR cc_start: 0.8810 (m-10) cc_final: 0.8537 (m-10) REVERT: A 297 ASP cc_start: 0.6315 (OUTLIER) cc_final: 0.5962 (p0) REVERT: A 307 PHE cc_start: 0.6306 (m-10) cc_final: 0.5520 (m-80) REVERT: A 351 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6629 (pp) REVERT: A 435 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7640 (pp) REVERT: A 484 MET cc_start: 0.8377 (ptp) cc_final: 0.8028 (mpt) REVERT: C 47 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7904 (tm-30) REVERT: C 154 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8372 (t) REVERT: C 226 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7538 (m-10) REVERT: C 244 GLN cc_start: 0.8114 (tp-100) cc_final: 0.7770 (tp40) REVERT: C 260 MET cc_start: 0.8279 (mmm) cc_final: 0.7892 (mmm) REVERT: C 297 ASP cc_start: 0.6327 (OUTLIER) cc_final: 0.6005 (p0) REVERT: C 484 MET cc_start: 0.8554 (ptp) cc_final: 0.8206 (mpt) outliers start: 38 outliers final: 22 residues processed: 195 average time/residue: 0.3351 time to fit residues: 72.1669 Evaluate side-chains 180 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 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 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 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 176 THR Chi-restraints excluded: chain C residue 226 TYR 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 360 THR Chi-restraints excluded: chain C residue 395 HIS 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: 0.6980 chunk 36 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 93 optimal weight: 0.1980 chunk 88 optimal weight: 0.0570 chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN C 345 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.138643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.110861 restraints weight = 17230.001| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.43 r_work: 0.3636 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8750 Z= 0.146 Angle : 0.829 13.009 11946 Z= 0.373 Chirality : 0.045 0.358 1398 Planarity : 0.004 0.045 1410 Dihedral : 10.929 141.108 2106 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 5.61 % Allowed : 27.80 % Favored : 66.59 % 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 aren not related in a simple way. whole: 1.15 (0.28), residues: 1038 helix: 1.77 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -2.51 (0.43), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 129 TYR 0.009 0.001 TYR C 226 PHE 0.016 0.001 PHE C 536 TRP 0.018 0.001 TRP C 452 HIS 0.002 0.001 HIS A 560 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8742) covalent geometry : angle 0.82720 (11932) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.23805 ( 8) hydrogen bonds : bond 0.04508 ( 594) hydrogen bonds : angle 4.45885 ( 1749) Misc. bond : bond 0.00028 ( 2) link_NAG-ASN : bond 0.00378 ( 2) link_NAG-ASN : angle 2.68617 ( 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 214 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8638 (tp30) cc_final: 0.8364 (tp30) REVERT: A 47 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8029 (tm-30) REVERT: A 222 PHE cc_start: 0.8410 (m-80) cc_final: 0.8140 (t80) REVERT: A 244 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7529 (tp40) REVERT: A 266 TYR cc_start: 0.8793 (m-10) cc_final: 0.8504 (m-10) REVERT: A 297 ASP cc_start: 0.6386 (OUTLIER) cc_final: 0.5975 (p0) REVERT: A 307 PHE cc_start: 0.6270 (m-10) cc_final: 0.5382 (m-80) REVERT: A 351 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6755 (pp) REVERT: A 409 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.9044 (ttm) REVERT: A 435 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7637 (pp) REVERT: A 484 MET cc_start: 0.8302 (ptp) cc_final: 0.8040 (mpt) REVERT: C 47 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7943 (tm-30) REVERT: C 226 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7572 (m-10) REVERT: C 244 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7792 (tp40) REVERT: C 260 MET cc_start: 0.8271 (mmm) cc_final: 0.7868 (mmm) REVERT: C 297 ASP cc_start: 0.6333 (OUTLIER) cc_final: 0.5943 (p0) REVERT: C 307 PHE cc_start: 0.6610 (m-10) cc_final: 0.5510 (m-80) REVERT: C 484 MET cc_start: 0.8425 (ptp) cc_final: 0.8085 (mpt) outliers start: 46 outliers final: 26 residues processed: 196 average time/residue: 0.3037 time to fit residues: 66.6119 Evaluate side-chains 184 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 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 351 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain C residue 62 LEU 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 220 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 TYR 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 370 THR Chi-restraints excluded: chain C residue 383 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 560 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 39 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN C 345 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.139470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.111104 restraints weight = 17037.008| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 3.45 r_work: 0.3650 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8750 Z= 0.146 Angle : 0.853 13.169 11946 Z= 0.379 Chirality : 0.045 0.373 1398 Planarity : 0.004 0.049 1410 Dihedral : 10.789 139.746 2106 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.63 % Allowed : 29.88 % 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 aren not related in a simple way. whole: 1.16 (0.28), residues: 1038 helix: 1.79 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -2.53 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 426 TYR 0.008 0.001 TYR C 226 PHE 0.015 0.001 PHE C 536 TRP 0.023 0.001 TRP A 452 HIS 0.003 0.001 HIS C 559 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8742) covalent geometry : angle 0.85097 (11932) SS BOND : bond 0.00037 ( 4) SS BOND : angle 0.27996 ( 8) hydrogen bonds : bond 0.04379 ( 594) hydrogen bonds : angle 4.45686 ( 1749) Misc. bond : bond 0.00028 ( 2) link_NAG-ASN : bond 0.00375 ( 2) link_NAG-ASN : angle 2.64813 ( 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 205 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.294 Fit side-chains REVERT: A 44 GLU cc_start: 0.8646 (tp30) cc_final: 0.8364 (tp30) REVERT: A 47 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8064 (tm-30) REVERT: A 222 PHE cc_start: 0.8399 (m-80) cc_final: 0.8140 (t80) REVERT: A 244 GLN cc_start: 0.8118 (tp-100) cc_final: 0.7579 (tp40) REVERT: A 297 ASP cc_start: 0.6244 (OUTLIER) cc_final: 0.5804 (p0) REVERT: A 307 PHE cc_start: 0.6390 (m-10) cc_final: 0.5694 (m-80) REVERT: A 309 GLU cc_start: 0.8869 (pm20) cc_final: 0.8638 (mm-30) REVERT: A 351 ILE cc_start: 0.6975 (OUTLIER) cc_final: 0.6699 (pp) REVERT: C 47 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7984 (tm-30) REVERT: C 215 TYR cc_start: 0.7645 (t80) cc_final: 0.7443 (t80) REVERT: C 226 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7573 (m-10) REVERT: C 244 GLN cc_start: 0.8128 (tp-100) cc_final: 0.7807 (tp40) REVERT: C 260 MET cc_start: 0.8278 (mmm) cc_final: 0.7900 (mmm) REVERT: C 297 ASP cc_start: 0.6308 (OUTLIER) cc_final: 0.5768 (p0) REVERT: C 307 PHE cc_start: 0.6577 (m-10) cc_final: 0.5546 (m-80) REVERT: C 314 ASP cc_start: 0.8201 (m-30) cc_final: 0.7988 (m-30) REVERT: C 345 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7443 (tp-100) REVERT: C 484 MET cc_start: 0.8294 (ptp) cc_final: 0.8058 (mpt) outliers start: 38 outliers final: 21 residues processed: 192 average time/residue: 0.3471 time to fit residues: 73.6685 Evaluate side-chains 175 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 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 395 HIS 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 79 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 226 TYR 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 345 GLN Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 560 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 66 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.139048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.110648 restraints weight = 17039.513| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 3.44 r_work: 0.3641 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 0.056 8750 Z= 0.155 Angle : 0.882 12.782 11946 Z= 0.396 Chirality : 0.046 0.394 1398 Planarity : 0.004 0.048 1410 Dihedral : 10.689 138.868 2106 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.54 % Allowed : 31.22 % Favored : 65.24 % 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 aren not related in a simple way. whole: 1.08 (0.27), residues: 1038 helix: 1.72 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -2.53 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 350 TYR 0.007 0.001 TYR C 226 PHE 0.015 0.001 PHE C 536 TRP 0.026 0.001 TRP A 452 HIS 0.009 0.001 HIS C 559 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8742) covalent geometry : angle 0.88023 (11932) SS BOND : bond 0.00054 ( 4) SS BOND : angle 0.25420 ( 8) hydrogen bonds : bond 0.04532 ( 594) hydrogen bonds : angle 4.54527 ( 1749) Misc. bond : bond 0.00030 ( 2) link_NAG-ASN : bond 0.00332 ( 2) link_NAG-ASN : angle 2.60829 ( 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: 29 poor density : 165 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8660 (tp30) cc_final: 0.8442 (tp30) REVERT: A 47 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8166 (tm-30) REVERT: A 222 PHE cc_start: 0.8372 (m-80) cc_final: 0.8108 (t80) REVERT: A 244 GLN cc_start: 0.8147 (tp-100) cc_final: 0.7776 (tp40) REVERT: A 297 ASP cc_start: 0.6156 (OUTLIER) cc_final: 0.5698 (p0) REVERT: A 307 PHE cc_start: 0.6483 (m-10) cc_final: 0.5841 (m-80) REVERT: A 313 GLU cc_start: 0.8534 (mp0) cc_final: 0.8191 (pm20) REVERT: C 47 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7961 (tm-30) REVERT: C 226 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7495 (m-10) REVERT: C 244 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7642 (tp40) REVERT: C 260 MET cc_start: 0.8252 (mmm) cc_final: 0.7868 (mmm) REVERT: C 297 ASP cc_start: 0.6288 (OUTLIER) cc_final: 0.5746 (p0) REVERT: C 307 PHE cc_start: 0.6754 (m-10) cc_final: 0.5600 (m-80) REVERT: C 314 ASP cc_start: 0.8186 (m-30) cc_final: 0.7944 (m-30) REVERT: C 484 MET cc_start: 0.8300 (ptp) cc_final: 0.8065 (mpt) outliers start: 29 outliers final: 20 residues processed: 187 average time/residue: 0.3671 time to fit residues: 75.9501 Evaluate side-chains 175 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 383 LEU 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 62 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 226 TYR 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 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 Chi-restraints excluded: chain C residue 560 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 75 optimal weight: 0.0870 chunk 39 optimal weight: 0.0040 chunk 73 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.0770 overall best weight: 0.2528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN C 244 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.140359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.112135 restraints weight = 17061.169| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.46 r_work: 0.3674 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8750 Z= 0.155 Angle : 0.916 13.724 11946 Z= 0.411 Chirality : 0.046 0.384 1398 Planarity : 0.004 0.056 1410 Dihedral : 10.506 137.446 2106 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.56 % Allowed : 32.56 % Favored : 64.88 % 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 aren not related in a simple way. whole: 1.00 (0.27), residues: 1038 helix: 1.66 (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 0.004 0.000 ARG A 426 TYR 0.007 0.001 TYR C 226 PHE 0.014 0.001 PHE C 550 TRP 0.028 0.001 TRP A 452 HIS 0.002 0.000 HIS C 559 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8742) covalent geometry : angle 0.91425 (11932) SS BOND : bond 0.00012 ( 4) SS BOND : angle 0.21580 ( 8) hydrogen bonds : bond 0.04456 ( 594) hydrogen bonds : angle 4.56008 ( 1749) Misc. bond : bond 0.00020 ( 2) link_NAG-ASN : bond 0.00405 ( 2) link_NAG-ASN : angle 2.60517 ( 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 192 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.341 Fit side-chains REVERT: A 44 GLU cc_start: 0.8663 (tp30) cc_final: 0.8334 (tp30) REVERT: A 47 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 215 TYR cc_start: 0.7821 (t80) cc_final: 0.7616 (t80) REVERT: A 222 PHE cc_start: 0.8405 (m-80) cc_final: 0.8195 (t80) REVERT: A 244 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7631 (tp40) REVERT: A 297 ASP cc_start: 0.6179 (OUTLIER) cc_final: 0.5626 (p0) REVERT: A 307 PHE cc_start: 0.6677 (m-10) cc_final: 0.5806 (m-80) REVERT: C 47 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7949 (tm-30) REVERT: C 226 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7679 (m-10) REVERT: C 244 GLN cc_start: 0.8087 (tp40) cc_final: 0.7747 (tp40) REVERT: C 260 MET cc_start: 0.8230 (mmm) cc_final: 0.7838 (mmm) REVERT: C 297 ASP cc_start: 0.6236 (OUTLIER) cc_final: 0.5693 (p0) REVERT: C 307 PHE cc_start: 0.6686 (m-10) cc_final: 0.5639 (m-80) REVERT: C 314 ASP cc_start: 0.8245 (m-30) cc_final: 0.8023 (m-30) REVERT: C 484 MET cc_start: 0.8277 (ptp) cc_final: 0.8056 (mpt) outliers start: 21 outliers final: 18 residues processed: 186 average time/residue: 0.3453 time to fit residues: 71.0720 Evaluate side-chains 179 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 383 LEU 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 62 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 226 TYR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 308 THR 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 560 HIS 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: 1.9990 chunk 80 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.139248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.111612 restraints weight = 17105.946| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 3.40 r_work: 0.3655 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8750 Z= 0.162 Angle : 0.928 13.001 11946 Z= 0.422 Chirality : 0.047 0.385 1398 Planarity : 0.004 0.051 1410 Dihedral : 10.389 136.861 2106 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.05 % Allowed : 32.68 % Favored : 64.27 % 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 aren not related in a simple way. whole: 0.97 (0.27), residues: 1038 helix: 1.65 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -2.57 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 350 TYR 0.007 0.001 TYR C 226 PHE 0.013 0.001 PHE C 536 TRP 0.027 0.002 TRP A 452 HIS 0.004 0.001 HIS C 559 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8742) covalent geometry : angle 0.92676 (11932) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.24417 ( 8) hydrogen bonds : bond 0.04610 ( 594) hydrogen bonds : angle 4.63212 ( 1749) Misc. bond : bond 0.00029 ( 2) link_NAG-ASN : bond 0.00325 ( 2) link_NAG-ASN : angle 2.54558 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2581.86 seconds wall clock time: 44 minutes 52.22 seconds (2692.22 seconds total)