Starting phenix.real_space_refine on Mon May 12 14:21:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsl_18635/05_2025/8qsl_18635_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsl_18635/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qsl_18635/05_2025/8qsl_18635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsl_18635/05_2025/8qsl_18635.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsl_18635/05_2025/8qsl_18635_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsl_18635/05_2025/8qsl_18635_neut.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.018 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.39, per 1000 atoms: 0.63 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: 2.81 Conformation dependent library (CDL) restraints added in 944.5 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: 0.75 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: 2.19 Time building geometry restraints manager: 2.95 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: 0.04 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: 0.880 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.840 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (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 TRP 0.040 0.002 TRP C 452 HIS 0.004 0.001 HIS C 348 PHE 0.017 0.001 PHE A 194 TYR 0.006 0.001 TYR C 86 ARG 0.002 0.001 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 2) link_NAG-ASN : angle 1.41883 ( 6) hydrogen bonds : bond 0.14117 ( 594) hydrogen bonds : angle 5.43517 ( 1749) SS BOND : bond 0.00188 ( 4) SS BOND : angle 0.41924 ( 8) covalent geometry : bond 0.00362 ( 8742) covalent geometry : angle 0.67087 (11932) Misc. bond : bond 0.85041 ( 2) *********************** 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 : 0.960 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: 0.7392 time to fit residues: 155.5685 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 : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 30.0000 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.136161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.107602 restraints weight = 16893.209| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.43 r_work: 0.3575 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8750 Z= 0.179 Angle : 0.775 8.096 11946 Z= 0.371 Chirality : 0.042 0.214 1398 Planarity : 0.005 0.038 1410 Dihedral : 11.608 148.876 2106 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.27 % Allowed : 22.44 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.27), residues: 1038 helix: 2.06 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -2.55 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 452 HIS 0.003 0.001 HIS C 303 PHE 0.023 0.002 PHE A 194 TYR 0.014 0.002 TYR C 226 ARG 0.004 0.001 ARG C 426 Details of bonding type rmsd link_NAG-ASN : bond 0.00036 ( 2) link_NAG-ASN : angle 2.50142 ( 6) hydrogen bonds : bond 0.05324 ( 594) hydrogen bonds : angle 4.67258 ( 1749) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.50482 ( 8) covalent geometry : bond 0.00399 ( 8742) covalent geometry : angle 0.77357 (11932) Misc. bond : bond 0.00247 ( 2) *********************** 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 215 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8311 (m-80) cc_final: 0.8063 (t80) REVERT: A 351 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.6985 (pp) REVERT: C 215 TYR cc_start: 0.8001 (t80) cc_final: 0.7793 (t80) REVERT: C 226 TYR cc_start: 0.8633 (m-80) cc_final: 0.7567 (m-80) REVERT: C 260 MET cc_start: 0.8199 (mmm) cc_final: 0.7932 (mmm) REVERT: C 452 TRP cc_start: 0.8181 (m100) cc_final: 0.7958 (m100) REVERT: C 528 ASN cc_start: 0.6816 (t0) cc_final: 0.6524 (m-40) outliers start: 35 outliers final: 8 residues processed: 193 average time/residue: 0.6720 time to fit residues: 144.2938 Evaluate side-chains 157 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 308 THR 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 47 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 218 GLN C 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.135966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.107063 restraints weight = 16930.231| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.42 r_work: 0.3573 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8750 Z= 0.175 Angle : 0.813 10.180 11946 Z= 0.375 Chirality : 0.045 0.400 1398 Planarity : 0.004 0.033 1410 Dihedral : 11.575 146.174 2106 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.84 % Favored : 93.06 % Rotamer: Outliers : 5.00 % Allowed : 22.56 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 1038 helix: 1.94 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -2.72 (0.42), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 452 HIS 0.002 0.001 HIS C 560 PHE 0.023 0.002 PHE A 325 TYR 0.009 0.001 TYR A 535 ARG 0.002 0.000 ARG A 393 Details of bonding type rmsd link_NAG-ASN : bond 0.02886 ( 2) link_NAG-ASN : angle 6.16412 ( 6) hydrogen bonds : bond 0.05177 ( 594) hydrogen bonds : angle 4.53324 ( 1749) SS BOND : bond 0.00107 ( 4) SS BOND : angle 0.50140 ( 8) covalent geometry : bond 0.00394 ( 8742) covalent geometry : angle 0.80123 (11932) Misc. bond : bond 0.00034 ( 2) *********************** 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 226 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8351 (m-80) cc_final: 0.8006 (t80) REVERT: A 351 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.6912 (pp) REVERT: C 154 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8344 (t) REVERT: C 222 PHE cc_start: 0.8407 (m-80) cc_final: 0.7612 (m-80) REVERT: C 226 TYR cc_start: 0.8722 (m-80) cc_final: 0.7357 (m-80) REVERT: C 260 MET cc_start: 0.8197 (mmm) cc_final: 0.7839 (mmm) REVERT: C 344 LEU cc_start: 0.8536 (mp) cc_final: 0.8331 (tp) REVERT: C 423 GLU cc_start: 0.8633 (tp30) cc_final: 0.8409 (tp30) REVERT: C 452 TRP cc_start: 0.8223 (m100) cc_final: 0.7973 (m100) REVERT: C 528 ASN cc_start: 0.6791 (t0) cc_final: 0.6499 (m-40) outliers start: 41 outliers final: 15 residues processed: 206 average time/residue: 0.6096 time to fit residues: 140.2120 Evaluate side-chains 172 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 401 SER 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 312 VAL Chi-restraints excluded: chain C residue 313 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 454 GLN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 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 = 0.4128 r_free = 0.4128 target = 0.137016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.107421 restraints weight = 16978.331| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 3.48 r_work: 0.3592 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 8750 Z= 0.156 Angle : 0.795 10.683 11946 Z= 0.365 Chirality : 0.044 0.357 1398 Planarity : 0.004 0.028 1410 Dihedral : 11.373 144.442 2106 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.00 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.27), residues: 1038 helix: 1.88 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -2.64 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 453 HIS 0.002 0.001 HIS A 348 PHE 0.027 0.001 PHE A 550 TYR 0.007 0.001 TYR A 86 ARG 0.002 0.000 ARG A 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 2) link_NAG-ASN : angle 4.17738 ( 6) hydrogen bonds : bond 0.04843 ( 594) hydrogen bonds : angle 4.49889 ( 1749) SS BOND : bond 0.00124 ( 4) SS BOND : angle 0.28646 ( 8) covalent geometry : bond 0.00358 ( 8742) covalent geometry : angle 0.78942 (11932) Misc. bond : bond 0.00021 ( 2) *********************** 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 222 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8090 (tm-30) REVERT: A 222 PHE cc_start: 0.8405 (m-80) cc_final: 0.8054 (t80) REVERT: A 371 MET cc_start: 0.7910 (ttm) cc_final: 0.7685 (ttm) REVERT: C 47 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8106 (tm-30) REVERT: C 215 TYR cc_start: 0.7954 (t80) cc_final: 0.7750 (t80) REVERT: C 222 PHE cc_start: 0.8415 (m-80) cc_final: 0.7712 (m-80) REVERT: C 226 TYR cc_start: 0.8705 (m-80) cc_final: 0.7424 (m-80) REVERT: C 244 GLN cc_start: 0.8281 (tp-100) cc_final: 0.7716 (tp40) REVERT: C 260 MET cc_start: 0.8190 (mmm) cc_final: 0.7778 (mmm) REVERT: C 297 ASP cc_start: 0.6321 (OUTLIER) cc_final: 0.6100 (p0) REVERT: C 423 GLU cc_start: 0.8278 (tp30) cc_final: 0.6962 (tm-30) REVERT: C 427 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8386 (mm) REVERT: C 452 TRP cc_start: 0.8264 (m100) cc_final: 0.8001 (m100) outliers start: 44 outliers final: 19 residues processed: 206 average time/residue: 0.6662 time to fit residues: 152.1123 Evaluate side-chains 176 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 312 VAL 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 43 THR 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 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 401 SER Chi-restraints excluded: chain C residue 427 LEU 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 84 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 31 optimal weight: 0.0870 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.137164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.108634 restraints weight = 17079.402| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.43 r_work: 0.3600 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8750 Z= 0.153 Angle : 0.805 11.516 11946 Z= 0.368 Chirality : 0.045 0.370 1398 Planarity : 0.004 0.032 1410 Dihedral : 11.215 143.051 2106 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 5.24 % Allowed : 24.63 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.28), residues: 1038 helix: 1.82 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -2.61 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 368 HIS 0.006 0.001 HIS C 521 PHE 0.022 0.001 PHE A 536 TYR 0.008 0.001 TYR A 535 ARG 0.005 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 2) link_NAG-ASN : angle 3.41909 ( 6) hydrogen bonds : bond 0.04750 ( 594) hydrogen bonds : angle 4.55217 ( 1749) SS BOND : bond 0.00124 ( 4) SS BOND : angle 0.28819 ( 8) covalent geometry : bond 0.00345 ( 8742) covalent geometry : angle 0.80200 (11932) Misc. bond : bond 0.00020 ( 2) *********************** 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 211 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7759 (tm-30) REVERT: A 218 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8287 (mm-40) REVERT: A 222 PHE cc_start: 0.8387 (m-80) cc_final: 0.8080 (t80) REVERT: A 244 GLN cc_start: 0.8089 (tp-100) cc_final: 0.7562 (tp40) REVERT: A 297 ASP cc_start: 0.6445 (OUTLIER) cc_final: 0.6110 (p0) REVERT: A 351 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6626 (pp) REVERT: A 484 MET cc_start: 0.8510 (ptp) cc_final: 0.8154 (mpt) REVERT: C 47 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7784 (tm-30) REVERT: C 154 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8387 (t) REVERT: C 215 TYR cc_start: 0.7887 (t80) cc_final: 0.7684 (t80) REVERT: C 260 MET cc_start: 0.8192 (mmm) cc_final: 0.7752 (mmm) REVERT: C 423 GLU cc_start: 0.8181 (tp30) cc_final: 0.7033 (tm-30) REVERT: C 427 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8323 (mm) REVERT: C 452 TRP cc_start: 0.8315 (m100) cc_final: 0.8066 (m100) REVERT: C 484 MET cc_start: 0.8564 (ptp) cc_final: 0.8245 (mpt) outliers start: 43 outliers final: 18 residues processed: 195 average time/residue: 0.6291 time to fit residues: 136.6524 Evaluate side-chains 167 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR 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 312 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 351 ILE 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 154 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 345 GLN 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 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 32 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.0870 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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** ** C 543 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 = 0.4138 r_free = 0.4138 target = 0.137518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.109487 restraints weight = 16950.738| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.38 r_work: 0.3610 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8750 Z= 0.152 Angle : 0.813 12.473 11946 Z= 0.369 Chirality : 0.044 0.363 1398 Planarity : 0.004 0.031 1410 Dihedral : 11.089 141.737 2106 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 5.24 % Allowed : 26.46 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.28), residues: 1038 helix: 1.87 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -2.60 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 452 HIS 0.002 0.001 HIS C 521 PHE 0.020 0.001 PHE A 536 TYR 0.011 0.001 TYR C 226 ARG 0.006 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 2) link_NAG-ASN : angle 3.01257 ( 6) hydrogen bonds : bond 0.04628 ( 594) hydrogen bonds : angle 4.50902 ( 1749) SS BOND : bond 0.00075 ( 4) SS BOND : angle 0.24531 ( 8) covalent geometry : bond 0.00347 ( 8742) covalent geometry : angle 0.81017 (11932) Misc. bond : bond 0.00014 ( 2) *********************** 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 216 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 222 PHE cc_start: 0.8404 (m-80) cc_final: 0.8084 (t80) REVERT: A 244 GLN cc_start: 0.8091 (tp-100) cc_final: 0.7579 (tp40) REVERT: A 297 ASP cc_start: 0.6354 (OUTLIER) cc_final: 0.5993 (p0) REVERT: A 307 PHE cc_start: 0.6479 (m-10) cc_final: 0.5625 (m-80) REVERT: A 351 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6712 (pp) REVERT: C 47 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7852 (tm-30) REVERT: C 222 PHE cc_start: 0.8448 (m-80) cc_final: 0.8024 (t80) REVERT: C 244 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7643 (tp40) REVERT: C 260 MET cc_start: 0.8272 (mmm) cc_final: 0.7836 (mmm) REVERT: C 297 ASP cc_start: 0.6391 (OUTLIER) cc_final: 0.6056 (p0) REVERT: C 307 PHE cc_start: 0.6243 (m-10) cc_final: 0.5467 (m-80) REVERT: C 423 GLU cc_start: 0.8089 (tp30) cc_final: 0.6416 (tp30) REVERT: C 452 TRP cc_start: 0.8309 (m100) cc_final: 0.8015 (m100) REVERT: C 484 MET cc_start: 0.8458 (ptp) cc_final: 0.8152 (mpt) outliers start: 43 outliers final: 21 residues processed: 205 average time/residue: 0.6704 time to fit residues: 152.7719 Evaluate side-chains 175 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR 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 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 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 312 VAL 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 Chi-restraints excluded: chain C residue 551 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 36 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.0050 chunk 7 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.138329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.110005 restraints weight = 17071.230| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.42 r_work: 0.3623 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 8750 Z= 0.151 Angle : 0.830 12.688 11946 Z= 0.375 Chirality : 0.044 0.370 1398 Planarity : 0.004 0.031 1410 Dihedral : 11.012 140.551 2106 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.39 % Allowed : 28.66 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.27), residues: 1038 helix: 1.82 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -2.66 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 368 HIS 0.002 0.001 HIS A 348 PHE 0.050 0.001 PHE C 550 TYR 0.007 0.001 TYR C 226 ARG 0.004 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 2) link_NAG-ASN : angle 2.87328 ( 6) hydrogen bonds : bond 0.04641 ( 594) hydrogen bonds : angle 4.49873 ( 1749) SS BOND : bond 0.00058 ( 4) SS BOND : angle 0.30375 ( 8) covalent geometry : bond 0.00342 ( 8742) covalent geometry : angle 0.82780 (11932) Misc. bond : bond 0.00032 ( 2) *********************** 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 207 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7874 (tm-30) REVERT: A 215 TYR cc_start: 0.7864 (t80) cc_final: 0.7654 (t80) REVERT: A 222 PHE cc_start: 0.8396 (m-80) cc_final: 0.8077 (t80) REVERT: A 244 GLN cc_start: 0.8085 (tp-100) cc_final: 0.7740 (tp40) REVERT: A 297 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.5935 (p0) REVERT: A 307 PHE cc_start: 0.6406 (m-10) cc_final: 0.5555 (m-80) REVERT: A 351 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6650 (pp) REVERT: A 484 MET cc_start: 0.8409 (ptp) cc_final: 0.8080 (mpt) REVERT: C 47 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7932 (tm-30) REVERT: C 215 TYR cc_start: 0.7790 (t80) cc_final: 0.7574 (t80) REVERT: C 222 PHE cc_start: 0.8467 (m-80) cc_final: 0.8014 (t80) REVERT: C 244 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7642 (tp40) REVERT: C 260 MET cc_start: 0.8289 (mmm) cc_final: 0.7896 (mmm) REVERT: C 297 ASP cc_start: 0.6335 (OUTLIER) cc_final: 0.5975 (p0) REVERT: C 307 PHE cc_start: 0.6533 (m-10) cc_final: 0.5683 (m-80) REVERT: C 314 ASP cc_start: 0.8316 (m-30) cc_final: 0.8082 (m-30) REVERT: C 371 MET cc_start: 0.7748 (ttm) cc_final: 0.7501 (ttm) REVERT: C 427 LEU cc_start: 0.8786 (mm) cc_final: 0.8403 (mm) REVERT: C 452 TRP cc_start: 0.8309 (m100) cc_final: 0.8044 (m100) REVERT: C 484 MET cc_start: 0.8416 (ptp) cc_final: 0.8179 (mpt) outliers start: 36 outliers final: 21 residues processed: 195 average time/residue: 0.6522 time to fit residues: 141.2439 Evaluate side-chains 182 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR 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 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 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 312 VAL 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 429 LEU Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 504 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 92 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 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 = 0.4154 r_free = 0.4154 target = 0.138541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.110534 restraints weight = 17167.944| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.41 r_work: 0.3633 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 8750 Z= 0.156 Angle : 0.855 13.164 11946 Z= 0.390 Chirality : 0.045 0.387 1398 Planarity : 0.004 0.031 1410 Dihedral : 10.888 139.351 2106 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.54 % Allowed : 30.73 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.28), residues: 1038 helix: 1.78 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -2.68 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 368 HIS 0.001 0.000 HIS A 348 PHE 0.017 0.001 PHE A 325 TYR 0.006 0.001 TYR C 226 ARG 0.004 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 2) link_NAG-ASN : angle 2.78094 ( 6) hydrogen bonds : bond 0.04592 ( 594) hydrogen bonds : angle 4.58861 ( 1749) SS BOND : bond 0.00050 ( 4) SS BOND : angle 0.25710 ( 8) covalent geometry : bond 0.00351 ( 8742) covalent geometry : angle 0.85304 (11932) Misc. bond : bond 0.00029 ( 2) *********************** 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 192 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7813 (tm-30) REVERT: A 215 TYR cc_start: 0.7856 (t80) cc_final: 0.7631 (t80) REVERT: A 222 PHE cc_start: 0.8378 (m-80) cc_final: 0.8122 (t80) REVERT: A 244 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7603 (tp40) REVERT: A 297 ASP cc_start: 0.6378 (OUTLIER) cc_final: 0.5941 (p0) REVERT: A 307 PHE cc_start: 0.6533 (m-10) cc_final: 0.5684 (m-80) REVERT: A 314 ASP cc_start: 0.8289 (m-30) cc_final: 0.8046 (m-30) REVERT: A 484 MET cc_start: 0.8366 (ptp) cc_final: 0.8087 (mpt) REVERT: C 47 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7965 (tm-30) REVERT: C 215 TYR cc_start: 0.7761 (t80) cc_final: 0.7537 (t80) REVERT: C 222 PHE cc_start: 0.8450 (m-80) cc_final: 0.8114 (t80) REVERT: C 244 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7659 (tp40) REVERT: C 260 MET cc_start: 0.8263 (mmm) cc_final: 0.7861 (mmm) REVERT: C 297 ASP cc_start: 0.6345 (OUTLIER) cc_final: 0.5921 (p0) REVERT: C 307 PHE cc_start: 0.6565 (m-10) cc_final: 0.5916 (m-80) REVERT: C 314 ASP cc_start: 0.8181 (m-30) cc_final: 0.7915 (m-30) REVERT: C 371 MET cc_start: 0.7819 (ttm) cc_final: 0.7599 (ttm) REVERT: C 423 GLU cc_start: 0.7548 (tp30) cc_final: 0.6592 (tp30) REVERT: C 427 LEU cc_start: 0.8706 (mm) cc_final: 0.8457 (mm) REVERT: C 452 TRP cc_start: 0.8336 (m100) cc_final: 0.8062 (m100) REVERT: C 484 MET cc_start: 0.8388 (ptp) cc_final: 0.8162 (mpt) outliers start: 29 outliers final: 15 residues processed: 182 average time/residue: 0.6637 time to fit residues: 134.5303 Evaluate side-chains 165 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 360 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.138332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.110029 restraints weight = 17210.666| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.41 r_work: 0.3623 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8750 Z= 0.161 Angle : 0.877 13.096 11946 Z= 0.397 Chirality : 0.046 0.382 1398 Planarity : 0.004 0.033 1410 Dihedral : 10.749 137.987 2106 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.32 % Allowed : 32.20 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.28), residues: 1038 helix: 1.76 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -2.71 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 368 HIS 0.002 0.001 HIS A 348 PHE 0.019 0.001 PHE A 325 TYR 0.006 0.001 TYR A 113 ARG 0.004 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 2) link_NAG-ASN : angle 2.67260 ( 6) hydrogen bonds : bond 0.04714 ( 594) hydrogen bonds : angle 4.63793 ( 1749) SS BOND : bond 0.00057 ( 4) SS BOND : angle 0.26119 ( 8) covalent geometry : bond 0.00371 ( 8742) covalent geometry : angle 0.87588 (11932) Misc. bond : bond 0.00023 ( 2) *********************** 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 179 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7837 (tm-30) REVERT: A 215 TYR cc_start: 0.7901 (t80) cc_final: 0.7693 (t80) REVERT: A 222 PHE cc_start: 0.8363 (m-80) cc_final: 0.8134 (t80) REVERT: A 244 GLN cc_start: 0.8147 (tp-100) cc_final: 0.7648 (tp40) REVERT: A 266 TYR cc_start: 0.8705 (m-10) cc_final: 0.8434 (m-10) REVERT: A 297 ASP cc_start: 0.6510 (OUTLIER) cc_final: 0.5939 (p0) REVERT: A 307 PHE cc_start: 0.6775 (m-10) cc_final: 0.6032 (m-80) REVERT: A 314 ASP cc_start: 0.8273 (m-30) cc_final: 0.7975 (m-30) REVERT: A 484 MET cc_start: 0.8361 (ptp) cc_final: 0.8130 (mpt) REVERT: C 47 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7855 (tm-30) REVERT: C 244 GLN cc_start: 0.8174 (tp-100) cc_final: 0.7672 (tp40) REVERT: C 260 MET cc_start: 0.8259 (mmm) cc_final: 0.7872 (mmm) REVERT: C 297 ASP cc_start: 0.6393 (OUTLIER) cc_final: 0.5847 (p0) REVERT: C 307 PHE cc_start: 0.6829 (m-10) cc_final: 0.5949 (m-80) REVERT: C 314 ASP cc_start: 0.8273 (m-30) cc_final: 0.7978 (m-30) REVERT: C 371 MET cc_start: 0.7813 (ttm) cc_final: 0.7533 (ttm) REVERT: C 423 GLU cc_start: 0.7814 (tp30) cc_final: 0.6853 (tp30) REVERT: C 427 LEU cc_start: 0.8735 (mm) cc_final: 0.8385 (mm) REVERT: C 452 TRP cc_start: 0.8292 (m100) cc_final: 0.7996 (m100) REVERT: C 484 MET cc_start: 0.8412 (ptp) cc_final: 0.8139 (mpt) outliers start: 19 outliers final: 13 residues processed: 175 average time/residue: 0.6474 time to fit residues: 126.3421 Evaluate side-chains 165 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 351 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 297 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 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 = 0.4150 r_free = 0.4150 target = 0.138039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.109727 restraints weight = 17070.376| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.40 r_work: 0.3621 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3340 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= 0.167 Angle : 0.897 13.170 11946 Z= 0.408 Chirality : 0.046 0.391 1398 Planarity : 0.004 0.033 1410 Dihedral : 10.612 136.584 2106 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.32 % Allowed : 32.68 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 1038 helix: 1.72 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -2.75 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 368 HIS 0.002 0.001 HIS A 348 PHE 0.025 0.001 PHE C 325 TYR 0.006 0.001 TYR C 557 ARG 0.004 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 2) link_NAG-ASN : angle 2.63887 ( 6) hydrogen bonds : bond 0.04736 ( 594) hydrogen bonds : angle 4.68280 ( 1749) SS BOND : bond 0.00053 ( 4) SS BOND : angle 0.24890 ( 8) covalent geometry : bond 0.00385 ( 8742) covalent geometry : angle 0.89574 (11932) Misc. bond : bond 0.00023 ( 2) ********************** 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 182 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7776 (tm-30) REVERT: A 222 PHE cc_start: 0.8386 (m-80) cc_final: 0.8159 (t80) REVERT: A 244 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7677 (tp40) REVERT: A 297 ASP cc_start: 0.6483 (OUTLIER) cc_final: 0.5925 (p0) REVERT: A 307 PHE cc_start: 0.6931 (m-10) cc_final: 0.6005 (m-80) REVERT: A 314 ASP cc_start: 0.8313 (m-30) cc_final: 0.8012 (m-30) REVERT: A 484 MET cc_start: 0.8332 (ptp) cc_final: 0.8095 (mpt) REVERT: C 47 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7839 (tm-30) REVERT: C 215 TYR cc_start: 0.7668 (t80) cc_final: 0.7450 (t80) REVERT: C 260 MET cc_start: 0.8267 (mmm) cc_final: 0.7886 (mmm) REVERT: C 297 ASP cc_start: 0.6404 (OUTLIER) cc_final: 0.5831 (p0) REVERT: C 307 PHE cc_start: 0.6741 (m-10) cc_final: 0.5880 (m-80) REVERT: C 314 ASP cc_start: 0.8287 (m-30) cc_final: 0.7940 (m-30) REVERT: C 423 GLU cc_start: 0.7851 (tp30) cc_final: 0.6899 (tp30) REVERT: C 427 LEU cc_start: 0.8699 (mm) cc_final: 0.8438 (mm) REVERT: C 452 TRP cc_start: 0.8311 (m100) cc_final: 0.8013 (m100) REVERT: C 484 MET cc_start: 0.8400 (ptp) cc_final: 0.8111 (mpt) outliers start: 19 outliers final: 16 residues processed: 178 average time/residue: 0.6505 time to fit residues: 128.9687 Evaluate side-chains 165 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 112 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 351 ILE Chi-restraints excluded: chain A residue 360 THR 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 80 LEU Chi-restraints excluded: chain C residue 297 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.138582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.110336 restraints weight = 17170.085| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 3.39 r_work: 0.3630 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3440 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= 0.159 Angle : 0.898 13.679 11946 Z= 0.404 Chirality : 0.047 0.389 1398 Planarity : 0.004 0.040 1410 Dihedral : 10.485 135.076 2106 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.32 % Allowed : 32.93 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 1038 helix: 1.72 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -2.74 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 368 HIS 0.002 0.001 HIS A 559 PHE 0.046 0.002 PHE C 550 TYR 0.005 0.001 TYR A 557 ARG 0.004 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 2) link_NAG-ASN : angle 2.60157 ( 6) hydrogen bonds : bond 0.04740 ( 594) hydrogen bonds : angle 4.65999 ( 1749) SS BOND : bond 0.00038 ( 4) SS BOND : angle 0.23844 ( 8) covalent geometry : bond 0.00358 ( 8742) covalent geometry : angle 0.89651 (11932) Misc. bond : bond 0.00031 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5221.27 seconds wall clock time: 91 minutes 1.16 seconds (5461.16 seconds total)