Starting phenix.real_space_refine on Thu Mar 13 16:52:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsl_18635/03_2025/8qsl_18635_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsl_18635/03_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_18635/03_2025/8qsl_18635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsl_18635/03_2025/8qsl_18635.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsl_18635/03_2025/8qsl_18635_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsl_18635/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.60, per 1000 atoms: 0.66 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: 2.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.78 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: 2.43 Time building geometry restraints manager: 3.21 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: 0.05 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: 1.030 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: 0.080 Process input model: 23.680 Find NCS groups from input model: 0.320 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:14.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.290 ------------------------------------------------------------------------------- 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 : 0.004 0.040 8742 Z= 0.236 Angle : 0.671 8.420 11932 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 *********************** 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 : 0.884 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: 0.9303 time to fit residues: 194.1787 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 : 1.083 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.136254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.107720 restraints weight = 16892.680| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.43 r_work: 0.3578 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8742 Z= 0.262 Angle : 0.774 8.097 11932 Z= 0.371 Chirality : 0.042 0.214 1398 Planarity : 0.005 0.038 1410 Dihedral : 11.608 148.875 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 *********************** 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 : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8311 (m-80) cc_final: 0.8068 (t80) REVERT: A 351 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.6985 (pp) REVERT: C 215 TYR cc_start: 0.7999 (t80) cc_final: 0.7794 (t80) REVERT: C 226 TYR cc_start: 0.8632 (m-80) cc_final: 0.7572 (m-80) REVERT: C 260 MET cc_start: 0.8205 (mmm) cc_final: 0.7938 (mmm) REVERT: C 452 TRP cc_start: 0.8181 (m100) cc_final: 0.7958 (m100) REVERT: C 528 ASN cc_start: 0.6824 (t0) cc_final: 0.6530 (m-40) outliers start: 35 outliers final: 8 residues processed: 193 average time/residue: 0.7952 time to fit residues: 170.5641 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 : 0.813 ------------------------------------------------------------------------------- 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: 8.9990 chunk 78 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 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 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 = 0.4132 r_free = 0.4132 target = 0.137721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.108771 restraints weight = 16828.758| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 3.43 r_work: 0.3594 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8742 Z= 0.221 Angle : 0.786 10.121 11932 Z= 0.364 Chirality : 0.044 0.392 1398 Planarity : 0.004 0.034 1410 Dihedral : 11.526 146.716 2106 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.15 % Allowed : 23.78 % Favored : 72.07 % 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: 1.33 (0.27), residues: 1038 helix: 1.97 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -2.60 (0.43), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 452 HIS 0.002 0.001 HIS A 348 PHE 0.022 0.001 PHE A 325 TYR 0.008 0.001 TYR C 86 ARG 0.002 0.000 ARG A 393 *********************** 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: 34 poor density : 192 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8370 (m-80) cc_final: 0.8029 (t80) REVERT: A 244 GLN cc_start: 0.8219 (tp-100) cc_final: 0.7552 (tp40) REVERT: C 222 PHE cc_start: 0.8421 (m-80) cc_final: 0.7632 (m-80) REVERT: C 226 TYR cc_start: 0.8659 (m-80) cc_final: 0.7291 (m-80) REVERT: C 260 MET cc_start: 0.8189 (mmm) cc_final: 0.7854 (mmm) REVERT: C 452 TRP cc_start: 0.8182 (m100) cc_final: 0.7945 (m100) REVERT: C 528 ASN cc_start: 0.6733 (t0) cc_final: 0.6465 (m-40) outliers start: 34 outliers final: 14 residues processed: 207 average time/residue: 0.8099 time to fit residues: 187.0602 Evaluate side-chains 165 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 401 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain C residue 43 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 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: 3.9990 chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 C 218 GLN ** C 521 HIS ** 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 = 0.4119 r_free = 0.4119 target = 0.136289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.106795 restraints weight = 17033.237| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.45 r_work: 0.3573 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 8742 Z= 0.275 Angle : 0.800 11.182 11932 Z= 0.370 Chirality : 0.044 0.348 1398 Planarity : 0.004 0.060 1410 Dihedral : 11.379 144.449 2106 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 6.22 % Allowed : 23.78 % 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: 1.92 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -2.76 (0.42), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 452 HIS 0.005 0.001 HIS C 521 PHE 0.023 0.002 PHE A 550 TYR 0.008 0.001 TYR A 535 ARG 0.003 0.000 ARG A 426 *********************** 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 227 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.6189 (OUTLIER) cc_final: 0.5643 (pmt-80) REVERT: A 222 PHE cc_start: 0.8404 (m-80) cc_final: 0.8053 (t80) REVERT: A 351 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6755 (pp) REVERT: C 154 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8361 (t) REVERT: C 215 TYR cc_start: 0.7931 (t80) cc_final: 0.7719 (t80) REVERT: C 222 PHE cc_start: 0.8422 (m-80) cc_final: 0.7747 (m-80) REVERT: C 226 TYR cc_start: 0.8734 (m-80) cc_final: 0.7432 (m-80) REVERT: C 244 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7656 (tp40) REVERT: C 260 MET cc_start: 0.8183 (mmm) cc_final: 0.7779 (mmm) REVERT: C 297 ASP cc_start: 0.6313 (OUTLIER) cc_final: 0.6083 (p0) REVERT: C 452 TRP cc_start: 0.8293 (m100) cc_final: 0.8012 (m100) outliers start: 51 outliers final: 18 residues processed: 207 average time/residue: 0.7202 time to fit residues: 165.2252 Evaluate side-chains 177 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 151 ARG 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 429 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 7.9990 chunk 49 optimal weight: 0.0030 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.137614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.108957 restraints weight = 17034.684| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.43 r_work: 0.3619 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8742 Z= 0.219 Angle : 0.795 11.810 11932 Z= 0.364 Chirality : 0.044 0.366 1398 Planarity : 0.004 0.054 1410 Dihedral : 11.194 142.938 2106 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 6.59 % Allowed : 23.66 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.28), residues: 1038 helix: 1.83 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -2.65 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 368 HIS 0.002 0.001 HIS C 521 PHE 0.019 0.001 PHE A 550 TYR 0.007 0.001 TYR C 226 ARG 0.006 0.000 ARG A 350 *********************** 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 232 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 178 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9072 (tt) cc_final: 0.8760 (tt) REVERT: A 47 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7951 (tm-30) REVERT: A 82 MET cc_start: 0.9177 (tpp) cc_final: 0.8972 (mmp) REVERT: A 215 TYR cc_start: 0.8055 (t80) cc_final: 0.7841 (t80) REVERT: A 222 PHE cc_start: 0.8377 (m-80) cc_final: 0.8055 (t80) REVERT: A 244 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7539 (tp40) REVERT: A 297 ASP cc_start: 0.6436 (OUTLIER) cc_final: 0.6096 (p0) REVERT: A 351 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6631 (pp) REVERT: A 371 MET cc_start: 0.7956 (ttm) cc_final: 0.7733 (ttt) REVERT: C 47 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8168 (tm-30) REVERT: C 154 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8379 (t) REVERT: C 260 MET cc_start: 0.8195 (mmm) cc_final: 0.7789 (mmm) REVERT: C 427 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8516 (mm) REVERT: C 452 TRP cc_start: 0.8306 (m100) cc_final: 0.8021 (m100) REVERT: C 484 MET cc_start: 0.8512 (ptp) cc_final: 0.8166 (mpt) outliers start: 54 outliers final: 25 residues processed: 213 average time/residue: 0.6669 time to fit residues: 157.8708 Evaluate side-chains 175 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 LEU 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 395 HIS Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 LEU 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 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 395 HIS Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 429 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: 7.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 36 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5320 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.137879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.109735 restraints weight = 16957.393| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.39 r_work: 0.3615 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8742 Z= 0.224 Angle : 0.816 12.551 11932 Z= 0.369 Chirality : 0.045 0.367 1398 Planarity : 0.004 0.051 1410 Dihedral : 11.075 141.630 2106 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 5.24 % Allowed : 27.07 % Favored : 67.68 % 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 (0.28), residues: 1038 helix: 1.85 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -2.61 (0.43), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 368 HIS 0.001 0.000 HIS A 521 PHE 0.016 0.001 PHE A 325 TYR 0.008 0.001 TYR C 226 ARG 0.005 0.000 ARG A 350 *********************** 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 : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9070 (tt) cc_final: 0.8766 (tt) REVERT: A 47 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 215 TYR cc_start: 0.7883 (t80) cc_final: 0.7668 (t80) REVERT: A 222 PHE cc_start: 0.8417 (m-80) cc_final: 0.8100 (t80) REVERT: A 244 GLN cc_start: 0.8110 (tp-100) cc_final: 0.7592 (tp40) REVERT: A 266 TYR cc_start: 0.8790 (m-10) cc_final: 0.8524 (m-10) REVERT: A 297 ASP cc_start: 0.6340 (OUTLIER) cc_final: 0.5974 (p0) REVERT: A 307 PHE cc_start: 0.6478 (m-10) cc_final: 0.5625 (m-80) REVERT: A 351 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6751 (pp) REVERT: A 371 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7746 (ttm) REVERT: A 484 MET cc_start: 0.8436 (ptp) cc_final: 0.8135 (mpt) REVERT: C 44 GLU cc_start: 0.8660 (tp30) cc_final: 0.8459 (tp30) REVERT: C 47 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7796 (tm-30) REVERT: C 222 PHE cc_start: 0.8465 (m-80) cc_final: 0.8076 (t80) REVERT: C 244 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7761 (tp40) REVERT: C 260 MET cc_start: 0.8282 (mmm) cc_final: 0.7893 (mmm) REVERT: C 297 ASP cc_start: 0.6367 (OUTLIER) cc_final: 0.6024 (p0) REVERT: C 307 PHE cc_start: 0.6175 (m-10) cc_final: 0.5404 (m-80) REVERT: C 423 GLU cc_start: 0.8163 (tp30) cc_final: 0.7581 (tp30) REVERT: C 427 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8495 (mm) REVERT: C 452 TRP cc_start: 0.8322 (m100) cc_final: 0.8081 (m100) REVERT: C 484 MET cc_start: 0.8492 (ptp) cc_final: 0.8162 (mpt) outliers start: 43 outliers final: 24 residues processed: 200 average time/residue: 0.6668 time to fit residues: 148.4676 Evaluate side-chains 183 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 59 VAL 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 371 MET 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 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 313 GLU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 457 GLN 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: 0.2980 chunk 67 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.0970 chunk 7 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 1 optimal weight: 0.0870 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN A 454 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.139068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.111245 restraints weight = 17125.424| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.40 r_work: 0.3662 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8742 Z= 0.213 Angle : 0.817 12.978 11932 Z= 0.369 Chirality : 0.044 0.356 1398 Planarity : 0.004 0.048 1410 Dihedral : 10.921 139.993 2106 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.76 % Allowed : 28.41 % Favored : 66.83 % 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: 1.26 (0.28), residues: 1038 helix: 1.88 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -2.62 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 368 HIS 0.002 0.001 HIS C 560 PHE 0.053 0.001 PHE C 550 TYR 0.008 0.001 TYR C 557 ARG 0.005 0.000 ARG A 350 *********************** 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 216 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9059 (tt) cc_final: 0.8793 (tt) REVERT: A 47 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7831 (tm-30) REVERT: A 222 PHE cc_start: 0.8404 (m-80) cc_final: 0.8052 (t80) REVERT: A 244 GLN cc_start: 0.8095 (tp-100) cc_final: 0.7574 (tp40) REVERT: A 266 TYR cc_start: 0.8773 (m-10) cc_final: 0.8486 (m-10) REVERT: A 297 ASP cc_start: 0.6319 (OUTLIER) cc_final: 0.5921 (p0) REVERT: A 307 PHE cc_start: 0.6514 (m-10) cc_final: 0.5678 (m-80) REVERT: A 351 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6741 (pp) REVERT: A 484 MET cc_start: 0.8335 (ptp) cc_final: 0.8092 (mpt) REVERT: C 47 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 222 PHE cc_start: 0.8510 (m-80) cc_final: 0.8105 (t80) REVERT: C 244 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7791 (tp40) REVERT: C 260 MET cc_start: 0.8279 (mmm) cc_final: 0.7903 (mmm) REVERT: C 297 ASP cc_start: 0.6291 (OUTLIER) cc_final: 0.5871 (p0) REVERT: C 307 PHE cc_start: 0.6239 (m-10) cc_final: 0.5560 (m-80) REVERT: C 371 MET cc_start: 0.7669 (ttm) cc_final: 0.7173 (ttm) REVERT: C 423 GLU cc_start: 0.8040 (tp30) cc_final: 0.7603 (tp30) REVERT: C 427 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8405 (mm) REVERT: C 452 TRP cc_start: 0.8359 (m100) cc_final: 0.8094 (m100) outliers start: 39 outliers final: 19 residues processed: 199 average time/residue: 0.7071 time to fit residues: 156.1344 Evaluate side-chains 185 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL 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 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 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 383 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 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: 1.9990 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 92 optimal weight: 0.0570 chunk 100 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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** ** A 543 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 = 0.4160 r_free = 0.4160 target = 0.139031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.110845 restraints weight = 17224.332| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 3.42 r_work: 0.3637 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8742 Z= 0.221 Angle : 0.843 13.440 11932 Z= 0.378 Chirality : 0.044 0.374 1398 Planarity : 0.004 0.050 1410 Dihedral : 10.768 138.571 2106 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.54 % Allowed : 31.71 % 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: 1.30 (0.28), residues: 1038 helix: 1.92 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -2.64 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 452 HIS 0.001 0.000 HIS A 348 PHE 0.021 0.001 PHE A 536 TYR 0.007 0.001 TYR C 557 ARG 0.004 0.000 ARG A 350 *********************** 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 196 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7801 (tm-30) REVERT: A 215 TYR cc_start: 0.7775 (t80) cc_final: 0.7556 (t80) REVERT: A 222 PHE cc_start: 0.8379 (m-80) cc_final: 0.8172 (t80) REVERT: A 244 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7641 (tp40) REVERT: A 297 ASP cc_start: 0.6228 (OUTLIER) cc_final: 0.5773 (p0) REVERT: A 307 PHE cc_start: 0.6646 (m-10) cc_final: 0.5919 (m-80) REVERT: A 309 GLU cc_start: 0.8820 (pm20) cc_final: 0.8596 (mm-30) REVERT: A 484 MET cc_start: 0.8275 (ptp) cc_final: 0.8072 (mpt) REVERT: C 47 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7839 (tm-30) REVERT: C 215 TYR cc_start: 0.7680 (t80) cc_final: 0.7474 (t80) REVERT: C 222 PHE cc_start: 0.8495 (m-80) cc_final: 0.8214 (t80) REVERT: C 260 MET cc_start: 0.8301 (mmm) cc_final: 0.7937 (mmm) REVERT: C 297 ASP cc_start: 0.6100 (OUTLIER) cc_final: 0.5681 (p0) REVERT: C 307 PHE cc_start: 0.6276 (m-10) cc_final: 0.5597 (m-80) REVERT: C 371 MET cc_start: 0.7506 (ttm) cc_final: 0.7181 (ttm) REVERT: C 423 GLU cc_start: 0.8067 (tp30) cc_final: 0.7335 (tp30) REVERT: C 427 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8395 (mm) REVERT: C 452 TRP cc_start: 0.8321 (m100) cc_final: 0.8069 (m100) outliers start: 29 outliers final: 15 residues processed: 184 average time/residue: 0.6992 time to fit residues: 143.4668 Evaluate side-chains 177 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 312 VAL 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 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 383 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.138419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.110144 restraints weight = 17306.876| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.39 r_work: 0.3625 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8742 Z= 0.242 Angle : 0.867 13.097 11932 Z= 0.391 Chirality : 0.046 0.380 1398 Planarity : 0.004 0.047 1410 Dihedral : 10.651 137.250 2106 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.90 % Allowed : 31.34 % 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: 1.24 (0.28), residues: 1038 helix: 1.88 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -2.63 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 452 HIS 0.002 0.001 HIS A 348 PHE 0.024 0.001 PHE C 325 TYR 0.007 0.001 TYR C 535 ARG 0.003 0.000 ARG A 350 *********************** 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 195 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7730 (tm-30) REVERT: A 215 TYR cc_start: 0.7899 (t80) cc_final: 0.7679 (t80) REVERT: A 222 PHE cc_start: 0.8373 (m-80) cc_final: 0.8151 (t80) REVERT: A 244 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7814 (tp40) REVERT: A 266 TYR cc_start: 0.8740 (m-10) cc_final: 0.8466 (m-10) REVERT: A 297 ASP cc_start: 0.6449 (OUTLIER) cc_final: 0.5869 (p0) REVERT: A 307 PHE cc_start: 0.6836 (m-10) cc_final: 0.6037 (m-80) REVERT: A 371 MET cc_start: 0.7664 (ttm) cc_final: 0.7325 (ttm) REVERT: C 47 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7827 (tm-30) REVERT: C 244 GLN cc_start: 0.8183 (tp40) cc_final: 0.7788 (tp40) REVERT: C 260 MET cc_start: 0.8250 (mmm) cc_final: 0.7925 (mmm) REVERT: C 297 ASP cc_start: 0.6302 (OUTLIER) cc_final: 0.5738 (p0) REVERT: C 307 PHE cc_start: 0.6458 (m-10) cc_final: 0.5677 (m-80) REVERT: C 371 MET cc_start: 0.7574 (ttm) cc_final: 0.7262 (ttm) REVERT: C 423 GLU cc_start: 0.8206 (tp30) cc_final: 0.7383 (tp30) REVERT: C 427 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8428 (mm) REVERT: C 452 TRP cc_start: 0.8335 (m100) cc_final: 0.8064 (m100) outliers start: 32 outliers final: 17 residues processed: 184 average time/residue: 0.8471 time to fit residues: 172.9025 Evaluate side-chains 170 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL 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 351 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 383 LEU 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 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 383 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 0.0040 chunk 61 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.138323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.110718 restraints weight = 17128.501| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.34 r_work: 0.3633 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 8742 Z= 0.263 Angle : 0.891 13.519 11932 Z= 0.403 Chirality : 0.046 0.388 1398 Planarity : 0.004 0.054 1410 Dihedral : 10.536 136.007 2106 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.93 % Allowed : 32.20 % 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 (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: 1.15 (0.27), residues: 1038 helix: 1.80 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -2.66 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 452 HIS 0.002 0.001 HIS A 348 PHE 0.022 0.001 PHE C 536 TYR 0.006 0.001 TYR C 535 ARG 0.004 0.000 ARG A 350 ********************** 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 185 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7743 (tm-30) REVERT: A 82 MET cc_start: 0.9157 (tpp) cc_final: 0.8880 (mmp) REVERT: A 215 TYR cc_start: 0.7860 (t80) cc_final: 0.7634 (t80) REVERT: A 222 PHE cc_start: 0.8384 (m-80) cc_final: 0.8151 (t80) REVERT: A 244 GLN cc_start: 0.8157 (tp-100) cc_final: 0.7669 (tp40) REVERT: A 266 TYR cc_start: 0.8711 (m-10) cc_final: 0.8432 (m-10) REVERT: A 297 ASP cc_start: 0.6247 (OUTLIER) cc_final: 0.5696 (p0) REVERT: A 307 PHE cc_start: 0.6978 (m-10) cc_final: 0.6021 (m-80) REVERT: A 371 MET cc_start: 0.7638 (ttm) cc_final: 0.7316 (ttm) REVERT: C 47 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7706 (tm-30) REVERT: C 215 TYR cc_start: 0.7597 (t80) cc_final: 0.7394 (t80) REVERT: C 244 GLN cc_start: 0.8127 (tp40) cc_final: 0.7662 (tp40) REVERT: C 260 MET cc_start: 0.8255 (mmm) cc_final: 0.7931 (mmm) REVERT: C 266 TYR cc_start: 0.8719 (m-10) cc_final: 0.8450 (m-10) REVERT: C 297 ASP cc_start: 0.6235 (OUTLIER) cc_final: 0.5722 (p0) REVERT: C 307 PHE cc_start: 0.6430 (m-10) cc_final: 0.5695 (m-80) REVERT: C 423 GLU cc_start: 0.8113 (tp30) cc_final: 0.7585 (tp30) REVERT: C 427 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8354 (mm) REVERT: C 452 TRP cc_start: 0.8359 (m100) cc_final: 0.8057 (m100) outliers start: 24 outliers final: 15 residues processed: 178 average time/residue: 0.7027 time to fit residues: 139.1790 Evaluate side-chains 168 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 297 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 383 LEU 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 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 383 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.138453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.110264 restraints weight = 17210.632| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.38 r_work: 0.3629 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 8742 Z= 0.247 Angle : 0.902 12.989 11932 Z= 0.403 Chirality : 0.046 0.384 1398 Planarity : 0.005 0.049 1410 Dihedral : 10.437 134.718 2106 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.17 % Allowed : 32.68 % Favored : 64.15 % 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: 1.14 (0.27), residues: 1038 helix: 1.80 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -2.64 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 452 HIS 0.002 0.001 HIS A 348 PHE 0.053 0.002 PHE C 550 TYR 0.006 0.001 TYR C 535 ARG 0.004 0.000 ARG A 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5602.20 seconds wall clock time: 98 minutes 1.21 seconds (5881.21 seconds total)