Starting phenix.real_space_refine on Thu Jul 2 17:21:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b70_15894/07_2026/8b70_15894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b70_15894/07_2026/8b70_15894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8b70_15894/07_2026/8b70_15894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b70_15894/07_2026/8b70_15894.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b70_15894/07_2026/8b70_15894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b70_15894/07_2026/8b70_15894.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8b70_15894/07_2026/8b70_15894.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b70_15894/07_2026/8b70_15894.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 34 5.16 5 C 6138 2.51 5 N 1456 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9258 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4444 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 24, 'TRANS': 547} Chain breaks: 2 Chain: "A" Number of atoms: 4444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4444 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 24, 'TRANS': 547} Chain breaks: 2 Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {' K': 1, '2BA': 1, 'LMT': 3} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "A" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 220 Unusual residues: {' K': 1, '2BA': 1, 'LMT': 5} Classifications: {'RNA_mixed': 1, 'undetermined': 6} Link IDs: {None: 6} Time building chain proxies: 1.87, per 1000 atoms: 0.20 Number of scatterers: 9258 At special positions: 0 Unit cell: (112.158, 86.211, 103.788, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 34 16.00 P 4 15.00 O 1624 8.00 N 1456 7.00 C 6138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 290.2 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 1 sheets defined 76.9% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'B' and resid 25 through 34 Processing helix chain 'B' and resid 39 through 42 removed outlier: 3.795A pdb=" N ALA B 42 " --> pdb=" O SER B 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 39 through 42' Processing helix chain 'B' and resid 43 through 54 removed outlier: 3.703A pdb=" N GLN B 47 " --> pdb=" O TYR B 43 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 6.846A pdb=" N ALA B 58 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TRP B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 88 removed outlier: 3.856A pdb=" N TYR B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 103 Processing helix chain 'B' and resid 104 through 137 Processing helix chain 'B' and resid 138 through 142 removed outlier: 4.779A pdb=" N ASP B 142 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 171 through 195 removed outlier: 3.911A pdb=" N TYR B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 232 through 237 removed outlier: 4.709A pdb=" N SER B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 232 through 237' Processing helix chain 'B' and resid 245 through 276 Processing helix chain 'B' and resid 284 through 295 Processing helix chain 'B' and resid 297 through 331 Proline residue: B 323 - end of helix Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 347 through 367 Processing helix chain 'B' and resid 369 through 400 Proline residue: B 375 - end of helix Proline residue: B 384 - end of helix Processing helix chain 'B' and resid 403 through 429 removed outlier: 3.694A pdb=" N LYS B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 462 Proline residue: B 435 - end of helix removed outlier: 3.584A pdb=" N ILE B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 3.576A pdb=" N ARG B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 498 Processing helix chain 'B' and resid 509 through 523 removed outlier: 3.727A pdb=" N GLU B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS B 514 " --> pdb=" O ARG B 510 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS B 515 " --> pdb=" O GLU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 557 removed outlier: 4.026A pdb=" N PHE B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 removed outlier: 4.211A pdb=" N ILE B 577 " --> pdb=" O TRP B 574 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS B 579 " --> pdb=" O THR B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 590 removed outlier: 3.896A pdb=" N PHE B 584 " --> pdb=" O ASN B 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 39 through 42 removed outlier: 3.794A pdb=" N ALA A 42 " --> pdb=" O SER A 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 42' Processing helix chain 'A' and resid 43 through 54 removed outlier: 3.704A pdb=" N GLN A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 removed outlier: 6.845A pdb=" N ALA A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 88 removed outlier: 3.856A pdb=" N TYR A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 104 through 137 Processing helix chain 'A' and resid 138 through 142 removed outlier: 4.779A pdb=" N ASP A 142 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 171 through 195 removed outlier: 3.911A pdb=" N TYR A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.708A pdb=" N SER A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 237' Processing helix chain 'A' and resid 245 through 276 Processing helix chain 'A' and resid 284 through 295 Processing helix chain 'A' and resid 297 through 331 Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 347 through 367 Processing helix chain 'A' and resid 369 through 400 Proline residue: A 375 - end of helix Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 403 through 429 removed outlier: 3.694A pdb=" N LYS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 462 Proline residue: A 435 - end of helix removed outlier: 3.584A pdb=" N ILE A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.576A pdb=" N ARG A 462 " --> pdb=" O GLY A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 498 Processing helix chain 'A' and resid 509 through 523 removed outlier: 3.727A pdb=" N GLU A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS A 514 " --> pdb=" O ARG A 510 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 557 removed outlier: 4.026A pdb=" N PHE A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 4.211A pdb=" N ILE A 577 " --> pdb=" O TRP A 574 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS A 579 " --> pdb=" O THR A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 590 removed outlier: 3.896A pdb=" N PHE A 584 " --> pdb=" O ASN A 580 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 528 through 533 removed outlier: 6.614A pdb=" N ALA B 503 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU B 532 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N HIS B 505 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE B 502 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL B 476 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL B 504 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL B 478 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL B 506 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET B 597 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 598 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 598 " --> pdb=" O THR B 600 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A 597 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE A 502 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A 476 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 504 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL A 478 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL A 506 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 503 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU A 532 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N HIS A 505 " --> pdb=" O LEU A 532 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2685 1.34 - 1.46: 2066 1.46 - 1.57: 4655 1.57 - 1.69: 14 1.69 - 1.81: 62 Bond restraints: 9482 Sorted by residual: bond pdb="C3'1 2BA B 901 " pdb="O3'1 2BA B 901 " ideal model delta sigma weight residual 1.418 1.343 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb="C3'1 2BA A1001 " pdb="O3'1 2BA A1001 " ideal model delta sigma weight residual 1.418 1.344 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5' 2BA A1001 " pdb=" O5' 2BA A1001 " ideal model delta sigma weight residual 1.433 1.362 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C5' 2BA B 901 " pdb=" O5' 2BA B 901 " ideal model delta sigma weight residual 1.433 1.362 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C3' 2BA A1001 " pdb=" O3' 2BA A1001 " ideal model delta sigma weight residual 1.410 1.343 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 9477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 12366 2.00 - 4.00: 310 4.00 - 6.00: 134 6.00 - 8.00: 65 8.00 - 10.00: 15 Bond angle restraints: 12890 Sorted by residual: angle pdb=" C LEU B 373 " pdb=" N ILE B 374 " pdb=" CA ILE B 374 " ideal model delta sigma weight residual 120.24 123.22 -2.98 6.30e-01 2.52e+00 2.24e+01 angle pdb=" C LEU A 373 " pdb=" N ILE A 374 " pdb=" CA ILE A 374 " ideal model delta sigma weight residual 120.24 123.20 -2.96 6.30e-01 2.52e+00 2.20e+01 angle pdb=" N ILE A 438 " pdb=" CA ILE A 438 " pdb=" C ILE A 438 " ideal model delta sigma weight residual 111.81 108.52 3.29 8.60e-01 1.35e+00 1.46e+01 angle pdb=" N ILE B 438 " pdb=" CA ILE B 438 " pdb=" C ILE B 438 " ideal model delta sigma weight residual 111.81 108.55 3.26 8.60e-01 1.35e+00 1.44e+01 angle pdb=" C PHE B 382 " pdb=" N ILE B 383 " pdb=" CA ILE B 383 " ideal model delta sigma weight residual 120.33 117.64 2.69 8.00e-01 1.56e+00 1.13e+01 ... (remaining 12885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4898 17.35 - 34.70: 490 34.70 - 52.05: 128 52.05 - 69.40: 42 69.40 - 86.75: 10 Dihedral angle restraints: 5568 sinusoidal: 2258 harmonic: 3310 Sorted by residual: dihedral pdb=" CA GLU B 233 " pdb=" C GLU B 233 " pdb=" N ALA B 234 " pdb=" CA ALA B 234 " ideal model delta harmonic sigma weight residual -180.00 -161.51 -18.49 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLU A 233 " pdb=" C GLU A 233 " pdb=" N ALA A 234 " pdb=" CA ALA A 234 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN B 244 " pdb=" C ASN B 244 " pdb=" N PRO B 245 " pdb=" CA PRO B 245 " ideal model delta harmonic sigma weight residual 180.00 162.89 17.11 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1324 0.071 - 0.142: 197 0.142 - 0.213: 35 0.213 - 0.284: 24 0.284 - 0.355: 6 Chirality restraints: 1586 Sorted by residual: chirality pdb=" C3' LMT A1004 " pdb=" C2' LMT A1004 " pdb=" C4' LMT A1004 " pdb=" O3' LMT A1004 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" C3' LMT B 904 " pdb=" C2' LMT B 904 " pdb=" C4' LMT B 904 " pdb=" O3' LMT B 904 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C4' LMT A1005 " pdb=" C3' LMT A1005 " pdb=" C5' LMT A1005 " pdb=" O1B LMT A1005 " both_signs ideal model delta sigma weight residual False -2.55 -2.86 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 1583 not shown) Planarity restraints: 1504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 244 " -0.035 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 245 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 244 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO B 245 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 245 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 245 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 153 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.64e+00 pdb=" C LEU A 153 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU A 153 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 154 " -0.009 2.00e-02 2.50e+03 ... (remaining 1501 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.75: 1369 2.75 - 3.34: 11121 3.34 - 3.94: 17894 3.94 - 4.54: 25745 4.54 - 5.14: 37268 Nonbonded interactions: 93397 Sorted by model distance: nonbonded pdb=" O3' LMT A1002 " pdb=" O6' LMT A1005 " model vdw 2.148 3.040 nonbonded pdb=" OH TYR A 81 " pdb=" OE1 GLU A 233 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR B 81 " pdb=" OE1 GLU B 233 " model vdw 2.251 3.040 nonbonded pdb=" O3' LMT A1004 " pdb=" O5B LMT A1004 " model vdw 2.321 3.040 nonbonded pdb=" O3' LMT B 904 " pdb=" O5B LMT B 904 " model vdw 2.321 3.040 ... (remaining 93392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 1004) selection = (chain 'B' and resid 22 through 904) } 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: 0.990 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.920 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 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 : 0.007 0.161 9484 Z= 0.407 Angle : 1.018 10.004 12890 Z= 0.446 Chirality : 0.063 0.355 1586 Planarity : 0.005 0.052 1504 Dihedral : 15.807 86.752 3436 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.84 % Allowed : 0.00 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.27), residues: 1132 helix: 1.91 (0.19), residues: 796 sheet: -1.86 (0.47), residues: 90 loop : -0.70 (0.47), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 331 TYR 0.024 0.001 TYR B 493 PHE 0.008 0.001 PHE A 382 TRP 0.008 0.001 TRP A 592 HIS 0.002 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.33 ( 9482) covalent geometry : angle 1.01823 / 0.45 (12890) hydrogen bonds : bond 0.11881 / 8.10 ( 636) hydrogen bonds : angle 6.19447 / 4.38 ( 1872) Misc. bond : bond 0.16012 / 8.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.199 Fit side-chains REVERT: B 32 MET cc_start: 0.6824 (mtp) cc_final: 0.6581 (mtp) REVERT: B 252 ARG cc_start: 0.5420 (mtt180) cc_final: 0.5097 (mpt-90) REVERT: B 437 LEU cc_start: 0.6776 (mm) cc_final: 0.6523 (mp) REVERT: B 472 LYS cc_start: 0.7690 (mtmt) cc_final: 0.7391 (mttm) REVERT: B 514 LYS cc_start: 0.7550 (mmmt) cc_final: 0.7203 (mmtp) REVERT: B 518 LYS cc_start: 0.6371 (ttpt) cc_final: 0.6056 (tptm) REVERT: A 32 MET cc_start: 0.6736 (mtp) cc_final: 0.6453 (mtp) REVERT: A 243 LYS cc_start: 0.6273 (mmtp) cc_final: 0.5983 (mmmm) REVERT: A 338 MET cc_start: 0.8337 (ptm) cc_final: 0.8004 (ptm) REVERT: A 440 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5909 (mmm) REVERT: A 472 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7372 (mttm) outliers start: 8 outliers final: 1 residues processed: 135 average time/residue: 0.0886 time to fit residues: 16.2959 Evaluate side-chains 92 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 440 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0020 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 GLN B 411 ASN B 580 ASN A 196 GLN A 389 GLN A 580 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.120452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.102675 restraints weight = 10388.177| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.00 r_work: 0.2888 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9484 Z= 0.189 Angle : 0.692 10.715 12890 Z= 0.322 Chirality : 0.046 0.197 1586 Planarity : 0.005 0.048 1504 Dihedral : 10.207 59.944 1429 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.67 % Allowed : 7.83 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.26), residues: 1132 helix: 2.23 (0.18), residues: 792 sheet: -1.62 (0.50), residues: 90 loop : -0.42 (0.45), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 510 TYR 0.023 0.002 TYR A 81 PHE 0.011 0.002 PHE B 516 TRP 0.013 0.002 TRP B 574 HIS 0.004 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 ( 9482) covalent geometry : angle 0.69243 / 0.32 (12890) hydrogen bonds : bond 0.04625 / 3.06 ( 636) hydrogen bonds : angle 4.40754 / 3.12 ( 1872) Misc. bond : bond 0.00088 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.217 Fit side-chains REVERT: B 141 HIS cc_start: 0.7155 (m-70) cc_final: 0.6760 (m-70) REVERT: B 437 LEU cc_start: 0.7947 (mm) cc_final: 0.7682 (mp) REVERT: B 514 LYS cc_start: 0.8594 (mmmt) cc_final: 0.8127 (mmtp) REVERT: B 518 LYS cc_start: 0.7644 (ttpt) cc_final: 0.7222 (tptm) REVERT: B 536 TYR cc_start: 0.8009 (m-80) cc_final: 0.7674 (m-10) REVERT: B 553 LYS cc_start: 0.7850 (ttmt) cc_final: 0.6752 (tttt) REVERT: A 437 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8182 (mm) outliers start: 16 outliers final: 7 residues processed: 110 average time/residue: 0.0805 time to fit residues: 12.4413 Evaluate side-chains 96 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 113 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 144 HIS B 196 GLN B 580 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.123870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.101706 restraints weight = 10262.947| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.26 r_work: 0.2889 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9484 Z= 0.125 Angle : 0.577 8.061 12890 Z= 0.270 Chirality : 0.042 0.201 1586 Planarity : 0.004 0.040 1504 Dihedral : 9.364 57.778 1424 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.15 % Allowed : 11.06 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.26), residues: 1132 helix: 2.46 (0.18), residues: 792 sheet: -1.41 (0.49), residues: 90 loop : -0.32 (0.47), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 510 TYR 0.015 0.001 TYR B 81 PHE 0.012 0.001 PHE B 322 TRP 0.013 0.001 TRP B 574 HIS 0.002 0.000 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9482) covalent geometry : angle 0.57699 / 0.27 (12890) hydrogen bonds : bond 0.04097 / 2.69 ( 636) hydrogen bonds : angle 4.12776 / 2.91 ( 1872) Misc. bond : bond 0.00095 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.207 Fit side-chains REVERT: B 32 MET cc_start: 0.7931 (mtp) cc_final: 0.7680 (mtp) REVERT: B 215 LEU cc_start: 0.7602 (tp) cc_final: 0.7330 (tp) REVERT: B 437 LEU cc_start: 0.8029 (mm) cc_final: 0.7598 (mp) REVERT: B 514 LYS cc_start: 0.8397 (mmmt) cc_final: 0.7920 (mmtp) REVERT: B 518 LYS cc_start: 0.7309 (ttpt) cc_final: 0.6863 (tptm) REVERT: B 536 TYR cc_start: 0.7914 (m-80) cc_final: 0.7534 (m-80) REVERT: A 392 MET cc_start: 0.8342 (tpt) cc_final: 0.8079 (mmm) REVERT: A 437 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7968 (mm) outliers start: 11 outliers final: 4 residues processed: 99 average time/residue: 0.0716 time to fit residues: 10.2641 Evaluate side-chains 90 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 437 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 324 GLN B 389 GLN A 558 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.123670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.100530 restraints weight = 10325.511| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.35 r_work: 0.2888 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9484 Z= 0.124 Angle : 0.567 7.688 12890 Z= 0.265 Chirality : 0.042 0.209 1586 Planarity : 0.004 0.045 1504 Dihedral : 9.281 57.561 1424 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.46 % Allowed : 11.69 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.26), residues: 1132 helix: 2.44 (0.18), residues: 796 sheet: -1.23 (0.49), residues: 90 loop : -0.24 (0.47), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 510 TYR 0.015 0.001 TYR A 81 PHE 0.008 0.001 PHE B 319 TRP 0.015 0.001 TRP B 574 HIS 0.002 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9482) covalent geometry : angle 0.56693 / 0.27 (12890) hydrogen bonds : bond 0.03939 / 2.59 ( 636) hydrogen bonds : angle 4.01466 / 2.83 ( 1872) Misc. bond : bond 0.00102 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.196 Fit side-chains REVERT: B 141 HIS cc_start: 0.7234 (m-70) cc_final: 0.6750 (m-70) REVERT: B 437 LEU cc_start: 0.8110 (mm) cc_final: 0.7798 (mp) REVERT: B 514 LYS cc_start: 0.8437 (mmmt) cc_final: 0.8169 (mmmt) REVERT: B 518 LYS cc_start: 0.7358 (ttpt) cc_final: 0.6886 (tptm) REVERT: B 536 TYR cc_start: 0.7980 (m-80) cc_final: 0.7570 (m-80) REVERT: A 32 MET cc_start: 0.7942 (mtp) cc_final: 0.7671 (mtp) REVERT: A 392 MET cc_start: 0.8423 (tpt) cc_final: 0.8151 (mmm) REVERT: A 437 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8084 (mm) REVERT: A 459 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7302 (mt-10) REVERT: A 514 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8106 (mmmt) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.0731 time to fit residues: 10.2393 Evaluate side-chains 95 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 100 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 389 GLN A 324 GLN A 558 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.100316 restraints weight = 10233.843| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.30 r_work: 0.2869 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9484 Z= 0.125 Angle : 0.561 7.441 12890 Z= 0.262 Chirality : 0.042 0.209 1586 Planarity : 0.004 0.048 1504 Dihedral : 9.038 58.095 1424 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.88 % Allowed : 12.63 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.26), residues: 1132 helix: 2.37 (0.18), residues: 804 sheet: -0.86 (0.51), residues: 92 loop : -0.41 (0.47), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 510 TYR 0.015 0.001 TYR A 81 PHE 0.007 0.001 PHE A 319 TRP 0.017 0.001 TRP B 574 HIS 0.001 0.000 HIS B 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 9482) covalent geometry : angle 0.56149 / 0.26 (12890) hydrogen bonds : bond 0.03880 / 2.55 ( 636) hydrogen bonds : angle 3.96290 / 2.79 ( 1872) Misc. bond : bond 0.00088 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.225 Fit side-chains REVERT: B 32 MET cc_start: 0.7923 (mtp) cc_final: 0.7635 (mtp) REVERT: B 215 LEU cc_start: 0.7688 (tp) cc_final: 0.7261 (tt) REVERT: B 355 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8037 (tp) REVERT: B 514 LYS cc_start: 0.8426 (mmmt) cc_final: 0.7913 (mmtm) REVERT: B 518 LYS cc_start: 0.7304 (ttpt) cc_final: 0.6848 (tptm) REVERT: B 536 TYR cc_start: 0.8039 (m-80) cc_final: 0.7629 (m-80) REVERT: A 32 MET cc_start: 0.7933 (mtp) cc_final: 0.7674 (mtp) REVERT: A 437 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8156 (mm) REVERT: A 459 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7164 (mt-10) REVERT: A 514 LYS cc_start: 0.8382 (mmmt) cc_final: 0.8111 (mmmt) outliers start: 18 outliers final: 10 residues processed: 99 average time/residue: 0.0738 time to fit residues: 10.5796 Evaluate side-chains 96 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.125029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.102931 restraints weight = 10304.324| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.27 r_work: 0.2907 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9484 Z= 0.110 Angle : 0.540 7.372 12890 Z= 0.252 Chirality : 0.041 0.204 1586 Planarity : 0.004 0.046 1504 Dihedral : 8.825 58.827 1424 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.67 % Allowed : 13.26 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.26), residues: 1132 helix: 2.60 (0.18), residues: 792 sheet: -0.64 (0.52), residues: 92 loop : -0.49 (0.45), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 510 TYR 0.013 0.001 TYR A 81 PHE 0.006 0.001 PHE B 366 TRP 0.016 0.001 TRP B 574 HIS 0.001 0.000 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 9482) covalent geometry : angle 0.54000 / 0.25 (12890) hydrogen bonds : bond 0.03656 / 2.41 ( 636) hydrogen bonds : angle 3.87420 / 2.72 ( 1872) Misc. bond : bond 0.00062 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.223 Fit side-chains REVERT: B 215 LEU cc_start: 0.7737 (tp) cc_final: 0.7501 (tp) REVERT: B 486 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8127 (m) REVERT: B 514 LYS cc_start: 0.8378 (mmmt) cc_final: 0.7866 (mmtm) REVERT: B 518 LYS cc_start: 0.7242 (ttpt) cc_final: 0.6780 (tptm) REVERT: B 536 TYR cc_start: 0.7999 (m-80) cc_final: 0.7561 (m-80) REVERT: A 392 MET cc_start: 0.8295 (tpt) cc_final: 0.8032 (mmm) REVERT: A 437 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8137 (mm) REVERT: A 514 LYS cc_start: 0.8324 (mmmt) cc_final: 0.8044 (mmmt) outliers start: 16 outliers final: 11 residues processed: 97 average time/residue: 0.0780 time to fit residues: 10.8928 Evaluate side-chains 99 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 101 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 0.0050 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 141 HIS B 144 HIS A 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.124481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.102519 restraints weight = 10258.443| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.25 r_work: 0.2904 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9484 Z= 0.114 Angle : 0.544 7.341 12890 Z= 0.254 Chirality : 0.041 0.203 1586 Planarity : 0.004 0.046 1504 Dihedral : 8.767 58.134 1424 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.09 % Allowed : 13.15 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.26), residues: 1132 helix: 2.51 (0.18), residues: 804 sheet: -0.54 (0.52), residues: 92 loop : -0.42 (0.46), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 510 TYR 0.013 0.001 TYR A 81 PHE 0.006 0.001 PHE B 319 TRP 0.014 0.001 TRP B 574 HIS 0.003 0.000 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9482) covalent geometry : angle 0.54386 / 0.25 (12890) hydrogen bonds : bond 0.03685 / 2.43 ( 636) hydrogen bonds : angle 3.86222 / 2.71 ( 1872) Misc. bond : bond 0.00069 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.335 Fit side-chains REVERT: B 486 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8223 (m) REVERT: B 518 LYS cc_start: 0.7290 (ttpt) cc_final: 0.6819 (tptm) REVERT: A 355 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7890 (tp) REVERT: A 437 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8175 (mm) REVERT: A 486 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8199 (m) REVERT: A 514 LYS cc_start: 0.8341 (mmmt) cc_final: 0.8052 (mmmt) outliers start: 20 outliers final: 14 residues processed: 98 average time/residue: 0.0905 time to fit residues: 12.8962 Evaluate side-chains 104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 550 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 141 HIS A 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.122944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.100850 restraints weight = 10235.044| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.26 r_work: 0.2880 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9484 Z= 0.126 Angle : 0.565 7.673 12890 Z= 0.263 Chirality : 0.042 0.222 1586 Planarity : 0.004 0.046 1504 Dihedral : 8.846 59.667 1424 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.40 % Allowed : 13.36 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.26), residues: 1132 helix: 2.45 (0.18), residues: 804 sheet: -0.55 (0.52), residues: 92 loop : -0.48 (0.45), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 510 TYR 0.014 0.001 TYR A 81 PHE 0.007 0.001 PHE B 605 TRP 0.014 0.001 TRP B 574 HIS 0.002 0.000 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9482) covalent geometry : angle 0.56507 / 0.26 (12890) hydrogen bonds : bond 0.03853 / 2.54 ( 636) hydrogen bonds : angle 3.91639 / 2.75 ( 1872) Misc. bond : bond 0.00087 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.275 Fit side-chains REVERT: B 215 LEU cc_start: 0.7684 (tp) cc_final: 0.7304 (tt) REVERT: B 355 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7931 (tp) REVERT: B 486 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8189 (m) REVERT: B 518 LYS cc_start: 0.7249 (ttpt) cc_final: 0.6774 (tptm) REVERT: A 32 MET cc_start: 0.7898 (mtp) cc_final: 0.7609 (mtp) REVERT: A 355 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7874 (tp) REVERT: A 392 MET cc_start: 0.8334 (tpt) cc_final: 0.8074 (mmm) REVERT: A 437 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8171 (mm) REVERT: A 486 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8188 (m) outliers start: 23 outliers final: 17 residues processed: 99 average time/residue: 0.0848 time to fit residues: 12.1837 Evaluate side-chains 105 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 562 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 19 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 141 HIS B 144 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.124150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.102131 restraints weight = 10234.808| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.26 r_work: 0.2900 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9484 Z= 0.116 Angle : 0.548 7.357 12890 Z= 0.254 Chirality : 0.041 0.212 1586 Planarity : 0.004 0.046 1504 Dihedral : 8.704 57.524 1424 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.40 % Allowed : 13.88 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.26), residues: 1132 helix: 2.50 (0.18), residues: 808 sheet: -0.45 (0.53), residues: 92 loop : -0.31 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 510 TYR 0.013 0.001 TYR A 81 PHE 0.006 0.001 PHE B 605 TRP 0.014 0.001 TRP B 574 HIS 0.003 0.000 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9482) covalent geometry : angle 0.54826 / 0.25 (12890) hydrogen bonds : bond 0.03716 / 2.45 ( 636) hydrogen bonds : angle 3.85883 / 2.71 ( 1872) Misc. bond : bond 0.00073 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.357 Fit side-chains REVERT: B 355 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7905 (tp) REVERT: B 486 VAL cc_start: 0.8478 (OUTLIER) cc_final: 0.8209 (m) REVERT: B 512 GLN cc_start: 0.7757 (mp10) cc_final: 0.7190 (mt0) REVERT: B 518 LYS cc_start: 0.7249 (ttpt) cc_final: 0.6762 (tptm) REVERT: B 553 LYS cc_start: 0.7642 (ttmt) cc_final: 0.6431 (tttt) REVERT: A 32 MET cc_start: 0.7906 (mtp) cc_final: 0.7615 (mtp) REVERT: A 355 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7855 (tp) REVERT: A 392 MET cc_start: 0.8335 (tpt) cc_final: 0.8074 (mmm) REVERT: A 437 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8204 (mm) REVERT: A 486 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8249 (m) outliers start: 23 outliers final: 15 residues processed: 102 average time/residue: 0.0770 time to fit residues: 11.3422 Evaluate side-chains 104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 141 HIS B 144 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.124070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.101554 restraints weight = 10189.639| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.30 r_work: 0.2890 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9484 Z= 0.120 Angle : 0.554 7.405 12890 Z= 0.257 Chirality : 0.041 0.212 1586 Planarity : 0.004 0.047 1504 Dihedral : 8.787 57.986 1424 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.30 % Allowed : 13.99 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.26), residues: 1132 helix: 2.49 (0.18), residues: 808 sheet: -0.43 (0.53), residues: 92 loop : -0.31 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 510 TYR 0.013 0.001 TYR A 81 PHE 0.010 0.001 PHE B 366 TRP 0.021 0.001 TRP B 574 HIS 0.003 0.000 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9482) covalent geometry : angle 0.55381 / 0.26 (12890) hydrogen bonds : bond 0.03750 / 2.47 ( 636) hydrogen bonds : angle 3.85825 / 2.71 ( 1872) Misc. bond : bond 0.00085 / 0.04 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.314 Fit side-chains REVERT: B 215 LEU cc_start: 0.7660 (tp) cc_final: 0.7272 (tt) REVERT: B 355 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7949 (tp) REVERT: B 486 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8260 (m) REVERT: B 518 LYS cc_start: 0.7268 (ttpt) cc_final: 0.6778 (tptm) REVERT: B 553 LYS cc_start: 0.7695 (ttmt) cc_final: 0.6487 (tttt) REVERT: A 32 MET cc_start: 0.7929 (mtp) cc_final: 0.7646 (mtp) REVERT: A 355 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7923 (tp) REVERT: A 392 MET cc_start: 0.8374 (tpt) cc_final: 0.8110 (mmm) REVERT: A 437 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8204 (mm) REVERT: A 486 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8293 (m) outliers start: 22 outliers final: 16 residues processed: 99 average time/residue: 0.0912 time to fit residues: 13.2644 Evaluate side-chains 104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 84 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 34 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 69 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 141 HIS B 144 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.125956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.103573 restraints weight = 10140.799| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.29 r_work: 0.2919 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9484 Z= 0.107 Angle : 0.541 7.585 12890 Z= 0.251 Chirality : 0.041 0.202 1586 Planarity : 0.004 0.048 1504 Dihedral : 8.683 58.809 1424 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.77 % Allowed : 14.51 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.26), residues: 1132 helix: 2.56 (0.18), residues: 808 sheet: -0.35 (0.54), residues: 92 loop : -0.29 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 510 TYR 0.012 0.001 TYR A 81 PHE 0.009 0.001 PHE B 366 TRP 0.021 0.001 TRP B 574 HIS 0.005 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 9482) covalent geometry : angle 0.54135 / 0.25 (12890) hydrogen bonds : bond 0.03597 / 2.37 ( 636) hydrogen bonds : angle 3.80548 / 2.67 ( 1872) Misc. bond : bond 0.00074 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1796.69 seconds wall clock time: 31 minutes 40.57 seconds (1900.57 seconds total)