Starting phenix.real_space_refine on Sat Aug 23 03:32:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b70_15894/08_2025/8b70_15894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b70_15894/08_2025/8b70_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_15894/08_2025/8b70_15894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b70_15894/08_2025/8b70_15894.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b70_15894/08_2025/8b70_15894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b70_15894/08_2025/8b70_15894.map" } 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9258 Number of models: 1 Model: "" Number of chains: 3 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} 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} Restraints were copied for chains: B Time building chain proxies: 3.97, per 1000 atoms: 0.43 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: 0.97 Conformation dependent library (CDL) restraints added in 460.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.32 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: 1.74 Time building geometry restraints manager: 1.18 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 - 26.25: 5478 26.25 - 52.50: 351 52.50 - 78.75: 93 78.75 - 105.00: 16 105.00 - 131.25: 30 Dihedral angle restraints: 5968 sinusoidal: 2658 harmonic: 3310 Sorted by residual: dihedral pdb=" C1B LMT B 904 " pdb=" C5B LMT B 904 " pdb=" O5B LMT B 904 " pdb=" C6B LMT B 904 " ideal model delta sinusoidal sigma weight residual 175.31 -53.44 -131.25 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C1B LMT A1004 " pdb=" C5B LMT A1004 " pdb=" O5B LMT A1004 " pdb=" C6B LMT A1004 " ideal model delta sinusoidal sigma weight residual 175.31 -53.48 -131.21 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C1B LMT B 904 " pdb=" C5B LMT B 904 " pdb=" O5B LMT B 904 " pdb=" C4B LMT B 904 " ideal model delta sinusoidal sigma weight residual -59.84 67.26 -127.10 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 5965 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 12.410 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 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 : 20.776 131.249 3836 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 aren 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 covalent geometry : bond 0.00706 ( 9482) covalent geometry : angle 1.01823 (12890) hydrogen bonds : bond 0.11881 ( 636) hydrogen bonds : angle 6.19447 ( 1872) Misc. bond : bond 0.16012 ( 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 : 0.338 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: 0.5098 (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: 0.1178 time to fit residues: 21.5794 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 : 0.361 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3267 r_free = 0.3267 target = 0.120616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.103059 restraints weight = 10397.726| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 0.97 r_work: 0.2886 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9484 Z= 0.192 Angle : 0.764 11.640 12890 Z= 0.340 Chirality : 0.048 0.254 1586 Planarity : 0.005 0.049 1504 Dihedral : 14.861 83.572 1829 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.67 % Allowed : 7.93 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.26), residues: 1132 helix: 2.22 (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 0.012 0.002 TRP B 574 HIS 0.003 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 9482) covalent geometry : angle 0.76374 (12890) hydrogen bonds : bond 0.04631 ( 636) hydrogen bonds : angle 4.40573 ( 1872) Misc. bond : bond 0.00061 ( 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 116 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.369 Fit side-chains REVERT: B 141 HIS cc_start: 0.7156 (m-70) cc_final: 0.6764 (m-70) REVERT: B 437 LEU cc_start: 0.7954 (mm) cc_final: 0.7698 (mp) REVERT: B 514 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8127 (mmtp) REVERT: B 518 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7236 (tptm) REVERT: B 536 TYR cc_start: 0.8017 (m-80) cc_final: 0.7683 (m-80) REVERT: B 553 LYS cc_start: 0.7857 (ttmt) cc_final: 0.6762 (tttt) REVERT: A 437 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8188 (mm) outliers start: 16 outliers final: 7 residues processed: 110 average time/residue: 0.1064 time to fit residues: 16.3966 Evaluate side-chains 92 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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: 0.9980 chunk 95 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 0.0570 chunk 38 optimal weight: 1.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3282 r_free = 0.3282 target = 0.122201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.098580 restraints weight = 10343.400| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.36 r_work: 0.2838 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9484 Z= 0.146 Angle : 0.605 8.848 12890 Z= 0.282 Chirality : 0.043 0.298 1586 Planarity : 0.004 0.041 1504 Dihedral : 11.290 59.187 1824 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.46 % Allowed : 11.27 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.26), residues: 1132 helix: 2.45 (0.18), residues: 788 sheet: -1.46 (0.49), residues: 90 loop : -0.34 (0.46), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 510 TYR 0.016 0.001 TYR B 81 PHE 0.012 0.001 PHE B 605 TRP 0.013 0.001 TRP B 574 HIS 0.003 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9482) covalent geometry : angle 0.60546 (12890) hydrogen bonds : bond 0.04275 ( 636) hydrogen bonds : angle 4.17491 ( 1872) Misc. bond : bond 0.00103 ( 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 108 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.339 Fit side-chains REVERT: B 32 MET cc_start: 0.7962 (mtp) cc_final: 0.7708 (mtp) REVERT: B 153 LEU cc_start: 0.8376 (mt) cc_final: 0.8116 (mt) REVERT: B 215 LEU cc_start: 0.7696 (tp) cc_final: 0.7399 (tp) REVERT: B 437 LEU cc_start: 0.8158 (mm) cc_final: 0.7820 (mp) REVERT: B 514 LYS cc_start: 0.8405 (mmmt) cc_final: 0.7908 (mmtp) REVERT: B 518 LYS cc_start: 0.7378 (ttpt) cc_final: 0.6925 (tptm) REVERT: B 536 TYR cc_start: 0.7949 (m-80) cc_final: 0.7599 (m-80) REVERT: B 553 LYS cc_start: 0.7635 (ttmt) cc_final: 0.6505 (tttt) REVERT: A 32 MET cc_start: 0.7962 (mtp) cc_final: 0.7688 (mtp) REVERT: A 392 MET cc_start: 0.8445 (tpt) cc_final: 0.8182 (mmm) REVERT: A 437 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8068 (mm) outliers start: 14 outliers final: 8 residues processed: 101 average time/residue: 0.1015 time to fit residues: 14.5930 Evaluate side-chains 100 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 232 VAL 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: 0.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 0.0770 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN B 324 GLN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.122468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.098937 restraints weight = 10361.266| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.36 r_work: 0.2845 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9484 Z= 0.130 Angle : 0.579 8.606 12890 Z= 0.270 Chirality : 0.042 0.225 1586 Planarity : 0.004 0.044 1504 Dihedral : 10.696 59.842 1824 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.36 % Allowed : 12.73 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.26), residues: 1132 helix: 2.42 (0.18), residues: 792 sheet: -1.24 (0.49), residues: 90 loop : -0.40 (0.46), residues: 250 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 0.010 0.001 PHE B 605 TRP 0.014 0.001 TRP B 574 HIS 0.002 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9482) covalent geometry : angle 0.57863 (12890) hydrogen bonds : bond 0.03999 ( 636) hydrogen bonds : angle 4.06320 ( 1872) Misc. bond : bond 0.00098 ( 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 108 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.349 Fit side-chains REVERT: B 514 LYS cc_start: 0.8408 (mmmt) cc_final: 0.8132 (mmmt) REVERT: B 518 LYS cc_start: 0.7404 (ttpt) cc_final: 0.6941 (tptm) REVERT: B 536 TYR cc_start: 0.8038 (m-80) cc_final: 0.7647 (m-80) REVERT: A 32 MET cc_start: 0.7932 (mtp) cc_final: 0.7694 (mtp) REVERT: A 215 LEU cc_start: 0.7830 (tp) cc_final: 0.7617 (tp) REVERT: A 392 MET cc_start: 0.8434 (tpt) cc_final: 0.8145 (mmm) REVERT: A 437 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8169 (mm) REVERT: A 514 LYS cc_start: 0.8372 (mmmt) cc_final: 0.8084 (mmmt) outliers start: 13 outliers final: 10 residues processed: 100 average time/residue: 0.0984 time to fit residues: 14.0995 Evaluate side-chains 97 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE 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 232 VAL 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: 0.0670 chunk 1 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 GLN A 324 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.123808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.100916 restraints weight = 10191.612| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.31 r_work: 0.2873 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9484 Z= 0.118 Angle : 0.555 7.118 12890 Z= 0.260 Chirality : 0.041 0.208 1586 Planarity : 0.004 0.047 1504 Dihedral : 10.447 58.918 1824 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.09 % Allowed : 12.84 % 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 aren not related in a simple way. whole: 2.32 (0.26), residues: 1132 helix: 2.38 (0.18), residues: 804 sheet: -0.84 (0.51), residues: 92 loop : -0.42 (0.47), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 510 TYR 0.014 0.001 TYR A 81 PHE 0.011 0.001 PHE B 366 TRP 0.013 0.001 TRP B 574 HIS 0.002 0.000 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9482) covalent geometry : angle 0.55516 (12890) hydrogen bonds : bond 0.03840 ( 636) hydrogen bonds : angle 3.95358 ( 1872) Misc. bond : bond 0.00118 ( 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 111 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.424 Fit side-chains REVERT: B 32 MET cc_start: 0.7910 (mtp) cc_final: 0.7646 (mtp) REVERT: B 153 LEU cc_start: 0.8318 (mt) cc_final: 0.8085 (mt) REVERT: B 215 LEU cc_start: 0.7695 (tp) cc_final: 0.7279 (tt) REVERT: B 355 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8028 (tp) REVERT: B 460 GLN cc_start: 0.8072 (tt0) cc_final: 0.7819 (tt0) REVERT: B 514 LYS cc_start: 0.8385 (mmmt) cc_final: 0.8114 (mmmt) REVERT: B 518 LYS cc_start: 0.7316 (ttpt) cc_final: 0.6860 (tptm) REVERT: B 536 TYR cc_start: 0.8041 (m-80) cc_final: 0.7600 (m-80) REVERT: A 392 MET cc_start: 0.8380 (tpt) cc_final: 0.8088 (mmm) REVERT: A 437 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8139 (mm) REVERT: A 514 LYS cc_start: 0.8364 (mmmt) cc_final: 0.8093 (mmmt) outliers start: 20 outliers final: 12 residues processed: 104 average time/residue: 0.0996 time to fit residues: 14.8501 Evaluate side-chains 104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 355 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 232 VAL 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 Chi-restraints excluded: chain A residue 550 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0000 chunk 83 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN A 196 GLN A 460 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.124146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.101753 restraints weight = 10302.129| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.27 r_work: 0.2892 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9484 Z= 0.116 Angle : 0.548 6.866 12890 Z= 0.257 Chirality : 0.040 0.192 1586 Planarity : 0.004 0.046 1504 Dihedral : 10.194 59.925 1824 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.30 % Allowed : 12.84 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.26), residues: 1132 helix: 2.53 (0.18), residues: 792 sheet: -0.69 (0.52), residues: 92 loop : -0.50 (0.45), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 510 TYR 0.014 0.001 TYR A 81 PHE 0.007 0.001 PHE B 366 TRP 0.018 0.001 TRP B 574 HIS 0.002 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9482) covalent geometry : angle 0.54800 (12890) hydrogen bonds : bond 0.03756 ( 636) hydrogen bonds : angle 3.91044 ( 1872) Misc. bond : bond 0.00121 ( 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 110 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.341 Fit side-chains REVERT: B 32 MET cc_start: 0.7890 (mtp) cc_final: 0.7614 (mtp) REVERT: B 355 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7941 (tp) REVERT: B 486 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8162 (m) REVERT: B 518 LYS cc_start: 0.7246 (ttpt) cc_final: 0.6787 (tptm) REVERT: A 32 MET cc_start: 0.7919 (mtp) cc_final: 0.7591 (mtp) REVERT: A 355 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7853 (tp) REVERT: A 392 MET cc_start: 0.8311 (tpt) cc_final: 0.7998 (mmm) REVERT: A 437 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8117 (mm) REVERT: A 486 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8134 (m) REVERT: A 514 LYS cc_start: 0.8318 (mmmt) cc_final: 0.8035 (mmmt) outliers start: 22 outliers final: 14 residues processed: 104 average time/residue: 0.0959 time to fit residues: 14.4350 Evaluate side-chains 105 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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 232 VAL 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 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: 0.9990 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 49 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS B 144 HIS B 196 GLN B 324 GLN A 460 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.123918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.101530 restraints weight = 10265.809| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.27 r_work: 0.2884 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9484 Z= 0.119 Angle : 0.554 6.946 12890 Z= 0.258 Chirality : 0.041 0.201 1586 Planarity : 0.004 0.046 1504 Dihedral : 10.139 58.392 1824 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.51 % Allowed : 13.67 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.26), residues: 1132 helix: 2.42 (0.18), residues: 804 sheet: -0.63 (0.52), residues: 92 loop : -0.40 (0.47), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 510 TYR 0.013 0.001 TYR A 81 PHE 0.009 0.001 PHE A 605 TRP 0.014 0.001 TRP B 574 HIS 0.003 0.000 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9482) covalent geometry : angle 0.55393 (12890) hydrogen bonds : bond 0.03760 ( 636) hydrogen bonds : angle 3.89959 ( 1872) Misc. bond : bond 0.00122 ( 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 113 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.369 Fit side-chains REVERT: B 215 LEU cc_start: 0.7679 (tp) cc_final: 0.7297 (tt) REVERT: B 355 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7994 (tp) REVERT: B 486 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8235 (m) REVERT: B 518 LYS cc_start: 0.7285 (ttpt) cc_final: 0.6818 (tptm) REVERT: A 32 MET cc_start: 0.7916 (mtp) cc_final: 0.7622 (mtp) REVERT: A 355 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7896 (tp) REVERT: A 437 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8177 (mm) REVERT: A 486 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8198 (m) REVERT: A 514 LYS cc_start: 0.8311 (mmmt) cc_final: 0.8026 (mmmt) outliers start: 24 outliers final: 17 residues processed: 107 average time/residue: 0.0957 time to fit residues: 14.7937 Evaluate side-chains 110 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 232 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=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: 0.9990 chunk 65 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS B 144 HIS B 196 GLN A 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.123453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.101098 restraints weight = 10238.598| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.26 r_work: 0.2885 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9484 Z= 0.124 Angle : 0.561 6.967 12890 Z= 0.261 Chirality : 0.041 0.233 1586 Planarity : 0.004 0.047 1504 Dihedral : 10.135 59.952 1824 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.71 % Allowed : 13.78 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.26), residues: 1132 helix: 2.39 (0.18), residues: 808 sheet: -0.60 (0.52), residues: 92 loop : -0.27 (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 0.008 0.001 PHE A 605 TRP 0.018 0.001 TRP B 574 HIS 0.003 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9482) covalent geometry : angle 0.56076 (12890) hydrogen bonds : bond 0.03809 ( 636) hydrogen bonds : angle 3.90567 ( 1872) Misc. bond : bond 0.00123 ( 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 116 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.365 Fit side-chains REVERT: B 215 LEU cc_start: 0.7646 (tp) cc_final: 0.7389 (tp) REVERT: B 355 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7937 (tp) REVERT: B 486 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8203 (m) REVERT: B 518 LYS cc_start: 0.7246 (ttpt) cc_final: 0.6775 (tptm) REVERT: A 32 MET cc_start: 0.7886 (mtp) cc_final: 0.7602 (mtp) REVERT: A 355 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7853 (tp) REVERT: A 437 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8160 (mm) REVERT: A 486 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8159 (m) REVERT: A 514 LYS cc_start: 0.8283 (mmmt) cc_final: 0.8004 (mmmt) outliers start: 26 outliers final: 17 residues processed: 110 average time/residue: 0.0958 time to fit residues: 15.3952 Evaluate side-chains 109 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 232 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 316 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 19 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 104 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3310 r_free = 0.3310 target = 0.124486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.102180 restraints weight = 10212.349| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.26 r_work: 0.2898 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3102 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= 0.117 Angle : 0.555 6.983 12890 Z= 0.259 Chirality : 0.040 0.209 1586 Planarity : 0.004 0.047 1504 Dihedral : 10.014 59.137 1824 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.51 % Allowed : 13.99 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.26), residues: 1132 helix: 2.45 (0.18), residues: 808 sheet: -0.55 (0.52), residues: 92 loop : -0.27 (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 0.008 0.001 PHE A 605 TRP 0.019 0.001 TRP B 574 HIS 0.003 0.000 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9482) covalent geometry : angle 0.55486 (12890) hydrogen bonds : bond 0.03740 ( 636) hydrogen bonds : angle 3.88387 ( 1872) Misc. bond : bond 0.00117 ( 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: 24 poor density : 85 time to evaluate : 0.350 Fit side-chains REVERT: B 215 LEU cc_start: 0.7625 (tp) cc_final: 0.7387 (tp) REVERT: B 355 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7892 (tp) REVERT: B 486 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8174 (m) REVERT: B 512 GLN cc_start: 0.7711 (mp10) cc_final: 0.7138 (mt0) REVERT: B 518 LYS cc_start: 0.7235 (ttpt) cc_final: 0.6760 (tptm) REVERT: A 32 MET cc_start: 0.7890 (mtp) cc_final: 0.7606 (mtp) REVERT: A 355 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7811 (tp) REVERT: A 392 MET cc_start: 0.8292 (tpt) cc_final: 0.8052 (mmm) REVERT: A 437 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8168 (mm) REVERT: A 486 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8203 (m) outliers start: 24 outliers final: 17 residues processed: 102 average time/residue: 0.0956 time to fit residues: 14.1197 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 : 0.348 ------------------------------------------------------------------------------- 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 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 232 VAL Chi-restraints excluded: chain A residue 316 ASN 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=1.00 ------------------------------------------------------------------------------- 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: 2.9990 chunk 43 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 19 optimal weight: 0.1980 chunk 101 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.121123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.097771 restraints weight = 10252.431| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.35 r_work: 0.2830 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9484 Z= 0.150 Angle : 0.596 7.376 12890 Z= 0.279 Chirality : 0.042 0.246 1586 Planarity : 0.004 0.046 1504 Dihedral : 10.304 57.461 1824 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.51 % Allowed : 14.09 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.26), residues: 1132 helix: 2.30 (0.18), residues: 808 sheet: -0.64 (0.52), residues: 92 loop : -0.36 (0.46), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 510 TYR 0.014 0.001 TYR B 81 PHE 0.010 0.001 PHE B 605 TRP 0.015 0.001 TRP B 574 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9482) covalent geometry : angle 0.59569 (12890) hydrogen bonds : bond 0.04112 ( 636) hydrogen bonds : angle 4.00915 ( 1872) Misc. bond : bond 0.00167 ( 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 110 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.344 Fit side-chains REVERT: B 215 LEU cc_start: 0.7714 (tp) cc_final: 0.7498 (tp) REVERT: B 512 GLN cc_start: 0.7773 (mp10) cc_final: 0.7209 (mt0) REVERT: B 518 LYS cc_start: 0.7285 (ttpt) cc_final: 0.6803 (tptm) REVERT: B 553 LYS cc_start: 0.7701 (ttmt) cc_final: 0.6487 (ttpp) REVERT: A 32 MET cc_start: 0.7922 (mtp) cc_final: 0.7654 (mtp) REVERT: A 355 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7982 (tp) REVERT: A 437 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8207 (mm) outliers start: 24 outliers final: 18 residues processed: 104 average time/residue: 0.0968 time to fit residues: 14.5442 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 : 0.358 ------------------------------------------------------------------------------- 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 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 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 232 VAL Chi-restraints excluded: chain A residue 316 ASN 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 550 VAL Chi-restraints excluded: chain A residue 562 MET 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: 0.4980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.122811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.099908 restraints weight = 10212.796| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.31 r_work: 0.2864 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9484 Z= 0.128 Angle : 0.570 7.191 12890 Z= 0.267 Chirality : 0.041 0.218 1586 Planarity : 0.004 0.047 1504 Dihedral : 10.198 58.762 1824 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.98 % Allowed : 14.41 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.26), residues: 1132 helix: 2.37 (0.18), residues: 808 sheet: -0.60 (0.52), residues: 92 loop : -0.33 (0.46), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 510 TYR 0.014 0.001 TYR A 81 PHE 0.009 0.001 PHE B 605 TRP 0.017 0.001 TRP B 574 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9482) covalent geometry : angle 0.57042 (12890) hydrogen bonds : bond 0.03926 ( 636) hydrogen bonds : angle 3.95530 ( 1872) Misc. bond : bond 0.00138 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2194.76 seconds wall clock time: 38 minutes 40.26 seconds (2320.26 seconds total)