Starting phenix.real_space_refine on Fri Mar 14 01:54:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b70_15894/03_2025/8b70_15894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b70_15894/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8b70_15894/03_2025/8b70_15894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b70_15894/03_2025/8b70_15894.map" model { file = "/net/cci-nas-00/data/ceres_data/8b70_15894/03_2025/8b70_15894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b70_15894/03_2025/8b70_15894.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'LMT': 5} Classifications: {'RNA': 1, 'undetermined': 6} Link IDs: {None: 6} Restraints were copied for chains: B Time building chain proxies: 9.07, per 1000 atoms: 0.98 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: 2.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.94 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: 2.48 Time building geometry restraints manager: 3.05 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 606 or resid 1001 through 1004)) selection = (chain 'B' and (resid 22 through 606 or resid 901 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: 0.980 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 27.040 Find NCS groups from input model: 0.390 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.690 ------------------------------------------------------------------------------- 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 0.075 9482 Z= 0.455 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (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 TRP 0.008 0.001 TRP A 592 HIS 0.002 0.001 HIS B 505 PHE 0.008 0.001 PHE A 382 TYR 0.024 0.001 TYR B 493 ARG 0.002 0.000 ARG A 331 *********************** 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 : 0.994 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: 0.2809 time to fit residues: 52.6623 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 : 1.017 ------------------------------------------------------------------------------- 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 96 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 A 196 GLN A 389 GLN ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.125545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.108319 restraints weight = 10260.182| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 0.95 r_work: 0.2965 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9482 Z= 0.202 Angle : 0.703 11.319 12890 Z= 0.311 Chirality : 0.045 0.219 1586 Planarity : 0.005 0.048 1504 Dihedral : 15.070 86.451 1829 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.46 % Allowed : 6.37 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.26), residues: 1132 helix: 2.51 (0.18), residues: 788 sheet: -1.50 (0.51), residues: 90 loop : -0.35 (0.46), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 574 HIS 0.004 0.001 HIS A 372 PHE 0.008 0.001 PHE B 516 TYR 0.019 0.001 TYR A 81 ARG 0.003 0.000 ARG B 510 *********************** 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 120 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.971 Fit side-chains REVERT: B 252 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7513 (mpt-90) REVERT: B 357 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.6854 (t80) REVERT: B 437 LEU cc_start: 0.7745 (mm) cc_final: 0.7486 (mp) REVERT: B 514 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8119 (mmtp) REVERT: B 518 LYS cc_start: 0.7640 (ttpt) cc_final: 0.7264 (tptm) REVERT: B 536 TYR cc_start: 0.7838 (m-80) cc_final: 0.7558 (m-10) outliers start: 14 outliers final: 8 residues processed: 114 average time/residue: 0.2102 time to fit residues: 34.3264 Evaluate side-chains 96 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 357 PHE 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 389 GLN Chi-restraints excluded: chain A residue 436 VAL 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: 0.5980 chunk 33 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 0.0050 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 389 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.126905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.104295 restraints weight = 10170.565| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.29 r_work: 0.2924 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9482 Z= 0.162 Angle : 0.584 8.463 12890 Z= 0.270 Chirality : 0.042 0.303 1586 Planarity : 0.004 0.038 1504 Dihedral : 10.903 59.703 1824 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.04 % Allowed : 9.39 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.27), residues: 1132 helix: 2.63 (0.18), residues: 792 sheet: -1.28 (0.50), residues: 90 loop : -0.29 (0.47), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 574 HIS 0.003 0.001 HIS B 141 PHE 0.008 0.001 PHE B 605 TYR 0.015 0.001 TYR B 81 ARG 0.005 0.000 ARG B 510 *********************** 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 106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.912 Fit side-chains REVERT: B 215 LEU cc_start: 0.7614 (tp) cc_final: 0.7181 (tt) REVERT: B 252 ARG cc_start: 0.7260 (mtt90) cc_final: 0.6956 (mpt-90) REVERT: B 357 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6363 (t80) REVERT: B 437 LEU cc_start: 0.7844 (mm) cc_final: 0.7511 (mp) REVERT: B 514 LYS cc_start: 0.8383 (mmmt) cc_final: 0.7930 (mmtp) REVERT: B 518 LYS cc_start: 0.7377 (ttpt) cc_final: 0.6927 (tptm) REVERT: B 536 TYR cc_start: 0.7803 (m-80) cc_final: 0.7494 (m-10) REVERT: A 392 MET cc_start: 0.8340 (tpt) cc_final: 0.8090 (mmm) REVERT: A 437 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7808 (mm) outliers start: 10 outliers final: 6 residues processed: 102 average time/residue: 0.2158 time to fit residues: 31.9734 Evaluate side-chains 94 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 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 45 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN A 558 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.122696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.100159 restraints weight = 10298.376| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.31 r_work: 0.2866 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9482 Z= 0.198 Angle : 0.587 9.065 12890 Z= 0.275 Chirality : 0.042 0.197 1586 Planarity : 0.004 0.041 1504 Dihedral : 10.533 57.967 1824 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.57 % Allowed : 11.06 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.26), residues: 1132 helix: 2.53 (0.18), residues: 792 sheet: -1.10 (0.50), residues: 90 loop : -0.34 (0.46), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 574 HIS 0.003 0.001 HIS B 144 PHE 0.015 0.001 PHE A 605 TYR 0.017 0.001 TYR B 81 ARG 0.004 0.000 ARG B 510 *********************** 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: 15 poor density : 91 time to evaluate : 0.962 Fit side-chains REVERT: B 32 MET cc_start: 0.7955 (mtp) cc_final: 0.7661 (mtp) REVERT: B 141 HIS cc_start: 0.7288 (m-70) cc_final: 0.6879 (m-70) REVERT: B 252 ARG cc_start: 0.7213 (mtt90) cc_final: 0.6894 (mpt-90) REVERT: B 437 LEU cc_start: 0.8064 (mm) cc_final: 0.7751 (mp) REVERT: B 460 GLN cc_start: 0.8147 (tt0) cc_final: 0.7932 (tt0) REVERT: B 514 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8167 (mmmt) REVERT: B 518 LYS cc_start: 0.7341 (ttpt) cc_final: 0.6883 (tptm) REVERT: B 536 TYR cc_start: 0.7915 (m-80) cc_final: 0.7554 (m-80) REVERT: A 32 MET cc_start: 0.7897 (mtp) cc_final: 0.7618 (mtp) REVERT: A 392 MET cc_start: 0.8358 (tpt) cc_final: 0.8151 (tpt) REVERT: A 437 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 459 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7179 (mt-10) REVERT: A 514 LYS cc_start: 0.8358 (mmmt) cc_final: 0.8094 (mmmt) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 0.2086 time to fit residues: 29.7723 Evaluate side-chains 90 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 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 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 49 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 58 optimal weight: 0.0370 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.124595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.102344 restraints weight = 10225.869| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.26 r_work: 0.2899 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9482 Z= 0.161 Angle : 0.556 7.298 12890 Z= 0.258 Chirality : 0.041 0.198 1586 Planarity : 0.004 0.042 1504 Dihedral : 10.308 58.598 1824 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.46 % Allowed : 13.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.26), residues: 1132 helix: 2.57 (0.18), residues: 792 sheet: -1.02 (0.50), residues: 90 loop : -0.37 (0.46), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 574 HIS 0.003 0.001 HIS B 141 PHE 0.010 0.001 PHE B 366 TYR 0.015 0.001 TYR A 81 ARG 0.004 0.000 ARG B 510 *********************** 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 104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.979 Fit side-chains REVERT: B 32 MET cc_start: 0.7914 (mtp) cc_final: 0.7656 (mtp) REVERT: B 141 HIS cc_start: 0.7248 (m-70) cc_final: 0.7025 (m90) REVERT: B 215 LEU cc_start: 0.7656 (tp) cc_final: 0.7228 (tt) REVERT: B 252 ARG cc_start: 0.7056 (mtt90) cc_final: 0.6770 (mpt-90) REVERT: B 437 LEU cc_start: 0.8091 (mm) cc_final: 0.7804 (mt) REVERT: B 460 GLN cc_start: 0.8130 (tt0) cc_final: 0.7870 (tt0) REVERT: B 514 LYS cc_start: 0.8373 (mmmt) cc_final: 0.8107 (mmmt) REVERT: B 518 LYS cc_start: 0.7230 (ttpt) cc_final: 0.6773 (tptm) REVERT: B 536 TYR cc_start: 0.7913 (m-80) cc_final: 0.7521 (m-80) REVERT: A 32 MET cc_start: 0.7862 (mtp) cc_final: 0.7594 (mtp) REVERT: A 392 MET cc_start: 0.8292 (tpt) cc_final: 0.8012 (mmm) REVERT: A 437 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7771 (mm) REVERT: A 459 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7127 (mt-10) REVERT: A 514 LYS cc_start: 0.8319 (mmmt) cc_final: 0.8052 (mmmt) outliers start: 14 outliers final: 10 residues processed: 98 average time/residue: 0.2219 time to fit residues: 30.9203 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 : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 317 THR 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 370 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 9 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.120566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.097057 restraints weight = 10350.075| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.37 r_work: 0.2816 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9482 Z= 0.243 Angle : 0.599 7.305 12890 Z= 0.281 Chirality : 0.042 0.209 1586 Planarity : 0.004 0.044 1504 Dihedral : 10.576 59.481 1824 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.19 % Allowed : 11.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.26), residues: 1132 helix: 2.36 (0.18), residues: 792 sheet: -0.84 (0.51), residues: 92 loop : -0.52 (0.45), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 574 HIS 0.002 0.001 HIS B 141 PHE 0.009 0.001 PHE B 366 TYR 0.016 0.001 TYR B 81 ARG 0.004 0.000 ARG B 510 *********************** 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 108 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.014 Fit side-chains REVERT: B 460 GLN cc_start: 0.8017 (tt0) cc_final: 0.7817 (tt0) REVERT: B 514 LYS cc_start: 0.8425 (mmmt) cc_final: 0.7898 (mmtm) REVERT: B 518 LYS cc_start: 0.7344 (ttpt) cc_final: 0.6882 (tptm) REVERT: A 32 MET cc_start: 0.7947 (mtp) cc_final: 0.7718 (mtp) REVERT: A 437 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7902 (mm) REVERT: A 459 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7333 (mt-10) outliers start: 21 outliers final: 14 residues processed: 101 average time/residue: 0.2149 time to fit residues: 31.5108 Evaluate side-chains 99 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 370 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 243 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 370 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 62 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.123538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.101255 restraints weight = 10279.359| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.26 r_work: 0.2884 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9482 Z= 0.168 Angle : 0.558 7.215 12890 Z= 0.259 Chirality : 0.041 0.194 1586 Planarity : 0.004 0.048 1504 Dihedral : 10.252 59.457 1824 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.67 % Allowed : 13.05 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.26), residues: 1132 helix: 2.37 (0.18), residues: 804 sheet: -0.66 (0.52), residues: 92 loop : -0.38 (0.47), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 574 HIS 0.002 0.001 HIS B 144 PHE 0.008 0.001 PHE B 366 TYR 0.015 0.001 TYR A 81 ARG 0.008 0.000 ARG B 510 *********************** 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 106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.927 Fit side-chains REVERT: B 215 LEU cc_start: 0.7602 (tp) cc_final: 0.7229 (tt) REVERT: B 355 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7890 (tp) REVERT: B 460 GLN cc_start: 0.7955 (tt0) cc_final: 0.7733 (tt0) REVERT: B 486 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8166 (m) REVERT: B 518 LYS cc_start: 0.7241 (ttpt) cc_final: 0.6782 (tptm) REVERT: A 32 MET cc_start: 0.7888 (mtp) cc_final: 0.7615 (mtp) REVERT: A 392 MET cc_start: 0.8318 (tpt) cc_final: 0.8062 (mmm) REVERT: A 437 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7835 (mm) REVERT: A 459 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7281 (mt-10) REVERT: A 514 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7969 (mmmt) outliers start: 16 outliers final: 11 residues processed: 99 average time/residue: 0.2072 time to fit residues: 29.5011 Evaluate side-chains 103 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 104 optimal weight: 0.0040 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.124188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.101740 restraints weight = 10358.615| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.28 r_work: 0.2890 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9482 Z= 0.165 Angle : 0.554 7.087 12890 Z= 0.257 Chirality : 0.040 0.218 1586 Planarity : 0.004 0.045 1504 Dihedral : 10.098 59.300 1824 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.88 % Allowed : 13.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.26), residues: 1132 helix: 2.39 (0.18), residues: 808 sheet: -0.59 (0.53), residues: 92 loop : -0.29 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 574 HIS 0.003 0.001 HIS B 144 PHE 0.007 0.001 PHE B 366 TYR 0.014 0.001 TYR A 81 ARG 0.007 0.000 ARG B 510 *********************** 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 108 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.999 Fit side-chains REVERT: B 215 LEU cc_start: 0.7671 (tp) cc_final: 0.7421 (tp) REVERT: B 355 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7927 (tp) REVERT: B 486 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8250 (m) REVERT: B 518 LYS cc_start: 0.7276 (ttpt) cc_final: 0.6807 (tptm) REVERT: A 32 MET cc_start: 0.7930 (mtp) cc_final: 0.7633 (mtp) REVERT: A 392 MET cc_start: 0.8368 (tpt) cc_final: 0.8109 (mmm) REVERT: A 437 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7854 (mm) REVERT: A 486 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8209 (m) outliers start: 18 outliers final: 13 residues processed: 102 average time/residue: 0.2279 time to fit residues: 33.6489 Evaluate side-chains 106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 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 486 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 20 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.122109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.099769 restraints weight = 10315.235| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.27 r_work: 0.2864 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9482 Z= 0.200 Angle : 0.578 7.332 12890 Z= 0.270 Chirality : 0.041 0.242 1586 Planarity : 0.004 0.046 1504 Dihedral : 10.170 56.680 1824 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.98 % Allowed : 13.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.26), residues: 1132 helix: 2.32 (0.18), residues: 808 sheet: -0.62 (0.52), residues: 92 loop : -0.37 (0.46), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 574 HIS 0.003 0.001 HIS B 141 PHE 0.009 0.001 PHE B 605 TYR 0.014 0.001 TYR A 81 ARG 0.007 0.000 ARG B 510 *********************** 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: 19 poor density : 90 time to evaluate : 0.976 Fit side-chains REVERT: B 215 LEU cc_start: 0.7668 (tp) cc_final: 0.7452 (tp) REVERT: B 512 GLN cc_start: 0.7748 (mp10) cc_final: 0.7161 (mt0) REVERT: B 518 LYS cc_start: 0.7242 (ttpt) cc_final: 0.6770 (tptm) REVERT: A 32 MET cc_start: 0.7889 (mtp) cc_final: 0.7617 (mtp) REVERT: A 392 MET cc_start: 0.8331 (tpt) cc_final: 0.8054 (mmm) REVERT: A 437 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7843 (mm) REVERT: A 459 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7324 (mt-10) outliers start: 19 outliers final: 15 residues processed: 103 average time/residue: 0.2121 time to fit residues: 31.4617 Evaluate side-chains 103 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 101 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 99 optimal weight: 0.0770 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.124745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.102212 restraints weight = 10381.036| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.28 r_work: 0.2902 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9482 Z= 0.159 Angle : 0.550 7.676 12890 Z= 0.255 Chirality : 0.040 0.185 1586 Planarity : 0.004 0.047 1504 Dihedral : 10.018 56.460 1824 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.77 % Allowed : 13.57 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.26), residues: 1132 helix: 2.46 (0.18), residues: 808 sheet: -0.48 (0.53), residues: 92 loop : -0.30 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 574 HIS 0.003 0.001 HIS B 144 PHE 0.011 0.001 PHE B 366 TYR 0.013 0.001 TYR A 81 ARG 0.006 0.000 ARG B 510 ********************** 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 104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.990 Fit side-chains REVERT: B 215 LEU cc_start: 0.7664 (tp) cc_final: 0.7422 (tp) REVERT: B 355 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7875 (tp) REVERT: B 518 LYS cc_start: 0.7263 (ttpt) cc_final: 0.6779 (tptm) REVERT: A 32 MET cc_start: 0.7882 (mtp) cc_final: 0.7627 (mtp) REVERT: A 392 MET cc_start: 0.8337 (tpt) cc_final: 0.8084 (mmm) REVERT: A 437 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7875 (mm) REVERT: A 459 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7203 (mt-10) outliers start: 17 outliers final: 14 residues processed: 98 average time/residue: 0.2145 time to fit residues: 31.2692 Evaluate side-chains 98 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 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 442 ILE Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.123805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.101446 restraints weight = 10241.081| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.27 r_work: 0.2890 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9482 Z= 0.175 Angle : 0.557 7.100 12890 Z= 0.260 Chirality : 0.041 0.217 1586 Planarity : 0.004 0.048 1504 Dihedral : 9.953 58.403 1824 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.57 % Allowed : 13.88 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.26), residues: 1132 helix: 2.44 (0.18), residues: 808 sheet: -0.47 (0.53), residues: 92 loop : -0.34 (0.46), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 574 HIS 0.003 0.001 HIS B 144 PHE 0.008 0.001 PHE B 605 TYR 0.014 0.001 TYR A 81 ARG 0.007 0.000 ARG B 510 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4209.70 seconds wall clock time: 75 minutes 46.17 seconds (4546.17 seconds total)