Starting phenix.real_space_refine on Sun Dec 29 00:40:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b70_15894/12_2024/8b70_15894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b70_15894/12_2024/8b70_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_15894/12_2024/8b70_15894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b70_15894/12_2024/8b70_15894.map" model { file = "/net/cci-nas-00/data/ceres_data/8b70_15894/12_2024/8b70_15894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b70_15894/12_2024/8b70_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-5532/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: 8.90, per 1000 atoms: 0.96 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: 2.93 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: 0.72 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: 2.90 Time building geometry restraints manager: 3.19 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.200 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- 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 : 0.945 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: 0.2640 time to fit residues: 48.0357 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 : 1.137 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 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 : 0.979 Fit side-chains REVERT: B 32 MET cc_start: 0.6833 (mtp) cc_final: 0.6551 (mtp) REVERT: B 141 HIS cc_start: 0.6333 (m-70) cc_final: 0.5994 (m-70) REVERT: B 357 PHE cc_start: 0.4885 (OUTLIER) cc_final: 0.3826 (t80) REVERT: B 437 LEU cc_start: 0.6830 (mm) cc_final: 0.6519 (mp) REVERT: B 459 GLU cc_start: 0.7026 (pt0) cc_final: 0.6671 (pt0) REVERT: B 472 LYS cc_start: 0.7841 (mtmt) cc_final: 0.7637 (mttm) REVERT: B 514 LYS cc_start: 0.7610 (mmmt) cc_final: 0.7250 (mmtp) REVERT: B 518 LYS cc_start: 0.6443 (ttpt) cc_final: 0.6135 (tptm) REVERT: A 32 MET cc_start: 0.6756 (mtp) cc_final: 0.6475 (mtp) REVERT: A 472 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7489 (mttm) outliers start: 14 outliers final: 8 residues processed: 114 average time/residue: 0.2185 time to fit residues: 35.3139 Evaluate side-chains 97 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 57 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 A 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9482 Z= 0.189 Angle : 0.597 8.841 12890 Z= 0.277 Chirality : 0.043 0.322 1586 Planarity : 0.004 0.038 1504 Dihedral : 11.038 58.573 1824 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.25 % Allowed : 9.29 % Favored : 89.46 % 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: 2.47 (0.27), residues: 1132 helix: 2.57 (0.18), residues: 792 sheet: -1.34 (0.49), residues: 90 loop : -0.27 (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 372 PHE 0.011 0.001 PHE B 605 TYR 0.016 0.001 TYR B 81 ARG 0.004 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: 12 poor density : 94 time to evaluate : 1.003 Fit side-chains REVERT: B 32 MET cc_start: 0.6899 (mtp) cc_final: 0.6604 (mtp) REVERT: B 141 HIS cc_start: 0.6430 (m-70) cc_final: 0.5706 (m-70) REVERT: B 437 LEU cc_start: 0.6925 (mm) cc_final: 0.6616 (mp) REVERT: B 459 GLU cc_start: 0.7147 (pt0) cc_final: 0.6864 (pt0) REVERT: B 472 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7656 (mttm) REVERT: B 514 LYS cc_start: 0.7643 (mmmt) cc_final: 0.7283 (mmtp) REVERT: B 518 LYS cc_start: 0.6502 (ttpt) cc_final: 0.6189 (tptm) REVERT: A 32 MET cc_start: 0.6781 (mtp) cc_final: 0.6081 (mtt) REVERT: A 437 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6679 (mm) REVERT: A 472 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7504 (mttm) outliers start: 12 outliers final: 7 residues processed: 101 average time/residue: 0.2361 time to fit residues: 33.6474 Evaluate side-chains 93 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 0.0370 chunk 110 optimal weight: 0.0050 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 0.5272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9482 Z= 0.151 Angle : 0.553 7.570 12890 Z= 0.257 Chirality : 0.040 0.193 1586 Planarity : 0.004 0.039 1504 Dihedral : 10.347 56.710 1824 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.25 % Allowed : 11.38 % 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: 2.61 (0.27), residues: 1132 helix: 2.66 (0.18), residues: 792 sheet: -1.08 (0.50), residues: 90 loop : -0.24 (0.47), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 574 HIS 0.002 0.000 HIS B 144 PHE 0.010 0.001 PHE A 605 TYR 0.014 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 104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.972 Fit side-chains REVERT: B 32 MET cc_start: 0.6888 (mtp) cc_final: 0.6571 (mtp) REVERT: B 437 LEU cc_start: 0.6942 (mm) cc_final: 0.6648 (mp) REVERT: B 459 GLU cc_start: 0.7225 (pt0) cc_final: 0.6928 (pt0) REVERT: B 472 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7654 (mttm) REVERT: B 514 LYS cc_start: 0.7628 (mmmt) cc_final: 0.7254 (mmtp) REVERT: B 518 LYS cc_start: 0.6504 (ttpt) cc_final: 0.6185 (tptm) REVERT: B 562 MET cc_start: 0.7387 (ttt) cc_final: 0.7179 (ttt) REVERT: A 32 MET cc_start: 0.6736 (mtp) cc_final: 0.6038 (mtt) REVERT: A 437 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6618 (mm) REVERT: A 459 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6510 (mt-10) REVERT: A 472 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7581 (mttm) outliers start: 12 outliers final: 5 residues processed: 101 average time/residue: 0.2231 time to fit residues: 32.4557 Evaluate side-chains 90 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE 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 91 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 460 GLN A 460 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9482 Z= 0.216 Angle : 0.589 7.262 12890 Z= 0.276 Chirality : 0.043 0.230 1586 Planarity : 0.004 0.039 1504 Dihedral : 10.630 59.939 1824 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.98 % Allowed : 12.11 % 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: 2.35 (0.26), residues: 1132 helix: 2.46 (0.18), residues: 792 sheet: -1.01 (0.51), residues: 90 loop : -0.40 (0.45), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 574 HIS 0.003 0.001 HIS B 144 PHE 0.008 0.001 PHE B 382 TYR 0.016 0.001 TYR B 81 ARG 0.003 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 112 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 1.003 Fit side-chains REVERT: B 32 MET cc_start: 0.6789 (mtp) cc_final: 0.6461 (mtp) REVERT: B 144 HIS cc_start: 0.5816 (OUTLIER) cc_final: 0.5614 (m-70) REVERT: B 437 LEU cc_start: 0.7096 (mm) cc_final: 0.6780 (mp) REVERT: B 472 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7574 (mttm) REVERT: B 518 LYS cc_start: 0.6467 (ttpt) cc_final: 0.6149 (tptm) REVERT: A 32 MET cc_start: 0.6740 (mtp) cc_final: 0.6428 (mtp) REVERT: A 420 MET cc_start: 0.5650 (tmm) cc_final: 0.5410 (tmm) REVERT: A 437 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6829 (mm) REVERT: A 459 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6567 (mt-10) REVERT: A 472 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7664 (mttm) REVERT: A 514 LYS cc_start: 0.7698 (mmmt) cc_final: 0.7491 (mmmt) outliers start: 19 outliers final: 12 residues processed: 104 average time/residue: 0.2017 time to fit residues: 30.1969 Evaluate side-chains 99 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 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 B 144 HIS A 196 GLN A 460 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9482 Z= 0.175 Angle : 0.560 7.104 12890 Z= 0.262 Chirality : 0.041 0.199 1586 Planarity : 0.004 0.041 1504 Dihedral : 10.361 59.744 1824 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.57 % Allowed : 12.73 % Favored : 85.70 % 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: 2.38 (0.26), residues: 1132 helix: 2.47 (0.18), residues: 792 sheet: -0.71 (0.51), residues: 92 loop : -0.50 (0.45), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 574 HIS 0.015 0.001 HIS B 144 PHE 0.009 0.001 PHE B 366 TYR 0.014 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 102 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.091 Fit side-chains REVERT: B 32 MET cc_start: 0.6858 (mtp) cc_final: 0.6524 (mtp) REVERT: B 437 LEU cc_start: 0.7086 (mm) cc_final: 0.6836 (mt) REVERT: B 472 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7589 (mttm) REVERT: B 518 LYS cc_start: 0.6406 (ttpt) cc_final: 0.6095 (tptm) REVERT: B 536 TYR cc_start: 0.6908 (m-80) cc_final: 0.6481 (m-80) REVERT: A 32 MET cc_start: 0.6757 (mtp) cc_final: 0.6444 (mtp) REVERT: A 420 MET cc_start: 0.5608 (tmm) cc_final: 0.5368 (tmm) REVERT: A 437 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6804 (mm) REVERT: A 472 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7647 (mttm) REVERT: A 514 LYS cc_start: 0.7705 (mmmt) cc_final: 0.7497 (mmmt) outliers start: 15 outliers final: 10 residues processed: 96 average time/residue: 0.2188 time to fit residues: 29.9823 Evaluate side-chains 98 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 A residue 96 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0470 chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9482 Z= 0.169 Angle : 0.552 7.846 12890 Z= 0.257 Chirality : 0.040 0.189 1586 Planarity : 0.004 0.043 1504 Dihedral : 10.153 59.826 1824 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.88 % Allowed : 12.84 % 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: 2.45 (0.26), residues: 1132 helix: 2.52 (0.18), residues: 792 sheet: -0.57 (0.53), residues: 92 loop : -0.52 (0.45), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 574 HIS 0.002 0.001 HIS B 144 PHE 0.006 0.001 PHE A 319 TYR 0.014 0.001 TYR B 81 ARG 0.007 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 108 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.966 Fit side-chains REVERT: B 32 MET cc_start: 0.6790 (mtp) cc_final: 0.6459 (mtp) REVERT: B 355 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5567 (tp) REVERT: B 472 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7479 (mttt) REVERT: B 518 LYS cc_start: 0.6437 (ttpt) cc_final: 0.6125 (tptm) REVERT: B 536 TYR cc_start: 0.6995 (m-80) cc_final: 0.6477 (m-80) REVERT: A 32 MET cc_start: 0.6785 (mtp) cc_final: 0.6465 (mtp) REVERT: A 420 MET cc_start: 0.5595 (tmm) cc_final: 0.5376 (tmm) REVERT: A 437 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6792 (mm) REVERT: A 459 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6579 (mt-10) REVERT: A 472 LYS cc_start: 0.8056 (mtmt) cc_final: 0.7546 (mttt) REVERT: A 514 LYS cc_start: 0.7697 (mmmt) cc_final: 0.7473 (mmmt) outliers start: 18 outliers final: 12 residues processed: 101 average time/residue: 0.2196 time to fit residues: 31.7440 Evaluate side-chains 102 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 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 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 A 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9482 Z= 0.187 Angle : 0.568 8.235 12890 Z= 0.263 Chirality : 0.041 0.214 1586 Planarity : 0.004 0.045 1504 Dihedral : 10.158 59.807 1824 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.98 % Allowed : 12.53 % 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: 2.35 (0.26), residues: 1132 helix: 2.38 (0.18), residues: 804 sheet: -0.55 (0.52), residues: 92 loop : -0.48 (0.46), 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 0.009 0.001 PHE B 366 TYR 0.014 0.001 TYR B 81 ARG 0.008 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 106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.900 Fit side-chains REVERT: B 32 MET cc_start: 0.6797 (mtp) cc_final: 0.6459 (mtp) REVERT: B 355 LEU cc_start: 0.5854 (OUTLIER) cc_final: 0.5578 (tp) REVERT: B 472 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7605 (mttt) REVERT: B 518 LYS cc_start: 0.6440 (ttpt) cc_final: 0.6120 (tptm) REVERT: B 536 TYR cc_start: 0.7016 (m-80) cc_final: 0.6535 (m-80) REVERT: A 32 MET cc_start: 0.6783 (mtp) cc_final: 0.6456 (mtp) REVERT: A 420 MET cc_start: 0.5540 (tmm) cc_final: 0.5323 (tmm) REVERT: A 437 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6820 (mm) REVERT: A 472 LYS cc_start: 0.8074 (mtmt) cc_final: 0.7584 (mttt) outliers start: 19 outliers final: 15 residues processed: 99 average time/residue: 0.2300 time to fit residues: 32.1780 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 : 0.988 ------------------------------------------------------------------------------- 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 562 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 HIS A 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9482 Z= 0.176 Angle : 0.557 7.296 12890 Z= 0.259 Chirality : 0.041 0.215 1586 Planarity : 0.004 0.042 1504 Dihedral : 10.056 58.963 1824 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.98 % Allowed : 12.53 % 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: 2.44 (0.26), residues: 1132 helix: 2.41 (0.18), residues: 808 sheet: -0.48 (0.52), residues: 92 loop : -0.35 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 574 HIS 0.002 0.000 HIS A 604 PHE 0.009 0.001 PHE A 605 TYR 0.014 0.001 TYR B 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 : 1.001 Fit side-chains REVERT: B 32 MET cc_start: 0.6787 (mtp) cc_final: 0.6446 (mtp) REVERT: B 355 LEU cc_start: 0.5824 (OUTLIER) cc_final: 0.5564 (tp) REVERT: B 472 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7622 (mttt) REVERT: B 518 LYS cc_start: 0.6443 (ttpt) cc_final: 0.6117 (tptm) REVERT: B 536 TYR cc_start: 0.7024 (m-80) cc_final: 0.6551 (m-80) REVERT: A 32 MET cc_start: 0.6814 (mtp) cc_final: 0.6492 (mtp) REVERT: A 420 MET cc_start: 0.5540 (tmm) cc_final: 0.5325 (tmm) REVERT: A 437 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6791 (mm) REVERT: A 472 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7591 (mttt) outliers start: 19 outliers final: 16 residues processed: 102 average time/residue: 0.2224 time to fit residues: 32.2998 Evaluate side-chains 105 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 562 MET 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 51 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.3980 chunk 104 optimal weight: 0.0570 chunk 90 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 71 optimal weight: 0.0370 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9482 Z= 0.143 Angle : 0.548 8.734 12890 Z= 0.253 Chirality : 0.040 0.209 1586 Planarity : 0.004 0.041 1504 Dihedral : 9.932 59.747 1824 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.36 % Allowed : 13.47 % Favored : 85.18 % 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: 2.59 (0.26), residues: 1132 helix: 2.52 (0.18), residues: 808 sheet: -0.33 (0.52), residues: 92 loop : -0.32 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 574 HIS 0.003 0.000 HIS B 144 PHE 0.009 0.001 PHE B 366 TYR 0.012 0.001 TYR B 81 ARG 0.007 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 101 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.006 Fit side-chains REVERT: B 32 MET cc_start: 0.6780 (mtp) cc_final: 0.6445 (mtp) REVERT: B 472 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7589 (mttt) REVERT: B 518 LYS cc_start: 0.6434 (ttpt) cc_final: 0.6105 (tptm) REVERT: B 536 TYR cc_start: 0.7049 (m-80) cc_final: 0.6584 (m-80) REVERT: A 32 MET cc_start: 0.6819 (mtp) cc_final: 0.6501 (mtp) REVERT: A 437 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6781 (mm) REVERT: A 472 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7528 (mttt) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.2332 time to fit residues: 31.0964 Evaluate side-chains 96 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 484 THR Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3272 r_free = 0.3272 target = 0.121181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.102257 restraints weight = 10324.946| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.06 r_work: 0.2894 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9482 Z= 0.209 Angle : 0.577 7.232 12890 Z= 0.269 Chirality : 0.042 0.251 1586 Planarity : 0.004 0.037 1504 Dihedral : 10.073 57.413 1824 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.36 % Allowed : 13.57 % 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 (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: 2.44 (0.26), residues: 1132 helix: 2.40 (0.18), residues: 808 sheet: -0.38 (0.52), residues: 92 loop : -0.35 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 574 HIS 0.001 0.001 HIS B 604 PHE 0.011 0.001 PHE A 605 TYR 0.014 0.001 TYR B 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: 1877.95 seconds wall clock time: 35 minutes 29.75 seconds (2129.75 seconds total)