Starting phenix.real_space_refine on Fri Jul 3 01:10:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l7j_23214/07_2026/7l7j_23214.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l7j_23214/07_2026/7l7j_23214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7l7j_23214/07_2026/7l7j_23214.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l7j_23214/07_2026/7l7j_23214.cif" model { file = "/net/cci-nas-00/data/ceres_data/7l7j_23214/07_2026/7l7j_23214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l7j_23214/07_2026/7l7j_23214.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l7j_23214/07_2026/7l7j_23214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l7j_23214/07_2026/7l7j_23214.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 52 5.16 5 C 7082 2.51 5 N 1897 2.21 5 O 2159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11196 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 920 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "A" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5107 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 1 Chain: "B" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5107 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.36, per 1000 atoms: 0.21 Number of scatterers: 11196 At special positions: 0 Unit cell: (96.866, 98.494, 130.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 6 15.00 O 2159 8.00 N 1897 7.00 C 7082 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=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 383.2 milliseconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 43.6% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.604A pdb=" N SER A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 43 through 66 removed outlier: 4.028A pdb=" N THR A 65 " --> pdb=" O TYR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 113 through 122 removed outlier: 3.545A pdb=" N LEU A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 139 Processing helix chain 'A' and resid 140 through 144 removed outlier: 4.312A pdb=" N VAL A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 through 144' Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 405 through 428 removed outlier: 3.950A pdb=" N LEU A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 452 removed outlier: 4.616A pdb=" N GLN A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 460 Processing helix chain 'A' and resid 477 through 484 Processing helix chain 'A' and resid 498 through 504 Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 508 through 515 Processing helix chain 'A' and resid 524 through 533 removed outlier: 3.867A pdb=" N TYR A 528 " --> pdb=" O PRO A 524 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 579 removed outlier: 5.763A pdb=" N ASN A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 640 through 653 Processing helix chain 'A' and resid 656 through 674 Processing helix chain 'A' and resid 680 through 697 removed outlier: 3.523A pdb=" N HIS A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 688 " --> pdb=" O HIS A 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 43 through 65 removed outlier: 4.432A pdb=" N THR B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 99 through 107 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 136 through 143 Processing helix chain 'B' and resid 192 through 198 removed outlier: 3.882A pdb=" N THR B 195 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLU B 196 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.891A pdb=" N GLN B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 305 through 318 Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 406 through 428 removed outlier: 3.666A pdb=" N LYS B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 452 removed outlier: 4.367A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ASN B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 461 removed outlier: 3.681A pdb=" N GLU B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 484 Processing helix chain 'B' and resid 498 through 504 Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 508 through 515 Processing helix chain 'B' and resid 524 through 531 removed outlier: 3.879A pdb=" N TYR B 528 " --> pdb=" O PRO B 524 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 568 Processing helix chain 'B' and resid 568 through 579 Processing helix chain 'B' and resid 607 through 615 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 624 through 629 removed outlier: 3.746A pdb=" N ALA B 629 " --> pdb=" O MET B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 653 Processing helix chain 'B' and resid 656 through 674 Processing helix chain 'B' and resid 680 through 697 removed outlier: 3.670A pdb=" N HIS B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 687 " --> pdb=" O THR B 683 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.516A pdb=" N ALA C 6 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 25 through 32 removed outlier: 5.404A pdb=" N ASP C 26 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU C 41 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 21 Processing sheet with id=AA4, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.806A pdb=" N GLN A 23 " --> pdb=" O ILE B 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 removed outlier: 6.557A pdb=" N ILE A 78 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE A 221 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 80 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 147 " --> pdb=" O HIS A 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 331 removed outlier: 3.777A pdb=" N ALA A 325 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 365 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 475 through 476 removed outlier: 4.164A pdb=" N TYR A 466 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ILE A 519 " --> pdb=" O HIS A 490 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N TYR A 492 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N MET A 521 " --> pdb=" O TYR A 492 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 494 " --> pdb=" O MET A 521 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE A 491 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 585 through 588 removed outlier: 6.627A pdb=" N LYS A 585 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE A 636 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 587 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 323 through 331 removed outlier: 6.770A pdb=" N VAL B 343 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 326 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 341 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS B 328 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA B 339 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER B 330 " --> pdb=" O PHE B 337 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N PHE B 337 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL B 365 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 475 through 476 removed outlier: 4.168A pdb=" N TYR B 466 " --> pdb=" O TYR B 520 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE B 491 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 585 through 588 removed outlier: 6.804A pdb=" N LYS B 585 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE B 636 " --> pdb=" O LYS B 585 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1413 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1967 1.31 - 1.43: 2776 1.43 - 1.56: 6552 1.56 - 1.69: 8 1.69 - 1.82: 87 Bond restraints: 11390 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.535 0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.536 0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" O5' ANP B 801 " pdb=" PA ANP B 801 " ideal model delta sigma weight residual 1.655 1.543 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.551 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 11385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 13706 2.82 - 5.65: 1560 5.65 - 8.47: 49 8.47 - 11.30: 5 11.30 - 14.12: 5 Bond angle restraints: 15325 Sorted by residual: angle pdb=" CA ASP B 286 " pdb=" CB ASP B 286 " pdb=" CG ASP B 286 " ideal model delta sigma weight residual 112.60 118.93 -6.33 1.00e+00 1.00e+00 4.00e+01 angle pdb=" CA PHE A 221 " pdb=" CB PHE A 221 " pdb=" CG PHE A 221 " ideal model delta sigma weight residual 113.80 120.07 -6.27 1.00e+00 1.00e+00 3.93e+01 angle pdb=" CA ASP A 322 " pdb=" CB ASP A 322 " pdb=" CG ASP A 322 " ideal model delta sigma weight residual 112.60 118.52 -5.92 1.00e+00 1.00e+00 3.50e+01 angle pdb=" N ARG B 591 " pdb=" CA ARG B 591 " pdb=" C ARG B 591 " ideal model delta sigma weight residual 113.16 120.45 -7.29 1.24e+00 6.50e-01 3.45e+01 angle pdb=" CA ASN B 622 " pdb=" CB ASN B 622 " pdb=" CG ASN B 622 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 15320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.41: 6813 31.41 - 62.81: 141 62.81 - 94.22: 30 94.22 - 125.63: 0 125.63 - 157.03: 2 Dihedral angle restraints: 6986 sinusoidal: 2965 harmonic: 4021 Sorted by residual: dihedral pdb=" CA GLU A 392 " pdb=" C GLU A 392 " pdb=" N ASP A 393 " pdb=" CA ASP A 393 " ideal model delta harmonic sigma weight residual 180.00 -151.14 -28.86 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASP B 286 " pdb=" C ASP B 286 " pdb=" N GLN B 287 " pdb=" CA GLN B 287 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA MET A 521 " pdb=" C MET A 521 " pdb=" N ILE A 522 " pdb=" CA ILE A 522 " ideal model delta harmonic sigma weight residual -180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 6983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 984 0.070 - 0.139: 519 0.139 - 0.209: 154 0.209 - 0.278: 22 0.278 - 0.348: 14 Chirality restraints: 1693 Sorted by residual: chirality pdb=" CA PHE A 329 " pdb=" N PHE A 329 " pdb=" C PHE A 329 " pdb=" CB PHE A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA ALA A 111 " pdb=" N ALA A 111 " pdb=" C ALA A 111 " pdb=" CB ALA A 111 " both_signs ideal model delta sigma weight residual False 2.48 2.15 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA ARG A 367 " pdb=" N ARG A 367 " pdb=" C ARG A 367 " pdb=" CB ARG A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 1690 not shown) Planarity restraints: 1946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 297 " 0.081 2.00e-02 2.50e+03 6.09e-02 9.27e+01 pdb=" CG TRP A 297 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 297 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 297 " -0.043 2.00e-02 2.50e+03 pdb=" NE1 TRP A 297 " -0.088 2.00e-02 2.50e+03 pdb=" CE2 TRP A 297 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 297 " -0.080 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 297 " 0.080 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 297 " -0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP A 297 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 309 " 0.120 2.00e-02 2.50e+03 6.30e-02 7.94e+01 pdb=" CG TYR A 309 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 309 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR A 309 " -0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR A 309 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 309 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 309 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 309 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 109 " 0.110 2.00e-02 2.50e+03 5.47e-02 7.49e+01 pdb=" CG TRP C 109 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP C 109 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP C 109 " -0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP C 109 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP C 109 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 109 " -0.082 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 109 " 0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 109 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 109 " 0.061 2.00e-02 2.50e+03 ... (remaining 1943 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 4217 2.92 - 3.42: 10757 3.42 - 3.91: 19288 3.91 - 4.41: 21924 4.41 - 4.90: 37222 Nonbonded interactions: 93408 Sorted by model distance: nonbonded pdb=" ND2 ASN B 51 " pdb=" O1A ANP B 801 " model vdw 2.427 3.120 nonbonded pdb=" N GLU A 200 " pdb=" OE1 GLU A 200 " model vdw 2.505 3.120 nonbonded pdb=" ND2 ASN A 51 " pdb=" O1A ANP A 801 " model vdw 2.526 3.120 nonbonded pdb=" OG SER B 589 " pdb=" OE1 GLU B 635 " model vdw 2.552 3.040 nonbonded pdb=" OD1 ASP B 57 " pdb=" OH TYR B 216 " model vdw 2.564 3.040 ... (remaining 93403 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' selection = chain 'B' } 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: 4.610 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.040 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.012 0.165 11390 Z= 0.707 Angle : 1.770 14.121 15325 Z= 1.164 Chirality : 0.090 0.348 1693 Planarity : 0.012 0.103 1946 Dihedral : 14.032 157.032 4378 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.28 % Favored : 95.58 % Rotamer: Outliers : 0.73 % Allowed : 3.14 % Favored : 96.13 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.21), residues: 1356 helix: -1.76 (0.18), residues: 488 sheet: 0.22 (0.34), residues: 232 loop : -0.49 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 687 TYR 0.120 0.021 TYR A 309 PHE 0.082 0.014 PHE A 507 TRP 0.110 0.022 TRP C 109 HIS 0.016 0.004 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.01211 / 0.71 (11390) covalent geometry : angle 1.76955 / 1.16 (15325) hydrogen bonds : bond 0.16471 / 11.18 ( 511) hydrogen bonds : angle 7.73910 / 5.27 ( 1413) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 200 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 THR cc_start: 0.8047 (p) cc_final: 0.7722 (m) REVERT: B 498 THR cc_start: 0.8030 (p) cc_final: 0.7698 (m) outliers start: 9 outliers final: 2 residues processed: 206 average time/residue: 0.1302 time to fit residues: 35.2629 Evaluate side-chains 107 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 591 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 GLN A 633 HIS B 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.130497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100017 restraints weight = 16842.938| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.86 r_work: 0.3216 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11390 Z= 0.154 Angle : 0.599 7.622 15325 Z= 0.328 Chirality : 0.043 0.192 1693 Planarity : 0.004 0.031 1946 Dihedral : 7.840 150.557 1491 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.37 % Allowed : 7.33 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.22), residues: 1356 helix: 0.35 (0.22), residues: 520 sheet: 0.13 (0.32), residues: 262 loop : -0.06 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 366 TYR 0.017 0.002 TYR B 434 PHE 0.026 0.002 PHE C 103 TRP 0.021 0.002 TRP B 162 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (11390) covalent geometry : angle 0.59945 / 0.33 (15325) hydrogen bonds : bond 0.04249 / 2.84 ( 511) hydrogen bonds : angle 5.09776 / 3.45 ( 1413) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 LYS cc_start: 0.6949 (mtpp) cc_final: 0.6327 (mtpt) REVERT: A 319 ASP cc_start: 0.8044 (t0) cc_final: 0.7804 (t70) REVERT: A 614 MET cc_start: 0.8351 (mmm) cc_final: 0.7386 (mmm) outliers start: 17 outliers final: 9 residues processed: 130 average time/residue: 0.1075 time to fit residues: 19.8451 Evaluate side-chains 99 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 594 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 52 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.131448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.098945 restraints weight = 16859.119| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.79 r_work: 0.3225 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11390 Z= 0.138 Angle : 0.521 5.528 15325 Z= 0.285 Chirality : 0.042 0.150 1693 Planarity : 0.003 0.032 1946 Dihedral : 7.110 138.867 1490 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.21 % Allowed : 8.86 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.23), residues: 1356 helix: 1.22 (0.23), residues: 498 sheet: -0.19 (0.31), residues: 269 loop : 0.10 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 620 TYR 0.016 0.002 TYR B 434 PHE 0.023 0.001 PHE C 103 TRP 0.018 0.001 TRP B 162 HIS 0.005 0.001 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (11390) covalent geometry : angle 0.52145 / 0.29 (15325) hydrogen bonds : bond 0.03718 / 2.49 ( 511) hydrogen bonds : angle 4.69006 / 3.17 ( 1413) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 TYR cc_start: 0.7510 (m-80) cc_final: 0.6996 (m-80) REVERT: C 45 ASP cc_start: 0.7135 (p0) cc_final: 0.5712 (t0) REVERT: C 63 ASP cc_start: 0.8249 (t0) cc_final: 0.7712 (t0) REVERT: C 107 LYS cc_start: 0.6946 (mtpp) cc_final: 0.6368 (mtpt) REVERT: A 193 ASP cc_start: 0.8216 (p0) cc_final: 0.7749 (t0) REVERT: A 319 ASP cc_start: 0.7923 (t0) cc_final: 0.7632 (t70) REVERT: B 402 MET cc_start: 0.9194 (ptp) cc_final: 0.8843 (ptm) REVERT: B 610 MET cc_start: 0.8522 (tpt) cc_final: 0.8091 (tpt) outliers start: 15 outliers final: 10 residues processed: 129 average time/residue: 0.1122 time to fit residues: 20.7222 Evaluate side-chains 116 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain B residue 636 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 65 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 0.3980 chunk 122 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 490 HIS A 633 HIS B 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.129318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.096268 restraints weight = 17077.675| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.81 r_work: 0.3185 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11390 Z= 0.178 Angle : 0.535 7.428 15325 Z= 0.287 Chirality : 0.043 0.155 1693 Planarity : 0.003 0.031 1946 Dihedral : 6.911 137.722 1486 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.37 % Allowed : 9.51 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1356 helix: 1.36 (0.23), residues: 498 sheet: -0.34 (0.31), residues: 264 loop : 0.03 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 620 TYR 0.019 0.002 TYR B 434 PHE 0.016 0.001 PHE C 103 TRP 0.018 0.001 TRP B 162 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (11390) covalent geometry : angle 0.53533 / 0.29 (15325) hydrogen bonds : bond 0.03623 / 2.42 ( 511) hydrogen bonds : angle 4.69616 / 3.19 ( 1413) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 TYR cc_start: 0.7553 (m-80) cc_final: 0.7015 (m-80) REVERT: C 45 ASP cc_start: 0.7117 (p0) cc_final: 0.5710 (t0) REVERT: C 63 ASP cc_start: 0.8337 (t0) cc_final: 0.7633 (t0) REVERT: A 193 ASP cc_start: 0.8136 (p0) cc_final: 0.7785 (t0) REVERT: A 201 ARG cc_start: 0.7775 (ptm-80) cc_final: 0.7456 (ttp-110) REVERT: A 319 ASP cc_start: 0.7877 (t0) cc_final: 0.7561 (t70) REVERT: A 654 LYS cc_start: 0.8424 (tttp) cc_final: 0.7616 (mmmm) REVERT: B 151 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8522 (mm) REVERT: B 393 ASP cc_start: 0.7795 (t70) cc_final: 0.7503 (t70) REVERT: B 402 MET cc_start: 0.9190 (ptp) cc_final: 0.8830 (ptm) outliers start: 17 outliers final: 9 residues processed: 123 average time/residue: 0.1184 time to fit residues: 21.2212 Evaluate side-chains 112 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 594 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 130 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 114 optimal weight: 0.0000 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 633 HIS ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.130371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.097663 restraints weight = 16872.026| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.80 r_work: 0.3210 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11390 Z= 0.132 Angle : 0.495 8.013 15325 Z= 0.266 Chirality : 0.041 0.152 1693 Planarity : 0.003 0.032 1946 Dihedral : 6.672 132.886 1486 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.21 % Allowed : 10.15 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1356 helix: 1.52 (0.23), residues: 498 sheet: -0.22 (0.31), residues: 260 loop : 0.02 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 620 TYR 0.017 0.002 TYR B 434 PHE 0.013 0.001 PHE C 103 TRP 0.018 0.001 TRP B 162 HIS 0.004 0.001 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (11390) covalent geometry : angle 0.49452 / 0.27 (15325) hydrogen bonds : bond 0.03321 / 2.23 ( 511) hydrogen bonds : angle 4.56881 / 3.11 ( 1413) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ASP cc_start: 0.7094 (p0) cc_final: 0.5817 (t0) REVERT: C 63 ASP cc_start: 0.8360 (t0) cc_final: 0.8014 (t0) REVERT: A 193 ASP cc_start: 0.8062 (p0) cc_final: 0.7762 (t0) REVERT: A 201 ARG cc_start: 0.7747 (ptm-80) cc_final: 0.7358 (ttp-110) REVERT: A 319 ASP cc_start: 0.7847 (t0) cc_final: 0.7526 (t70) REVERT: B 151 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8488 (mm) REVERT: B 393 ASP cc_start: 0.7748 (t70) cc_final: 0.7452 (t70) REVERT: B 402 MET cc_start: 0.9204 (ptp) cc_final: 0.8864 (ptm) REVERT: B 610 MET cc_start: 0.8585 (tpt) cc_final: 0.8175 (tpt) REVERT: B 644 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7667 (tt0) outliers start: 15 outliers final: 9 residues processed: 123 average time/residue: 0.1020 time to fit residues: 18.1142 Evaluate side-chains 113 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 644 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 72 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 633 HIS ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096099 restraints weight = 17180.453| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.83 r_work: 0.3179 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11390 Z= 0.177 Angle : 0.525 8.801 15325 Z= 0.280 Chirality : 0.042 0.146 1693 Planarity : 0.003 0.034 1946 Dihedral : 6.750 135.354 1486 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.37 % Allowed : 10.15 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1356 helix: 1.53 (0.23), residues: 496 sheet: -0.35 (0.31), residues: 264 loop : 0.01 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 620 TYR 0.019 0.002 TYR B 434 PHE 0.011 0.001 PHE B 342 TRP 0.018 0.001 TRP B 162 HIS 0.004 0.001 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (11390) covalent geometry : angle 0.52492 / 0.28 (15325) hydrogen bonds : bond 0.03433 / 2.31 ( 511) hydrogen bonds : angle 4.63334 / 3.15 ( 1413) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ASP cc_start: 0.7072 (p0) cc_final: 0.5835 (t0) REVERT: C 63 ASP cc_start: 0.8336 (t0) cc_final: 0.7965 (t0) REVERT: A 193 ASP cc_start: 0.8061 (p0) cc_final: 0.7822 (t0) REVERT: A 201 ARG cc_start: 0.7790 (ptm-80) cc_final: 0.7470 (ttp-110) REVERT: A 319 ASP cc_start: 0.7870 (t0) cc_final: 0.7533 (t70) REVERT: A 521 MET cc_start: 0.8507 (mtt) cc_final: 0.8298 (mtt) REVERT: A 600 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7685 (m) REVERT: B 40 ASN cc_start: 0.8441 (t0) cc_final: 0.8045 (m-40) REVERT: B 151 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8494 (mm) REVERT: B 393 ASP cc_start: 0.7790 (t70) cc_final: 0.7504 (t70) REVERT: B 402 MET cc_start: 0.9209 (ptp) cc_final: 0.8854 (ptm) REVERT: B 644 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7713 (tt0) outliers start: 17 outliers final: 9 residues processed: 115 average time/residue: 0.0938 time to fit residues: 15.6315 Evaluate side-chains 112 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 644 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 60 optimal weight: 8.9990 chunk 76 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 100 optimal weight: 0.0470 chunk 87 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 633 HIS ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.129441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096605 restraints weight = 17052.713| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.80 r_work: 0.3188 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11390 Z= 0.152 Angle : 0.498 8.062 15325 Z= 0.267 Chirality : 0.041 0.147 1693 Planarity : 0.003 0.035 1946 Dihedral : 6.695 134.653 1486 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.37 % Allowed : 10.72 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.23), residues: 1356 helix: 1.59 (0.23), residues: 496 sheet: -0.30 (0.32), residues: 264 loop : -0.03 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 620 TYR 0.018 0.002 TYR B 434 PHE 0.009 0.001 PHE B 342 TRP 0.018 0.001 TRP B 162 HIS 0.006 0.001 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (11390) covalent geometry : angle 0.49841 / 0.27 (15325) hydrogen bonds : bond 0.03266 / 2.19 ( 511) hydrogen bonds : angle 4.55732 / 3.09 ( 1413) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ASP cc_start: 0.7067 (p0) cc_final: 0.5745 (t0) REVERT: C 63 ASP cc_start: 0.8345 (t0) cc_final: 0.7900 (t0) REVERT: A 193 ASP cc_start: 0.8035 (p0) cc_final: 0.7835 (t0) REVERT: A 201 ARG cc_start: 0.7774 (ptm-80) cc_final: 0.7456 (ttp-110) REVERT: A 319 ASP cc_start: 0.7867 (t0) cc_final: 0.7547 (t70) REVERT: A 429 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: B 40 ASN cc_start: 0.8433 (t0) cc_final: 0.8043 (m-40) REVERT: B 151 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8487 (mm) REVERT: B 393 ASP cc_start: 0.7795 (t70) cc_final: 0.7512 (t70) REVERT: B 402 MET cc_start: 0.9198 (ptp) cc_final: 0.8856 (ptm) REVERT: B 610 MET cc_start: 0.8638 (tpt) cc_final: 0.8196 (tpt) REVERT: B 644 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7713 (tt0) outliers start: 17 outliers final: 9 residues processed: 120 average time/residue: 0.0885 time to fit residues: 15.4532 Evaluate side-chains 111 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 644 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 30 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 55 optimal weight: 0.0980 chunk 9 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 116 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.131139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.098285 restraints weight = 16954.797| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.80 r_work: 0.3215 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11390 Z= 0.119 Angle : 0.482 8.254 15325 Z= 0.257 Chirality : 0.040 0.142 1693 Planarity : 0.003 0.035 1946 Dihedral : 6.522 131.494 1486 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.05 % Allowed : 11.28 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.23), residues: 1356 helix: 1.72 (0.23), residues: 496 sheet: -0.20 (0.32), residues: 260 loop : -0.08 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 620 TYR 0.017 0.001 TYR B 434 PHE 0.008 0.001 PHE C 103 TRP 0.019 0.001 TRP B 162 HIS 0.003 0.001 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (11390) covalent geometry : angle 0.48211 / 0.26 (15325) hydrogen bonds : bond 0.03079 / 2.08 ( 511) hydrogen bonds : angle 4.44872 / 3.02 ( 1413) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ASP cc_start: 0.7066 (p0) cc_final: 0.5784 (t0) REVERT: C 63 ASP cc_start: 0.8319 (t0) cc_final: 0.7932 (t0) REVERT: A 201 ARG cc_start: 0.7835 (ptm-80) cc_final: 0.7448 (ttp-110) REVERT: A 319 ASP cc_start: 0.7859 (t0) cc_final: 0.7550 (t70) REVERT: A 358 LYS cc_start: 0.8592 (mmtp) cc_final: 0.8288 (mmtm) REVERT: A 521 MET cc_start: 0.8527 (mtt) cc_final: 0.8307 (mtt) REVERT: B 40 ASN cc_start: 0.8428 (t0) cc_final: 0.8074 (m-40) REVERT: B 151 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8483 (mm) REVERT: B 393 ASP cc_start: 0.7815 (t70) cc_final: 0.7536 (t70) REVERT: B 402 MET cc_start: 0.9174 (ptp) cc_final: 0.8848 (ptm) outliers start: 13 outliers final: 8 residues processed: 117 average time/residue: 0.0914 time to fit residues: 15.8078 Evaluate side-chains 110 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 594 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 102 optimal weight: 0.0060 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.131940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.099209 restraints weight = 16928.014| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.80 r_work: 0.3223 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11390 Z= 0.112 Angle : 0.486 7.717 15325 Z= 0.259 Chirality : 0.040 0.141 1693 Planarity : 0.003 0.034 1946 Dihedral : 6.422 129.779 1486 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.89 % Allowed : 11.85 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1356 helix: 1.57 (0.23), residues: 510 sheet: -0.19 (0.32), residues: 260 loop : -0.18 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 226 TYR 0.016 0.001 TYR B 434 PHE 0.008 0.001 PHE C 103 TRP 0.019 0.001 TRP B 162 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (11390) covalent geometry : angle 0.48556 / 0.26 (15325) hydrogen bonds : bond 0.03005 / 2.04 ( 511) hydrogen bonds : angle 4.35968 / 2.96 ( 1413) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 LYS cc_start: 0.6080 (mttt) cc_final: 0.5670 (mtmt) REVERT: C 45 ASP cc_start: 0.7055 (p0) cc_final: 0.5796 (t0) REVERT: C 63 ASP cc_start: 0.8336 (t0) cc_final: 0.7969 (t0) REVERT: A 201 ARG cc_start: 0.7830 (ptm-80) cc_final: 0.7452 (ttp-110) REVERT: A 319 ASP cc_start: 0.7892 (t0) cc_final: 0.7588 (t70) REVERT: B 40 ASN cc_start: 0.8442 (t0) cc_final: 0.8108 (m-40) REVERT: B 130 MET cc_start: 0.8602 (mtt) cc_final: 0.8334 (mtt) REVERT: B 151 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8469 (mm) REVERT: B 393 ASP cc_start: 0.7819 (t70) cc_final: 0.7541 (t70) REVERT: B 402 MET cc_start: 0.9177 (ptp) cc_final: 0.8863 (ptm) REVERT: B 610 MET cc_start: 0.8621 (tpt) cc_final: 0.8145 (tpt) REVERT: B 628 MET cc_start: 0.7391 (mmm) cc_final: 0.7073 (tpt) outliers start: 11 outliers final: 7 residues processed: 124 average time/residue: 0.1028 time to fit residues: 18.2933 Evaluate side-chains 116 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 594 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 74 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.130902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099249 restraints weight = 16748.139| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.67 r_work: 0.3264 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11390 Z= 0.119 Angle : 0.485 7.642 15325 Z= 0.259 Chirality : 0.041 0.141 1693 Planarity : 0.003 0.034 1946 Dihedral : 6.390 129.882 1486 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.89 % Allowed : 11.76 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.23), residues: 1356 helix: 1.61 (0.23), residues: 510 sheet: -0.20 (0.32), residues: 260 loop : -0.18 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 226 TYR 0.016 0.001 TYR B 434 PHE 0.008 0.001 PHE C 103 TRP 0.018 0.001 TRP B 162 HIS 0.005 0.001 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (11390) covalent geometry : angle 0.48511 / 0.26 (15325) hydrogen bonds : bond 0.03006 / 2.04 ( 511) hydrogen bonds : angle 4.33982 / 2.94 ( 1413) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 LYS cc_start: 0.7696 (mtpt) cc_final: 0.7252 (mttp) REVERT: C 45 ASP cc_start: 0.7005 (p0) cc_final: 0.5723 (t0) REVERT: C 54 ASP cc_start: 0.6741 (m-30) cc_final: 0.6360 (m-30) REVERT: C 63 ASP cc_start: 0.8333 (t0) cc_final: 0.8019 (t0) REVERT: C 91 LYS cc_start: 0.7034 (ptpp) cc_final: 0.6441 (ptpp) REVERT: A 201 ARG cc_start: 0.8011 (ptm-80) cc_final: 0.7630 (ttp-110) REVERT: A 319 ASP cc_start: 0.7948 (t0) cc_final: 0.7616 (t70) REVERT: A 521 MET cc_start: 0.8669 (mtt) cc_final: 0.8451 (mtt) REVERT: A 581 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7561 (tptt) REVERT: B 40 ASN cc_start: 0.8619 (t0) cc_final: 0.8265 (m-40) REVERT: B 151 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8598 (mm) REVERT: B 393 ASP cc_start: 0.7961 (t70) cc_final: 0.7701 (t70) REVERT: B 402 MET cc_start: 0.9241 (ptp) cc_final: 0.8932 (ptm) REVERT: B 610 MET cc_start: 0.8806 (tpt) cc_final: 0.8407 (tpt) REVERT: B 628 MET cc_start: 0.7421 (mmm) cc_final: 0.7152 (tpt) outliers start: 11 outliers final: 7 residues processed: 121 average time/residue: 0.1221 time to fit residues: 20.8015 Evaluate side-chains 107 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 594 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 124 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.129702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.097918 restraints weight = 16680.582| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.66 r_work: 0.3242 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11390 Z= 0.149 Angle : 0.509 7.469 15325 Z= 0.270 Chirality : 0.041 0.145 1693 Planarity : 0.003 0.033 1946 Dihedral : 6.541 133.857 1486 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.81 % Allowed : 11.85 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.23), residues: 1356 helix: 1.56 (0.23), residues: 510 sheet: -0.24 (0.32), residues: 260 loop : -0.18 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 400 TYR 0.019 0.002 TYR B 434 PHE 0.010 0.001 PHE B 342 TRP 0.017 0.001 TRP B 162 HIS 0.004 0.001 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (11390) covalent geometry : angle 0.50876 / 0.27 (15325) hydrogen bonds : bond 0.03153 / 2.14 ( 511) hydrogen bonds : angle 4.42491 / 3.00 ( 1413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2339.56 seconds wall clock time: 41 minutes 1.36 seconds (2461.36 seconds total)