Starting phenix.real_space_refine on Tue Jul 29 11:34:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l7j_23214/07_2025/7l7j_23214.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l7j_23214/07_2025/7l7j_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7l7j_23214/07_2025/7l7j_23214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l7j_23214/07_2025/7l7j_23214.map" model { file = "/net/cci-nas-00/data/ceres_data/7l7j_23214/07_2025/7l7j_23214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l7j_23214/07_2025/7l7j_23214.cif" } resolution = 3.1 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.19, per 1000 atoms: 0.64 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: 2.53 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.43 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: 3.97 Time building geometry restraints manager: 3.06 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: 6867 31.41 - 62.81: 141 62.81 - 94.22: 32 94.22 - 125.63: 0 125.63 - 157.03: 2 Dihedral angle restraints: 7042 sinusoidal: 3021 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 7039 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: 3.470 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.430 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 14.104 157.032 4434 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 (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: -1.39 (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 TRP 0.110 0.022 TRP C 109 HIS 0.016 0.004 HIS A 633 PHE 0.082 0.014 PHE A 507 TYR 0.120 0.021 TYR A 309 ARG 0.008 0.001 ARG A 687 Details of bonding type rmsd hydrogen bonds : bond 0.16471 ( 511) hydrogen bonds : angle 7.73910 ( 1413) covalent geometry : bond 0.01211 (11390) covalent geometry : angle 1.76955 (15325) *********************** 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 : 1.345 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: 0.3498 time to fit residues: 95.7914 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 : 1.413 ------------------------------------------------------------------------------- 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 113 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.0470 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3830 r_free = 0.3830 target = 0.130914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.100510 restraints weight = 16834.992| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.87 r_work: 0.3224 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11390 Z= 0.144 Angle : 0.599 7.693 15325 Z= 0.327 Chirality : 0.043 0.191 1693 Planarity : 0.004 0.032 1946 Dihedral : 8.333 148.627 1547 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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 (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: 0.09 (0.22), residues: 1356 helix: 0.34 (0.21), residues: 520 sheet: 0.15 (0.32), residues: 262 loop : -0.05 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 162 HIS 0.004 0.001 HIS B 189 PHE 0.028 0.001 PHE C 103 TYR 0.018 0.002 TYR B 434 ARG 0.004 0.001 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 511) hydrogen bonds : angle 5.10299 ( 1413) covalent geometry : bond 0.00323 (11390) covalent geometry : angle 0.59882 (15325) *********************** 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 138 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 LYS cc_start: 0.6951 (mtpp) cc_final: 0.6326 (mtpt) REVERT: A 319 ASP cc_start: 0.8048 (t0) cc_final: 0.7825 (t70) REVERT: A 614 MET cc_start: 0.8359 (mmm) cc_final: 0.7361 (mmm) outliers start: 17 outliers final: 10 residues processed: 131 average time/residue: 0.2725 time to fit residues: 50.0173 Evaluate side-chains 100 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 A residue 662 LEU 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 111 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 103 optimal weight: 0.0570 chunk 134 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.131431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.098758 restraints weight = 16868.163| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.80 r_work: 0.3226 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11390 Z= 0.137 Angle : 0.519 5.490 15325 Z= 0.284 Chirality : 0.042 0.152 1693 Planarity : 0.003 0.030 1946 Dihedral : 7.650 135.273 1546 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.13 % Allowed : 8.78 % Favored : 90.09 % 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: 0.59 (0.23), residues: 1356 helix: 1.21 (0.23), residues: 498 sheet: -0.18 (0.31), residues: 269 loop : 0.11 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 162 HIS 0.005 0.001 HIS A 633 PHE 0.023 0.001 PHE C 103 TYR 0.016 0.002 TYR B 434 ARG 0.006 0.000 ARG B 620 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 511) hydrogen bonds : angle 4.67721 ( 1413) covalent geometry : bond 0.00322 (11390) covalent geometry : angle 0.51880 (15325) *********************** 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 132 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 TYR cc_start: 0.7512 (m-80) cc_final: 0.7001 (m-80) REVERT: C 45 ASP cc_start: 0.7112 (p0) cc_final: 0.5691 (t0) REVERT: C 63 ASP cc_start: 0.8250 (t0) cc_final: 0.7708 (t0) REVERT: C 107 LYS cc_start: 0.6928 (mtpp) cc_final: 0.6335 (mtpt) REVERT: A 193 ASP cc_start: 0.8211 (p0) cc_final: 0.7741 (t0) REVERT: A 319 ASP cc_start: 0.7922 (t0) cc_final: 0.7623 (t70) REVERT: A 402 MET cc_start: 0.8969 (ptp) cc_final: 0.8690 (ptm) REVERT: A 654 LYS cc_start: 0.8438 (tttp) cc_final: 0.7736 (mmtp) REVERT: B 402 MET cc_start: 0.9183 (ptp) cc_final: 0.8820 (ptm) REVERT: B 610 MET cc_start: 0.8460 (tpt) cc_final: 0.8009 (tpt) outliers start: 14 outliers final: 8 residues processed: 127 average time/residue: 0.2650 time to fit residues: 47.6295 Evaluate side-chains 110 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 662 LEU Chi-restraints excluded: chain B residue 65 THR 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 636 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 95 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS B 28 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.130928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.098274 restraints weight = 16814.065| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.78 r_work: 0.3219 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11390 Z= 0.137 Angle : 0.503 7.216 15325 Z= 0.272 Chirality : 0.042 0.152 1693 Planarity : 0.003 0.031 1946 Dihedral : 7.088 130.302 1542 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.37 % Allowed : 8.94 % Favored : 89.69 % 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: 0.70 (0.23), residues: 1356 helix: 1.45 (0.23), residues: 498 sheet: -0.25 (0.31), residues: 264 loop : 0.10 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 162 HIS 0.004 0.001 HIS A 633 PHE 0.017 0.001 PHE C 103 TYR 0.017 0.002 TYR C 9 ARG 0.006 0.000 ARG B 620 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 511) hydrogen bonds : angle 4.58402 ( 1413) covalent geometry : bond 0.00323 (11390) covalent geometry : angle 0.50294 (15325) *********************** 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 130 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 TYR cc_start: 0.7504 (m-80) cc_final: 0.6991 (m-80) REVERT: C 45 ASP cc_start: 0.7108 (p0) cc_final: 0.5743 (t0) REVERT: C 63 ASP cc_start: 0.8346 (t0) cc_final: 0.7650 (t0) REVERT: A 193 ASP cc_start: 0.8090 (p0) cc_final: 0.7719 (t0) REVERT: A 201 ARG cc_start: 0.7709 (ptm-80) cc_final: 0.7414 (ttp-110) REVERT: A 319 ASP cc_start: 0.7857 (t0) cc_final: 0.7555 (t70) REVERT: A 654 LYS cc_start: 0.8498 (tttp) cc_final: 0.7682 (mmmm) REVERT: B 151 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8517 (mm) REVERT: B 393 ASP cc_start: 0.7764 (t70) cc_final: 0.7459 (t70) REVERT: B 402 MET cc_start: 0.9172 (ptp) cc_final: 0.8833 (ptm) outliers start: 17 outliers final: 10 residues processed: 126 average time/residue: 0.3010 time to fit residues: 54.2787 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 : 1.279 ------------------------------------------------------------------------------- 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 394 LEU Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 633 HIS 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 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 83 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 0.0030 chunk 2 optimal weight: 0.6980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.131694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.099317 restraints weight = 16815.020| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.78 r_work: 0.3235 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11390 Z= 0.113 Angle : 0.476 8.348 15325 Z= 0.257 Chirality : 0.041 0.146 1693 Planarity : 0.003 0.032 1946 Dihedral : 6.751 125.755 1542 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.05 % Allowed : 9.59 % Favored : 89.36 % 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: 0.83 (0.23), residues: 1356 helix: 1.63 (0.23), residues: 496 sheet: -0.16 (0.31), residues: 260 loop : 0.08 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 162 HIS 0.012 0.001 HIS A 633 PHE 0.012 0.001 PHE C 103 TYR 0.016 0.001 TYR B 434 ARG 0.006 0.000 ARG B 620 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 511) hydrogen bonds : angle 4.47000 ( 1413) covalent geometry : bond 0.00259 (11390) covalent geometry : angle 0.47647 (15325) *********************** 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 123 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ASP cc_start: 0.7069 (p0) cc_final: 0.5832 (t0) REVERT: C 63 ASP cc_start: 0.8366 (t0) cc_final: 0.7946 (t0) REVERT: A 193 ASP cc_start: 0.8066 (p0) cc_final: 0.7751 (t0) REVERT: A 201 ARG cc_start: 0.7705 (ptm-80) cc_final: 0.7398 (ttp-110) REVERT: A 319 ASP cc_start: 0.7836 (t0) cc_final: 0.7512 (t70) REVERT: A 522 ILE cc_start: 0.8348 (mm) cc_final: 0.8014 (mt) REVERT: A 646 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7829 (tt) REVERT: A 654 LYS cc_start: 0.8452 (tttp) cc_final: 0.7721 (mmtp) REVERT: B 393 ASP cc_start: 0.7728 (t70) cc_final: 0.7425 (t70) REVERT: B 402 MET cc_start: 0.9201 (ptp) cc_final: 0.8870 (ptm) REVERT: B 610 MET cc_start: 0.8482 (tpt) cc_final: 0.8089 (tpt) outliers start: 13 outliers final: 7 residues processed: 120 average time/residue: 0.3091 time to fit residues: 53.6173 Evaluate side-chains 110 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 633 HIS Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 390 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 96 optimal weight: 0.9980 chunk 128 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 74 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS A 633 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.130648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099388 restraints weight = 16962.297| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.68 r_work: 0.3238 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11390 Z= 0.114 Angle : 0.464 7.399 15325 Z= 0.250 Chirality : 0.040 0.145 1693 Planarity : 0.003 0.034 1946 Dihedral : 6.539 124.020 1542 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.05 % Allowed : 10.07 % Favored : 88.88 % 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: 0.89 (0.23), residues: 1356 helix: 1.77 (0.23), residues: 496 sheet: -0.17 (0.31), residues: 260 loop : 0.05 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 162 HIS 0.003 0.001 HIS B 189 PHE 0.009 0.001 PHE C 103 TYR 0.016 0.001 TYR B 434 ARG 0.008 0.000 ARG B 620 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 511) hydrogen bonds : angle 4.41672 ( 1413) covalent geometry : bond 0.00263 (11390) covalent geometry : angle 0.46392 (15325) *********************** 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 122 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ASP cc_start: 0.7044 (p0) cc_final: 0.5793 (t0) REVERT: C 63 ASP cc_start: 0.8295 (t0) cc_final: 0.7919 (t0) REVERT: A 193 ASP cc_start: 0.7998 (p0) cc_final: 0.7773 (t0) REVERT: A 201 ARG cc_start: 0.7672 (ptm-80) cc_final: 0.7414 (ttp-110) REVERT: A 319 ASP cc_start: 0.7803 (t0) cc_final: 0.7480 (t70) REVERT: A 581 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7679 (tptt) REVERT: A 646 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7817 (tt) REVERT: B 393 ASP cc_start: 0.7694 (t70) cc_final: 0.7389 (t70) REVERT: B 402 MET cc_start: 0.9230 (ptp) cc_final: 0.8873 (ptm) REVERT: B 610 MET cc_start: 0.8581 (tpt) cc_final: 0.8183 (tpt) outliers start: 13 outliers final: 9 residues processed: 121 average time/residue: 0.2549 time to fit residues: 44.6030 Evaluate side-chains 110 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 394 LEU Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 65 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 81 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 114 optimal weight: 0.0980 chunk 109 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3823 r_free = 0.3823 target = 0.131218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.098664 restraints weight = 17175.657| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.80 r_work: 0.3222 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11390 Z= 0.128 Angle : 0.489 9.765 15325 Z= 0.262 Chirality : 0.041 0.145 1693 Planarity : 0.003 0.035 1946 Dihedral : 6.544 125.233 1542 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.13 % Allowed : 10.80 % Favored : 88.07 % 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: 0.89 (0.23), residues: 1356 helix: 1.77 (0.23), residues: 496 sheet: -0.13 (0.31), residues: 260 loop : 0.03 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 162 HIS 0.003 0.001 HIS B 189 PHE 0.008 0.001 PHE C 103 TYR 0.017 0.001 TYR B 434 ARG 0.008 0.000 ARG B 620 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 511) hydrogen bonds : angle 4.40690 ( 1413) covalent geometry : bond 0.00300 (11390) covalent geometry : angle 0.48859 (15325) *********************** 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 117 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ASP cc_start: 0.7082 (p0) cc_final: 0.5750 (t0) REVERT: C 63 ASP cc_start: 0.8296 (t0) cc_final: 0.7899 (t0) REVERT: A 193 ASP cc_start: 0.8003 (p0) cc_final: 0.7785 (t0) REVERT: A 201 ARG cc_start: 0.7846 (ptm-80) cc_final: 0.7517 (ttp-110) REVERT: A 319 ASP cc_start: 0.7894 (t0) cc_final: 0.7581 (t70) REVERT: A 429 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: A 581 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7683 (tptt) REVERT: A 646 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7816 (tt) REVERT: B 151 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8500 (mm) REVERT: B 393 ASP cc_start: 0.7757 (t70) cc_final: 0.7468 (t70) REVERT: B 402 MET cc_start: 0.9229 (ptp) cc_final: 0.8890 (ptm) outliers start: 14 outliers final: 11 residues processed: 116 average time/residue: 0.2497 time to fit residues: 41.8096 Evaluate side-chains 114 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 394 LEU Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 646 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 484 MET Chi-restraints excluded: chain B residue 594 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 60 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 116 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3833 r_free = 0.3833 target = 0.131237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.098730 restraints weight = 16917.586| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.80 r_work: 0.3227 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11390 Z= 0.121 Angle : 0.479 8.715 15325 Z= 0.256 Chirality : 0.041 0.145 1693 Planarity : 0.003 0.036 1946 Dihedral : 6.500 125.027 1542 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.21 % Allowed : 10.64 % Favored : 88.15 % 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: 0.90 (0.23), residues: 1356 helix: 1.80 (0.23), residues: 496 sheet: -0.13 (0.31), residues: 260 loop : 0.01 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 162 HIS 0.004 0.001 HIS A 633 PHE 0.008 0.001 PHE C 103 TYR 0.017 0.001 TYR B 434 ARG 0.008 0.000 ARG B 620 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 511) hydrogen bonds : angle 4.39733 ( 1413) covalent geometry : bond 0.00284 (11390) covalent geometry : angle 0.47937 (15325) *********************** 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: 15 poor density : 103 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ASP cc_start: 0.7058 (p0) cc_final: 0.5754 (t0) REVERT: C 63 ASP cc_start: 0.8310 (t0) cc_final: 0.7926 (t0) REVERT: A 201 ARG cc_start: 0.7845 (ptm-80) cc_final: 0.7532 (ttp-110) REVERT: A 319 ASP cc_start: 0.7863 (t0) cc_final: 0.7574 (t70) REVERT: A 358 LYS cc_start: 0.8594 (mmtp) cc_final: 0.8283 (mmtm) REVERT: A 581 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7648 (tptt) REVERT: A 600 VAL cc_start: 0.7994 (OUTLIER) cc_final: 0.7752 (m) REVERT: A 646 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7816 (tt) REVERT: B 151 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8492 (mm) REVERT: B 393 ASP cc_start: 0.7749 (t70) cc_final: 0.7462 (t70) REVERT: B 402 MET cc_start: 0.9214 (ptp) cc_final: 0.8868 (ptm) REVERT: B 610 MET cc_start: 0.8593 (tpt) cc_final: 0.8367 (tpt) outliers start: 15 outliers final: 10 residues processed: 116 average time/residue: 0.2520 time to fit residues: 42.1485 Evaluate side-chains 109 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 394 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 646 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 484 MET 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 131 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 114 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3831 r_free = 0.3831 target = 0.131062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.098556 restraints weight = 16803.295| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.78 r_work: 0.3223 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11390 Z= 0.128 Angle : 0.486 8.502 15325 Z= 0.260 Chirality : 0.041 0.145 1693 Planarity : 0.003 0.035 1946 Dihedral : 6.533 126.419 1542 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.97 % Allowed : 11.44 % Favored : 87.59 % 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: 0.75 (0.23), residues: 1356 helix: 1.61 (0.23), residues: 510 sheet: -0.10 (0.31), residues: 260 loop : -0.11 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 162 HIS 0.003 0.001 HIS B 189 PHE 0.007 0.001 PHE B 342 TYR 0.018 0.001 TYR B 434 ARG 0.004 0.000 ARG B 620 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 511) hydrogen bonds : angle 4.38072 ( 1413) covalent geometry : bond 0.00300 (11390) covalent geometry : angle 0.48577 (15325) *********************** 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 114 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ASP cc_start: 0.7069 (p0) cc_final: 0.5788 (t0) REVERT: C 63 ASP cc_start: 0.8309 (t0) cc_final: 0.7925 (t0) REVERT: A 201 ARG cc_start: 0.7841 (ptm-80) cc_final: 0.7547 (ttp-110) REVERT: A 319 ASP cc_start: 0.7895 (t0) cc_final: 0.7532 (t70) REVERT: A 522 ILE cc_start: 0.8412 (mm) cc_final: 0.8098 (mt) REVERT: A 581 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7684 (tptt) REVERT: A 646 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7805 (tt) REVERT: B 151 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8492 (mm) REVERT: B 393 ASP cc_start: 0.7799 (t70) cc_final: 0.7519 (t70) REVERT: B 402 MET cc_start: 0.9222 (ptp) cc_final: 0.8916 (ptm) REVERT: B 610 MET cc_start: 0.8648 (tpt) cc_final: 0.8362 (tpt) outliers start: 12 outliers final: 9 residues processed: 113 average time/residue: 0.2405 time to fit residues: 39.7117 Evaluate side-chains 110 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 394 LEU Chi-restraints excluded: chain A residue 646 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 484 MET 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 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3824 r_free = 0.3824 target = 0.131312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.098553 restraints weight = 16992.515| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.80 r_work: 0.3217 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3977 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= 0.131 Angle : 0.484 8.373 15325 Z= 0.259 Chirality : 0.041 0.145 1693 Planarity : 0.003 0.036 1946 Dihedral : 6.551 128.033 1542 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.05 % Allowed : 11.52 % Favored : 87.43 % 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: 0.74 (0.23), residues: 1356 helix: 1.62 (0.23), residues: 510 sheet: -0.10 (0.32), residues: 260 loop : -0.15 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 162 HIS 0.004 0.001 HIS A 633 PHE 0.008 0.001 PHE B 342 TYR 0.018 0.001 TYR B 434 ARG 0.002 0.000 ARG A 226 Details of bonding type rmsd hydrogen bonds : bond 0.03070 ( 511) hydrogen bonds : angle 4.38201 ( 1413) covalent geometry : bond 0.00310 (11390) covalent geometry : angle 0.48366 (15325) ********************** 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 120 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 LYS cc_start: 0.5999 (mttt) cc_final: 0.5656 (mtmt) REVERT: C 45 ASP cc_start: 0.7098 (p0) cc_final: 0.5768 (t0) REVERT: C 63 ASP cc_start: 0.8312 (t0) cc_final: 0.7950 (t0) REVERT: C 67 LYS cc_start: 0.6266 (ttpt) cc_final: 0.5645 (tttp) REVERT: A 201 ARG cc_start: 0.7842 (ptm-80) cc_final: 0.7472 (ttp-110) REVERT: A 287 GLN cc_start: 0.7017 (tm-30) cc_final: 0.6797 (tm-30) REVERT: A 319 ASP cc_start: 0.7892 (t0) cc_final: 0.7525 (t70) REVERT: A 522 ILE cc_start: 0.8352 (mm) cc_final: 0.8033 (mt) REVERT: A 581 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7689 (tptt) REVERT: A 646 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7823 (tt) REVERT: B 151 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8480 (mm) REVERT: B 393 ASP cc_start: 0.7802 (t70) cc_final: 0.7518 (t70) REVERT: B 402 MET cc_start: 0.9207 (ptp) cc_final: 0.8863 (ptm) REVERT: B 610 MET cc_start: 0.8624 (tpt) cc_final: 0.8311 (tpt) REVERT: B 628 MET cc_start: 0.7465 (mmm) cc_final: 0.7190 (tpt) outliers start: 13 outliers final: 9 residues processed: 118 average time/residue: 0.2637 time to fit residues: 43.7175 Evaluate side-chains 118 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 394 LEU Chi-restraints excluded: chain A residue 646 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 484 MET 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 91 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3819 r_free = 0.3819 target = 0.130244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.097148 restraints weight = 16716.899| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.78 r_work: 0.3226 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11390 Z= 0.175 Angle : 0.520 8.111 15325 Z= 0.276 Chirality : 0.042 0.151 1693 Planarity : 0.003 0.035 1946 Dihedral : 6.818 134.175 1542 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.97 % Allowed : 11.68 % 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 (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: 0.62 (0.23), residues: 1356 helix: 1.53 (0.23), residues: 510 sheet: -0.15 (0.32), residues: 258 loop : -0.22 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 162 HIS 0.004 0.001 HIS A 154 PHE 0.011 0.001 PHE B 342 TYR 0.020 0.002 TYR B 434 ARG 0.003 0.000 ARG B 400 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 511) hydrogen bonds : angle 4.49089 ( 1413) covalent geometry : bond 0.00419 (11390) covalent geometry : angle 0.51956 (15325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5408.12 seconds wall clock time: 96 minutes 24.67 seconds (5784.67 seconds total)