Starting phenix.real_space_refine on Mon Dec 30 07:34:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wjo_32547/12_2024/7wjo_32547.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wjo_32547/12_2024/7wjo_32547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wjo_32547/12_2024/7wjo_32547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wjo_32547/12_2024/7wjo_32547.map" model { file = "/net/cci-nas-00/data/ceres_data/7wjo_32547/12_2024/7wjo_32547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wjo_32547/12_2024/7wjo_32547.cif" } resolution = 3.2 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8394 2.51 5 N 2156 2.21 5 O 2310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12932 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6431 Classifications: {'peptide': 801} Link IDs: {'PTRANS': 30, 'TRANS': 770} Chain breaks: 1 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'BGI': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 13.91, per 1000 atoms: 1.08 Number of scatterers: 12932 At special positions: 0 Unit cell: (116.63, 114.49, 129.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2310 8.00 N 2156 7.00 C 8394 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: 3.35 Conformation dependent library (CDL) restraints added in 1.6 seconds 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 65.8% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.612A pdb=" N SER A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 110 Processing helix chain 'A' and resid 112 through 134 removed outlier: 3.676A pdb=" N ALA A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 163 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 242 through 262 removed outlier: 3.801A pdb=" N LEU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 removed outlier: 3.505A pdb=" N GLN A 282 " --> pdb=" O ASP A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 357 through 374 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 423 through 447 removed outlier: 3.670A pdb=" N SER A 427 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.626A pdb=" N LEU A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.545A pdb=" N VAL A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 554 removed outlier: 3.782A pdb=" N LYS A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TRP A 539 " --> pdb=" O GLN A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 564 through 587 removed outlier: 3.682A pdb=" N PHE A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 606 Processing helix chain 'A' and resid 619 through 647 removed outlier: 3.882A pdb=" N ASP A 623 " --> pdb=" O GLN A 619 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 681 Processing helix chain 'A' and resid 684 through 705 removed outlier: 5.333A pdb=" N VAL A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 removed outlier: 5.265A pdb=" N THR A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N HIS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 Processing helix chain 'A' and resid 764 through 819 Processing helix chain 'A' and resid 824 through 857 removed outlier: 5.049A pdb=" N GLY A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 74 Processing helix chain 'B' and resid 76 through 90 removed outlier: 3.612A pdb=" N SER B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 110 Processing helix chain 'B' and resid 112 through 134 removed outlier: 3.676A pdb=" N ALA B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 163 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 242 through 262 removed outlier: 3.800A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 282 removed outlier: 3.505A pdb=" N GLN B 282 " --> pdb=" O ASP B 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 279 through 282' Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 357 through 374 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 423 through 447 removed outlier: 3.670A pdb=" N SER B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 480 through 485 removed outlier: 3.626A pdb=" N LEU B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 494 through 505 removed outlier: 3.545A pdb=" N VAL B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 554 removed outlier: 3.781A pdb=" N LYS B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TRP B 539 " --> pdb=" O GLN B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 564 through 587 removed outlier: 3.682A pdb=" N PHE B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 606 Processing helix chain 'B' and resid 619 through 647 removed outlier: 3.882A pdb=" N ASP B 623 " --> pdb=" O GLN B 619 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 681 Processing helix chain 'B' and resid 684 through 705 removed outlier: 5.333A pdb=" N VAL B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TYR B 698 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 720 removed outlier: 5.265A pdb=" N THR B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N HIS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 Processing helix chain 'B' and resid 764 through 819 Processing helix chain 'B' and resid 824 through 857 removed outlier: 5.049A pdb=" N GLY B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU B 855 " --> pdb=" O HIS B 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 removed outlier: 6.174A pdb=" N HIS B 175 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ARG B 200 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR B 332 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN B 346 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS B 352 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B 232 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N CYS B 287 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE B 234 " --> pdb=" O CYS B 287 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL B 289 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 236 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET B 233 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N MET B 381 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N CYS B 235 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B 461 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY B 406 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 11.464A pdb=" N ILE B 405 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 14.829A pdb=" N LYS B 517 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 16.238A pdb=" N GLY B 407 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 12.629A pdb=" N ALA B 519 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N CYS B 409 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA B 521 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN B 411 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR B 523 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR B 413 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 387 removed outlier: 11.464A pdb=" N ILE A 405 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 14.829A pdb=" N LYS A 517 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 16.238A pdb=" N GLY A 407 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 12.628A pdb=" N ALA A 519 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N CYS A 409 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA A 521 " --> pdb=" O CYS A 409 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLN A 411 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR A 523 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR A 413 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY A 406 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A 461 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET A 233 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N MET A 381 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N CYS A 235 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A 232 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N CYS A 287 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 234 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL A 289 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 236 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN A 346 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 352 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N THR A 332 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ARG A 200 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N HIS A 175 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 174 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N SER B 55 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS A 176 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 337 834 hydrogen bonds defined for protein. 2460 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: 4.47 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2030 1.29 - 1.42: 3786 1.42 - 1.55: 7348 1.55 - 1.68: 8 1.68 - 1.81: 112 Bond restraints: 13284 Sorted by residual: bond pdb=" C25 BGI B1001 " pdb=" O26 BGI B1001 " ideal model delta sigma weight residual 1.216 1.433 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C25 BGI A1001 " pdb=" O26 BGI A1001 " ideal model delta sigma weight residual 1.216 1.433 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C17 BGI B1001 " pdb=" C18 BGI B1001 " ideal model delta sigma weight residual 1.532 1.332 0.200 2.00e-02 2.50e+03 9.96e+01 bond pdb=" C17 BGI A1001 " pdb=" C18 BGI A1001 " ideal model delta sigma weight residual 1.532 1.333 0.199 2.00e-02 2.50e+03 9.88e+01 bond pdb=" C17 BGI B1001 " pdb=" O21 BGI B1001 " ideal model delta sigma weight residual 1.433 1.606 -0.173 2.00e-02 2.50e+03 7.46e+01 ... (remaining 13279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 17752 1.69 - 3.38: 214 3.38 - 5.06: 49 5.06 - 6.75: 15 6.75 - 8.44: 12 Bond angle restraints: 18042 Sorted by residual: angle pdb=" N GLU B 463 " pdb=" CA GLU B 463 " pdb=" C GLU B 463 " ideal model delta sigma weight residual 114.62 108.77 5.85 1.14e+00 7.69e-01 2.64e+01 angle pdb=" N GLU A 463 " pdb=" CA GLU A 463 " pdb=" C GLU A 463 " ideal model delta sigma weight residual 114.62 108.78 5.84 1.14e+00 7.69e-01 2.63e+01 angle pdb=" CA GLU A 463 " pdb=" C GLU A 463 " pdb=" N ALA A 464 " ideal model delta sigma weight residual 119.71 116.14 3.57 1.17e+00 7.31e-01 9.31e+00 angle pdb=" CA GLU B 463 " pdb=" C GLU B 463 " pdb=" N ALA B 464 " ideal model delta sigma weight residual 119.71 116.18 3.53 1.17e+00 7.31e-01 9.09e+00 angle pdb=" C18 BGI B1001 " pdb=" C19 BGI B1001 " pdb=" O30 BGI B1001 " ideal model delta sigma weight residual 116.99 108.55 8.44 3.00e+00 1.11e-01 7.91e+00 ... (remaining 18037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 7327 17.32 - 34.63: 398 34.63 - 51.95: 57 51.95 - 69.27: 18 69.27 - 86.58: 14 Dihedral angle restraints: 7814 sinusoidal: 3122 harmonic: 4692 Sorted by residual: dihedral pdb=" CA TYR A 617 " pdb=" C TYR A 617 " pdb=" N SER A 618 " pdb=" CA SER A 618 " ideal model delta harmonic sigma weight residual 180.00 -163.72 -16.28 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA TYR B 617 " pdb=" C TYR B 617 " pdb=" N SER B 618 " pdb=" CA SER B 618 " ideal model delta harmonic sigma weight residual -180.00 -163.75 -16.25 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB ARG B 797 " pdb=" CG ARG B 797 " pdb=" CD ARG B 797 " pdb=" NE ARG B 797 " ideal model delta sinusoidal sigma weight residual 180.00 123.01 56.99 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 7811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1722 0.056 - 0.112: 237 0.112 - 0.168: 23 0.168 - 0.223: 0 0.223 - 0.279: 2 Chirality restraints: 1984 Sorted by residual: chirality pdb=" C18 BGI A1001 " pdb=" C17 BGI A1001 " pdb=" C19 BGI A1001 " pdb=" O31 BGI A1001 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C18 BGI B1001 " pdb=" C17 BGI B1001 " pdb=" C19 BGI B1001 " pdb=" O31 BGI B1001 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C19 BGI B1001 " pdb=" C18 BGI B1001 " pdb=" C20 BGI B1001 " pdb=" O30 BGI B1001 " both_signs ideal model delta sigma weight residual False 2.48 2.63 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 1981 not shown) Planarity restraints: 2278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 598 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C PHE B 598 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE B 598 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE B 599 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 598 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C PHE A 598 " 0.037 2.00e-02 2.50e+03 pdb=" O PHE A 598 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 599 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 599 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C ILE B 599 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE B 599 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 600 " 0.012 2.00e-02 2.50e+03 ... (remaining 2275 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1248 2.74 - 3.28: 12232 3.28 - 3.82: 20984 3.82 - 4.36: 22611 4.36 - 4.90: 43325 Nonbonded interactions: 100400 Sorted by model distance: nonbonded pdb=" OH TYR A 88 " pdb=" OD1 ASP B 115 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR A 52 " pdb=" OE2 GLU B 225 " model vdw 2.207 3.040 nonbonded pdb=" O LYS A 269 " pdb=" OH TYR A 393 " model vdw 2.277 3.040 nonbonded pdb=" O LYS B 269 " pdb=" OH TYR B 393 " model vdw 2.277 3.040 nonbonded pdb=" OE2 GLU A 225 " pdb=" OH TYR B 52 " model vdw 2.284 3.040 ... (remaining 100395 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: 3.760 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 37.330 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.006 0.217 13284 Z= 0.363 Angle : 0.554 8.440 18042 Z= 0.282 Chirality : 0.040 0.279 1984 Planarity : 0.004 0.031 2278 Dihedral : 11.696 86.583 4802 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.29 % Allowed : 6.02 % Favored : 93.69 % 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: 1.94 (0.22), residues: 1594 helix: 2.59 (0.17), residues: 982 sheet: 0.13 (0.43), residues: 170 loop : -1.37 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 804 HIS 0.005 0.001 HIS A 403 PHE 0.016 0.001 PHE B 601 TYR 0.011 0.001 TYR A 365 ARG 0.002 0.000 ARG B 608 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 230 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ARG cc_start: 0.7539 (mtt180) cc_final: 0.5958 (mtt90) REVERT: A 264 MET cc_start: 0.7999 (tpp) cc_final: 0.7763 (ttt) REVERT: A 552 TRP cc_start: 0.7187 (t-100) cc_final: 0.6802 (m-10) REVERT: A 850 ILE cc_start: 0.8256 (tt) cc_final: 0.8026 (tt) REVERT: B 187 ASP cc_start: 0.7188 (p0) cc_final: 0.6596 (p0) REVERT: B 305 GLU cc_start: 0.7831 (tt0) cc_final: 0.7572 (tt0) REVERT: B 645 LEU cc_start: 0.8575 (tp) cc_final: 0.8364 (tt) REVERT: B 790 LYS cc_start: 0.7486 (mttt) cc_final: 0.7261 (mptt) REVERT: B 820 SER cc_start: 0.7917 (m) cc_final: 0.7712 (p) REVERT: B 850 ILE cc_start: 0.8487 (tt) cc_final: 0.8249 (tt) outliers start: 4 outliers final: 2 residues processed: 232 average time/residue: 0.3064 time to fit residues: 97.2264 Evaluate side-chains 144 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 326 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 0.0170 chunk 93 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13284 Z= 0.196 Angle : 0.520 7.046 18042 Z= 0.276 Chirality : 0.040 0.176 1984 Planarity : 0.004 0.031 2278 Dihedral : 6.670 46.465 1852 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.81 % Allowed : 9.36 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.83 (0.22), residues: 1594 helix: 2.44 (0.17), residues: 998 sheet: -0.00 (0.43), residues: 170 loop : -1.34 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 804 HIS 0.003 0.001 HIS A 578 PHE 0.015 0.001 PHE A 601 TYR 0.018 0.001 TYR A 732 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7803 (mp) REVERT: A 193 MET cc_start: 0.7182 (mmm) cc_final: 0.6730 (mmm) REVERT: A 238 MET cc_start: 0.7814 (ttm) cc_final: 0.7535 (ttm) REVERT: A 552 TRP cc_start: 0.7220 (t-100) cc_final: 0.6826 (m-10) REVERT: A 730 THR cc_start: 0.8645 (m) cc_final: 0.8312 (p) REVERT: A 850 ILE cc_start: 0.8301 (tt) cc_final: 0.8059 (tt) REVERT: B 187 ASP cc_start: 0.7134 (p0) cc_final: 0.6647 (p0) REVERT: B 305 GLU cc_start: 0.7834 (tt0) cc_final: 0.7521 (tt0) REVERT: B 325 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7521 (mp10) REVERT: B 850 ILE cc_start: 0.8543 (tt) cc_final: 0.8262 (tt) outliers start: 25 outliers final: 13 residues processed: 173 average time/residue: 0.2744 time to fit residues: 67.6308 Evaluate side-chains 153 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 684 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 HIS A 736 ASN B 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 13284 Z= 0.463 Angle : 0.663 8.665 18042 Z= 0.352 Chirality : 0.046 0.230 1984 Planarity : 0.005 0.035 2278 Dihedral : 5.597 36.688 1850 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.02 % Favored : 93.85 % Rotamer: Outliers : 2.98 % Allowed : 10.45 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.22), residues: 1594 helix: 1.85 (0.16), residues: 980 sheet: -0.49 (0.41), residues: 176 loop : -1.37 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 202 HIS 0.008 0.002 HIS A 578 PHE 0.020 0.002 PHE B 601 TYR 0.025 0.002 TYR A 365 ARG 0.007 0.001 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7977 (mp) REVERT: A 199 ARG cc_start: 0.7576 (mtt180) cc_final: 0.7330 (mtt-85) REVERT: A 552 TRP cc_start: 0.7358 (t-100) cc_final: 0.6776 (m-10) REVERT: A 850 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8474 (tt) REVERT: B 187 ASP cc_start: 0.7352 (p0) cc_final: 0.6856 (p0) REVERT: B 305 GLU cc_start: 0.7848 (tt0) cc_final: 0.7593 (tt0) REVERT: B 325 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7763 (mp10) REVERT: B 785 ARG cc_start: 0.7160 (mtt180) cc_final: 0.6733 (ptp-170) REVERT: B 850 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8300 (tt) outliers start: 41 outliers final: 24 residues processed: 176 average time/residue: 0.2741 time to fit residues: 69.0085 Evaluate side-chains 159 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 816 VAL Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 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 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN B 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13284 Z= 0.197 Angle : 0.525 7.620 18042 Z= 0.280 Chirality : 0.039 0.128 1984 Planarity : 0.004 0.034 2278 Dihedral : 4.922 29.812 1850 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.18 % Allowed : 12.99 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.22), residues: 1594 helix: 2.19 (0.17), residues: 974 sheet: -0.42 (0.42), residues: 174 loop : -1.34 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 202 HIS 0.002 0.001 HIS A 563 PHE 0.015 0.001 PHE B 601 TYR 0.015 0.001 TYR A 732 ARG 0.003 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7846 (mp) REVERT: A 552 TRP cc_start: 0.7319 (t-100) cc_final: 0.6762 (m-10) REVERT: A 850 ILE cc_start: 0.8429 (tt) cc_final: 0.8176 (tt) REVERT: B 187 ASP cc_start: 0.7311 (p0) cc_final: 0.6802 (p0) REVERT: B 199 ARG cc_start: 0.7632 (tpp80) cc_final: 0.7278 (mmt90) REVERT: B 451 SER cc_start: 0.8827 (t) cc_final: 0.8554 (p) REVERT: B 785 ARG cc_start: 0.7132 (mtt180) cc_final: 0.6742 (ptp-170) REVERT: B 850 ILE cc_start: 0.8494 (tt) cc_final: 0.8217 (tt) outliers start: 30 outliers final: 17 residues processed: 164 average time/residue: 0.2834 time to fit residues: 65.7705 Evaluate side-chains 151 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 820 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 0.0170 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13284 Z= 0.217 Angle : 0.520 7.777 18042 Z= 0.276 Chirality : 0.039 0.128 1984 Planarity : 0.004 0.033 2278 Dihedral : 4.763 28.237 1850 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.39 % Allowed : 12.92 % Favored : 84.69 % 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: 1.47 (0.22), residues: 1594 helix: 2.25 (0.17), residues: 974 sheet: -0.51 (0.42), residues: 174 loop : -1.36 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 202 HIS 0.003 0.001 HIS A 578 PHE 0.016 0.001 PHE A 601 TYR 0.017 0.001 TYR A 732 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7839 (mp) REVERT: A 199 ARG cc_start: 0.7544 (mtt180) cc_final: 0.7240 (mtt-85) REVERT: A 552 TRP cc_start: 0.7318 (t-100) cc_final: 0.6745 (m-10) REVERT: A 850 ILE cc_start: 0.8432 (tt) cc_final: 0.8165 (tt) REVERT: B 187 ASP cc_start: 0.7275 (p0) cc_final: 0.6723 (p0) REVERT: B 451 SER cc_start: 0.8801 (t) cc_final: 0.8553 (p) REVERT: B 785 ARG cc_start: 0.7091 (mtt180) cc_final: 0.6746 (ptp-170) REVERT: B 850 ILE cc_start: 0.8528 (tt) cc_final: 0.8221 (tt) outliers start: 33 outliers final: 21 residues processed: 163 average time/residue: 0.3004 time to fit residues: 69.9459 Evaluate side-chains 150 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13284 Z= 0.370 Angle : 0.591 7.864 18042 Z= 0.313 Chirality : 0.043 0.148 1984 Planarity : 0.004 0.033 2278 Dihedral : 5.162 33.335 1850 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.47 % Allowed : 14.15 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1594 helix: 2.03 (0.17), residues: 978 sheet: -0.70 (0.41), residues: 172 loop : -1.38 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 202 HIS 0.005 0.001 HIS B 578 PHE 0.018 0.002 PHE B 601 TYR 0.018 0.002 TYR A 365 ARG 0.003 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7911 (mp) REVERT: A 650 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7944 (mmmt) REVERT: A 850 ILE cc_start: 0.8586 (tt) cc_final: 0.8342 (tt) REVERT: B 75 MET cc_start: 0.2834 (mmt) cc_final: 0.2590 (mmt) REVERT: B 187 ASP cc_start: 0.7370 (p0) cc_final: 0.6805 (p0) REVERT: B 451 SER cc_start: 0.8832 (t) cc_final: 0.8556 (p) REVERT: B 529 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8454 (tt) REVERT: B 538 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6994 (mtt-85) REVERT: B 785 ARG cc_start: 0.7115 (mtt180) cc_final: 0.6757 (ptp90) REVERT: B 850 ILE cc_start: 0.8611 (tt) cc_final: 0.8281 (tt) outliers start: 34 outliers final: 25 residues processed: 156 average time/residue: 0.2957 time to fit residues: 64.8947 Evaluate side-chains 159 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 816 VAL Chi-restraints excluded: chain B residue 820 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13284 Z= 0.235 Angle : 0.524 8.189 18042 Z= 0.279 Chirality : 0.040 0.133 1984 Planarity : 0.004 0.034 2278 Dihedral : 4.888 30.360 1850 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.90 % Allowed : 13.93 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.22), residues: 1594 helix: 2.18 (0.17), residues: 978 sheet: -0.64 (0.41), residues: 170 loop : -1.39 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 202 HIS 0.003 0.001 HIS B 578 PHE 0.016 0.001 PHE A 601 TYR 0.016 0.001 TYR A 492 ARG 0.002 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7848 (mp) REVERT: A 552 TRP cc_start: 0.7407 (OUTLIER) cc_final: 0.6846 (m-10) REVERT: A 850 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8259 (tt) REVERT: B 75 MET cc_start: 0.2798 (mmt) cc_final: 0.2512 (mmt) REVERT: B 187 ASP cc_start: 0.7380 (p0) cc_final: 0.6815 (p0) REVERT: B 451 SER cc_start: 0.8725 (t) cc_final: 0.8524 (p) REVERT: B 529 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8365 (tt) REVERT: B 538 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6914 (mtt-85) REVERT: B 785 ARG cc_start: 0.7166 (mtt180) cc_final: 0.6858 (ptp-170) REVERT: B 850 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8282 (tt) outliers start: 40 outliers final: 28 residues processed: 161 average time/residue: 0.2954 time to fit residues: 66.8511 Evaluate side-chains 165 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 0.0040 chunk 76 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13284 Z= 0.216 Angle : 0.524 9.175 18042 Z= 0.278 Chirality : 0.039 0.130 1984 Planarity : 0.004 0.033 2278 Dihedral : 4.805 29.080 1850 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.19 % Allowed : 13.86 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1594 helix: 2.25 (0.17), residues: 978 sheet: -0.64 (0.41), residues: 170 loop : -1.37 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 184 HIS 0.003 0.001 HIS B 578 PHE 0.017 0.001 PHE B 601 TYR 0.018 0.001 TYR A 492 ARG 0.004 0.000 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7816 (mp) REVERT: A 552 TRP cc_start: 0.7339 (OUTLIER) cc_final: 0.6789 (m-10) REVERT: A 850 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8254 (tt) REVERT: B 75 MET cc_start: 0.2763 (mmt) cc_final: 0.2475 (mmt) REVERT: B 187 ASP cc_start: 0.7351 (p0) cc_final: 0.6787 (p0) REVERT: B 529 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8352 (tt) REVERT: B 538 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6892 (mtt-85) REVERT: B 785 ARG cc_start: 0.7155 (mtt180) cc_final: 0.6836 (ptp-170) REVERT: B 850 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8279 (tt) outliers start: 44 outliers final: 27 residues processed: 165 average time/residue: 0.3008 time to fit residues: 70.0556 Evaluate side-chains 164 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13284 Z= 0.328 Angle : 0.573 9.809 18042 Z= 0.304 Chirality : 0.042 0.146 1984 Planarity : 0.004 0.034 2278 Dihedral : 5.075 31.823 1850 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.12 % Allowed : 13.79 % Favored : 83.09 % 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: 1.25 (0.22), residues: 1594 helix: 2.05 (0.17), residues: 990 sheet: -0.77 (0.40), residues: 170 loop : -1.42 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 184 HIS 0.004 0.001 HIS B 578 PHE 0.018 0.002 PHE B 601 TYR 0.016 0.002 TYR A 492 ARG 0.003 0.000 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7822 (mp) REVERT: A 552 TRP cc_start: 0.7446 (OUTLIER) cc_final: 0.6868 (m-10) REVERT: A 850 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8437 (tt) REVERT: B 529 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8513 (tt) REVERT: B 538 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6944 (mtt-85) REVERT: B 785 ARG cc_start: 0.7161 (mtt180) cc_final: 0.6852 (ptp-170) REVERT: B 850 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8358 (tt) outliers start: 43 outliers final: 32 residues processed: 160 average time/residue: 0.3030 time to fit residues: 68.0551 Evaluate side-chains 171 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 98 optimal weight: 0.0040 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13284 Z= 0.228 Angle : 0.532 10.182 18042 Z= 0.282 Chirality : 0.040 0.132 1984 Planarity : 0.004 0.035 2278 Dihedral : 4.893 29.679 1850 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.98 % Allowed : 14.08 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.22), residues: 1594 helix: 2.15 (0.17), residues: 990 sheet: -0.59 (0.41), residues: 166 loop : -1.40 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 184 HIS 0.003 0.001 HIS B 578 PHE 0.018 0.001 PHE B 601 TYR 0.019 0.001 TYR A 492 ARG 0.003 0.000 ARG A 797 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7811 (mp) REVERT: A 552 TRP cc_start: 0.7465 (OUTLIER) cc_final: 0.6893 (m-10) REVERT: A 850 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8294 (tt) REVERT: B 513 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7274 (mtp) REVERT: B 529 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8496 (tt) REVERT: B 538 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6916 (mtt-85) REVERT: B 785 ARG cc_start: 0.7129 (mtt180) cc_final: 0.6842 (ptp-170) REVERT: B 850 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8349 (tt) outliers start: 41 outliers final: 30 residues processed: 153 average time/residue: 0.2893 time to fit residues: 62.7189 Evaluate side-chains 167 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 0.0060 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 111 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.110477 restraints weight = 15343.002| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.15 r_work: 0.3139 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13284 Z= 0.160 Angle : 0.500 9.970 18042 Z= 0.265 Chirality : 0.038 0.139 1984 Planarity : 0.004 0.037 2278 Dihedral : 4.540 25.146 1850 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.25 % Allowed : 15.09 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.22), residues: 1594 helix: 2.34 (0.17), residues: 990 sheet: -0.52 (0.41), residues: 166 loop : -1.32 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 184 HIS 0.002 0.001 HIS B 563 PHE 0.015 0.001 PHE B 601 TYR 0.019 0.001 TYR A 492 ARG 0.004 0.000 ARG A 200 =============================================================================== Job complete usr+sys time: 2668.21 seconds wall clock time: 49 minutes 44.43 seconds (2984.43 seconds total)