Starting phenix.real_space_refine on Thu Feb 13 07:29:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wiv_32537/02_2025/7wiv_32537.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wiv_32537/02_2025/7wiv_32537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wiv_32537/02_2025/7wiv_32537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wiv_32537/02_2025/7wiv_32537.map" model { file = "/net/cci-nas-00/data/ceres_data/7wiv_32537/02_2025/7wiv_32537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wiv_32537/02_2025/7wiv_32537.cif" } resolution = 2.88 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= 0.049 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 3 5.49 5 S 14 5.16 5 C 5511 2.51 5 N 1553 2.21 5 O 1565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8646 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4344 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 25, 'TRANS': 545} Chain: "B" Number of atoms: 4271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4271 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 25, 'TRANS': 550} Chain: "A" 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: 5.76, per 1000 atoms: 0.67 Number of scatterers: 8646 At special positions: 0 Unit cell: (71.34, 95.94, 132.84, 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 14 16.00 P 3 15.00 O 1565 8.00 N 1553 7.00 C 5511 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 7 sheets defined 63.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 309 through 323 removed outlier: 3.559A pdb=" N VAL A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 375 removed outlier: 3.756A pdb=" N GLY A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 385 removed outlier: 4.136A pdb=" N PHE A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.627A pdb=" N LYS A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 407 removed outlier: 3.564A pdb=" N LEU A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 430 removed outlier: 3.720A pdb=" N VAL A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.837A pdb=" N VAL A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.512A pdb=" N TYR A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 479 removed outlier: 4.076A pdb=" N GLN A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 490 through 509 removed outlier: 3.665A pdb=" N ASP A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 513 removed outlier: 4.139A pdb=" N GLY A 513 " --> pdb=" O PRO A 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 510 through 513' Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 523 through 541 removed outlier: 3.510A pdb=" N LEU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 548 Processing helix chain 'A' and resid 549 through 556 Processing helix chain 'A' and resid 558 through 571 removed outlier: 3.606A pdb=" N ARG A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 587 removed outlier: 4.104A pdb=" N ALA A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 586 " --> pdb=" O HIS A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 675 through 677 No H-bonds generated for 'chain 'A' and resid 675 through 677' Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.623A pdb=" N TYR A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 705 removed outlier: 3.632A pdb=" N ILE A 704 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 734 through 737 removed outlier: 4.042A pdb=" N ASP A 737 " --> pdb=" O ASP A 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 734 through 737' Processing helix chain 'A' and resid 751 through 763 removed outlier: 3.672A pdb=" N THR A 755 " --> pdb=" O ARG A 751 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'A' and resid 778 through 781 removed outlier: 3.672A pdb=" N GLU A 781 " --> pdb=" O PRO A 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 778 through 781' Processing helix chain 'A' and resid 782 through 792 removed outlier: 3.710A pdb=" N ARG A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 831 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'B' and resid 17 through 25 removed outlier: 3.816A pdb=" N ALA B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.773A pdb=" N ARG B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 46 removed outlier: 3.821A pdb=" N LEU B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 54 through 97 removed outlier: 3.505A pdb=" N VAL B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B 92 " --> pdb=" O HIS B 88 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 94 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B 95 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.642A pdb=" N ALA B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.571A pdb=" N VAL B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 removed outlier: 3.543A pdb=" N LEU B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) Proline residue: B 142 - end of helix removed outlier: 3.889A pdb=" N LEU B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 162 through 193 removed outlier: 4.057A pdb=" N LEU B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 202 Processing helix chain 'B' and resid 202 through 208 removed outlier: 3.610A pdb=" N LEU B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 removed outlier: 3.647A pdb=" N ALA B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 265 removed outlier: 3.991A pdb=" N LEU B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 5.916A pdb=" N PHE B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N SER B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 253 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.525A pdb=" N THR B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 312 removed outlier: 3.748A pdb=" N ARG B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 422 through 428 Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.842A pdb=" N VAL B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 457 through 461 removed outlier: 3.648A pdb=" N ASN B 460 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 503 through 514 Processing helix chain 'B' and resid 554 through 558 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.867A pdb=" N PHE B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 610 through 613 removed outlier: 3.811A pdb=" N GLN A 672 " --> pdb=" O VAL A 669 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 615 through 617 removed outlier: 5.112A pdb=" N VAL A 615 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 687 through 689 removed outlier: 6.527A pdb=" N THR A 639 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU A 823 " --> pdb=" O VAL A 815 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 698 through 699 removed outlier: 3.689A pdb=" N GLY A 698 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 355 through 356 Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 339 removed outlier: 7.359A pdb=" N PHE B 339 " --> pdb=" O ASP B 350 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP B 350 " --> pdb=" O PHE B 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 410 through 412 removed outlier: 6.397A pdb=" N LEU B 491 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL B 524 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B 493 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N THR B 362 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR B 361 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU B 538 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA B 363 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL B 540 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 365 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 547 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP B 541 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL B 545 " --> pdb=" O ASP B 541 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1405 1.27 - 1.41: 2094 1.41 - 1.54: 5206 1.54 - 1.67: 81 1.67 - 1.80: 25 Bond restraints: 8811 Sorted by residual: bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C LYS B 486 " pdb=" O LYS B 486 " ideal model delta sigma weight residual 1.235 1.141 0.093 1.26e-02 6.30e+03 5.48e+01 bond pdb=" C VAL B 270 " pdb=" O VAL B 270 " ideal model delta sigma weight residual 1.240 1.171 0.068 1.26e-02 6.30e+03 2.95e+01 bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C THR B 269 " pdb=" O THR B 269 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.32e-02 5.74e+03 2.71e+01 ... (remaining 8806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 11889 3.58 - 7.16: 139 7.16 - 10.75: 11 10.75 - 14.33: 3 14.33 - 17.91: 1 Bond angle restraints: 12043 Sorted by residual: angle pdb=" N GLY B 388 " pdb=" CA GLY B 388 " pdb=" C GLY B 388 " ideal model delta sigma weight residual 110.21 119.62 -9.41 9.10e-01 1.21e+00 1.07e+02 angle pdb=" C THR B 267 " pdb=" CA THR B 267 " pdb=" CB THR B 267 " ideal model delta sigma weight residual 110.96 123.88 -12.92 1.54e+00 4.22e-01 7.04e+01 angle pdb=" N ALA B 442 " pdb=" CA ALA B 442 " pdb=" C ALA B 442 " ideal model delta sigma weight residual 114.64 102.34 12.30 1.52e+00 4.33e-01 6.55e+01 angle pdb=" N ILE B 531 " pdb=" CA ILE B 531 " pdb=" C ILE B 531 " ideal model delta sigma weight residual 113.71 106.97 6.74 9.50e-01 1.11e+00 5.03e+01 angle pdb=" N GLN A 454 " pdb=" CA GLN A 454 " pdb=" C GLN A 454 " ideal model delta sigma weight residual 114.16 104.32 9.84 1.48e+00 4.57e-01 4.42e+01 ... (remaining 12038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4716 17.31 - 34.62: 414 34.62 - 51.93: 71 51.93 - 69.25: 19 69.25 - 86.56: 13 Dihedral angle restraints: 5233 sinusoidal: 1972 harmonic: 3261 Sorted by residual: dihedral pdb=" C THR B 267 " pdb=" N THR B 267 " pdb=" CA THR B 267 " pdb=" CB THR B 267 " ideal model delta harmonic sigma weight residual -122.00 -139.89 17.89 0 2.50e+00 1.60e-01 5.12e+01 dihedral pdb=" CA ARG B 389 " pdb=" C ARG B 389 " pdb=" N VAL B 390 " pdb=" CA VAL B 390 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA SER B 368 " pdb=" C SER B 368 " pdb=" N GLY B 369 " pdb=" CA GLY B 369 " ideal model delta harmonic sigma weight residual 180.00 152.37 27.63 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 5230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 1422 0.115 - 0.229: 37 0.229 - 0.344: 5 0.344 - 0.459: 1 0.459 - 0.573: 1 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CA THR B 267 " pdb=" N THR B 267 " pdb=" C THR B 267 " pdb=" CB THR B 267 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.57 2.00e-01 2.50e+01 8.22e+00 chirality pdb=" CA LEU B 268 " pdb=" N LEU B 268 " pdb=" C LEU B 268 " pdb=" CB LEU B 268 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA LYS B 486 " pdb=" N LYS B 486 " pdb=" C LYS B 486 " pdb=" CB LYS B 486 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1463 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 836 " -0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ARG A 836 " 0.075 2.00e-02 2.50e+03 pdb=" O ARG A 836 " -0.028 2.00e-02 2.50e+03 pdb=" N TYR A 837 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 342 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C ASP B 342 " -0.066 2.00e-02 2.50e+03 pdb=" O ASP B 342 " 0.025 2.00e-02 2.50e+03 pdb=" N GLY B 343 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 545 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO A 546 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 546 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 546 " 0.039 5.00e-02 4.00e+02 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1210 2.75 - 3.29: 8558 3.29 - 3.82: 13573 3.82 - 4.36: 17386 4.36 - 4.90: 29541 Nonbonded interactions: 70268 Sorted by model distance: nonbonded pdb=" NH2 ARG A 364 " pdb=" OG1 THR B 228 " model vdw 2.209 3.120 nonbonded pdb=" OG SER B 27 " pdb=" OD1 ASP B 71 " model vdw 2.220 3.040 nonbonded pdb=" N3B ANP A 901 " pdb=" O2A ANP A 901 " model vdw 2.251 3.120 nonbonded pdb=" OD1 ASN B 221 " pdb=" N ALA B 222 " model vdw 2.273 3.120 nonbonded pdb=" O LEU B 70 " pdb=" OG1 THR B 74 " model vdw 2.285 3.040 ... (remaining 70263 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.160 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.370 Find NCS groups from input model: 0.150 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:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 : 0.008 0.150 8811 Z= 0.573 Angle : 1.023 17.912 12043 Z= 0.626 Chirality : 0.056 0.573 1466 Planarity : 0.005 0.072 1537 Dihedral : 14.501 86.558 3131 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.36 % Favored : 90.20 % Rotamer: Outliers : 0.68 % Allowed : 5.34 % Favored : 93.98 % Cbeta Deviations : 0.38 % 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: -5.21 (0.19), residues: 1143 helix: -3.11 (0.15), residues: 698 sheet: -3.96 (0.47), residues: 60 loop : -3.68 (0.26), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 154 HIS 0.008 0.001 HIS A 818 PHE 0.016 0.002 PHE B 244 TYR 0.013 0.002 TYR A 837 ARG 0.006 0.001 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.958 Fit side-chains REVERT: A 359 ASP cc_start: 0.8596 (t70) cc_final: 0.8379 (OUTLIER) REVERT: A 392 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8476 (tmmt) REVERT: A 436 VAL cc_start: 0.9043 (t) cc_final: 0.8782 (m) REVERT: A 515 LYS cc_start: 0.8946 (mttt) cc_final: 0.8728 (mttp) REVERT: B 71 ASP cc_start: 0.7719 (m-30) cc_final: 0.7507 (m-30) outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 1.5729 time to fit residues: 126.5999 Evaluate side-chains 45 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 329 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 0.0270 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.0970 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS A 463 GLN A 597 HIS A 743 ASN A 752 GLN A 802 HIS B 11 ASN B 109 ASN B 237 GLN B 241 GLN B 426 ASN B 533 HIS B 568 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.089494 restraints weight = 13663.537| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.17 r_work: 0.3033 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8811 Z= 0.176 Angle : 0.697 9.014 12043 Z= 0.358 Chirality : 0.042 0.136 1466 Planarity : 0.005 0.057 1537 Dihedral : 7.924 56.106 1281 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.79 % Favored : 92.04 % Rotamer: Outliers : 1.48 % Allowed : 10.23 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.20 (0.22), residues: 1143 helix: -1.44 (0.18), residues: 713 sheet: -3.15 (0.48), residues: 75 loop : -3.04 (0.28), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 529 HIS 0.004 0.001 HIS A 818 PHE 0.008 0.001 PHE A 559 TYR 0.018 0.001 TYR A 568 ARG 0.006 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.961 Fit side-chains REVERT: A 392 LYS cc_start: 0.8838 (ttpp) cc_final: 0.8592 (tmtt) REVERT: A 515 LYS cc_start: 0.9107 (mttt) cc_final: 0.8869 (mttp) REVERT: A 517 LEU cc_start: 0.8904 (tp) cc_final: 0.8657 (mp) REVERT: B 48 GLU cc_start: 0.7915 (pm20) cc_final: 0.7696 (pm20) REVERT: B 71 ASP cc_start: 0.8684 (m-30) cc_final: 0.8425 (m-30) REVERT: B 161 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8751 (mt) REVERT: B 270 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.7990 (t) REVERT: B 435 SER cc_start: 0.7092 (p) cc_final: 0.6764 (t) REVERT: B 447 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7679 (mpt-90) outliers start: 13 outliers final: 2 residues processed: 77 average time/residue: 1.1826 time to fit residues: 98.2026 Evaluate side-chains 58 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 447 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 57 optimal weight: 0.0670 chunk 73 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 743 ASN B 130 ASN B 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.088845 restraints weight = 13918.768| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.21 r_work: 0.3009 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8811 Z= 0.201 Angle : 0.650 7.717 12043 Z= 0.331 Chirality : 0.042 0.140 1466 Planarity : 0.005 0.057 1537 Dihedral : 6.523 55.279 1281 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.61 % Favored : 92.30 % Rotamer: Outliers : 3.07 % Allowed : 10.57 % Favored : 86.36 % 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: -1.99 (0.24), residues: 1143 helix: -0.50 (0.20), residues: 711 sheet: -2.53 (0.52), residues: 75 loop : -2.57 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 56 HIS 0.004 0.001 HIS A 818 PHE 0.011 0.001 PHE B 244 TYR 0.012 0.001 TYR A 782 ARG 0.002 0.000 ARG B 560 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.929 Fit side-chains REVERT: A 392 LYS cc_start: 0.8874 (ttpp) cc_final: 0.8608 (tmtt) REVERT: A 515 LYS cc_start: 0.9050 (mttt) cc_final: 0.8790 (mttp) REVERT: A 517 LEU cc_start: 0.8910 (tp) cc_final: 0.8674 (mp) REVERT: A 781 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: B 71 ASP cc_start: 0.8666 (m-30) cc_final: 0.8361 (m-30) REVERT: B 161 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8675 (mt) REVERT: B 270 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8168 (t) REVERT: B 435 SER cc_start: 0.7097 (p) cc_final: 0.6774 (t) REVERT: B 447 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7718 (mpt-90) outliers start: 27 outliers final: 9 residues processed: 78 average time/residue: 1.0357 time to fit residues: 88.0102 Evaluate side-chains 63 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 577 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 69 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 GLN A 743 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.089378 restraints weight = 13709.659| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.20 r_work: 0.3016 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8811 Z= 0.196 Angle : 0.620 7.649 12043 Z= 0.316 Chirality : 0.042 0.134 1466 Planarity : 0.005 0.057 1537 Dihedral : 5.971 49.677 1281 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.35 % Favored : 92.56 % Rotamer: Outliers : 2.84 % Allowed : 11.93 % Favored : 85.23 % 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: -1.41 (0.25), residues: 1143 helix: -0.02 (0.20), residues: 710 sheet: -2.20 (0.55), residues: 75 loop : -2.39 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 56 HIS 0.005 0.001 HIS A 818 PHE 0.010 0.001 PHE B 244 TYR 0.012 0.001 TYR A 782 ARG 0.003 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.958 Fit side-chains REVERT: A 515 LYS cc_start: 0.9007 (mttt) cc_final: 0.8741 (mttp) REVERT: A 517 LEU cc_start: 0.8878 (tp) cc_final: 0.8656 (mp) REVERT: A 781 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: B 71 ASP cc_start: 0.8639 (m-30) cc_final: 0.8336 (m-30) REVERT: B 123 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: B 161 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8690 (mt) REVERT: B 270 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8107 (t) REVERT: B 435 SER cc_start: 0.6968 (p) cc_final: 0.6629 (t) REVERT: B 447 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7671 (mpt-90) outliers start: 25 outliers final: 7 residues processed: 74 average time/residue: 1.0906 time to fit residues: 87.3674 Evaluate side-chains 57 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 577 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 GLN A 743 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.089860 restraints weight = 13702.172| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.16 r_work: 0.3016 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8811 Z= 0.205 Angle : 0.625 7.508 12043 Z= 0.315 Chirality : 0.042 0.166 1466 Planarity : 0.005 0.057 1537 Dihedral : 5.726 45.077 1281 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.26 % Favored : 92.65 % Rotamer: Outliers : 3.07 % Allowed : 13.18 % Favored : 83.75 % 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: -1.10 (0.25), residues: 1143 helix: 0.23 (0.20), residues: 711 sheet: -1.93 (0.58), residues: 70 loop : -2.34 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 56 HIS 0.005 0.001 HIS A 818 PHE 0.011 0.001 PHE B 244 TYR 0.012 0.001 TYR A 782 ARG 0.005 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 0.935 Fit side-chains REVERT: A 515 LYS cc_start: 0.8987 (mttt) cc_final: 0.8726 (mttp) REVERT: A 517 LEU cc_start: 0.8877 (tp) cc_final: 0.8664 (mp) REVERT: A 519 ASP cc_start: 0.8805 (t0) cc_final: 0.8454 (t70) REVERT: A 781 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: B 71 ASP cc_start: 0.8638 (m-30) cc_final: 0.8353 (m-30) REVERT: B 161 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8718 (mt) REVERT: B 270 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8146 (t) REVERT: B 435 SER cc_start: 0.6894 (p) cc_final: 0.6582 (t) outliers start: 27 outliers final: 11 residues processed: 75 average time/residue: 1.0434 time to fit residues: 85.0566 Evaluate side-chains 61 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 501 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 627 GLN A 743 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.109227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.089272 restraints weight = 13660.626| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.18 r_work: 0.3012 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8811 Z= 0.221 Angle : 0.636 7.793 12043 Z= 0.319 Chirality : 0.043 0.174 1466 Planarity : 0.005 0.058 1537 Dihedral : 5.608 45.009 1281 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.17 % Favored : 92.74 % Rotamer: Outliers : 2.39 % Allowed : 14.43 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1143 helix: 0.42 (0.21), residues: 705 sheet: -1.81 (0.58), residues: 70 loop : -2.22 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 56 HIS 0.005 0.001 HIS A 818 PHE 0.011 0.001 PHE B 244 TYR 0.013 0.002 TYR A 568 ARG 0.004 0.000 ARG B 447 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.888 Fit side-chains REVERT: A 392 LYS cc_start: 0.8834 (ttpp) cc_final: 0.8593 (tmtt) REVERT: A 515 LYS cc_start: 0.8999 (mttt) cc_final: 0.8733 (mttp) REVERT: A 519 ASP cc_start: 0.8819 (t0) cc_final: 0.8461 (t70) REVERT: A 781 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: B 71 ASP cc_start: 0.8645 (m-30) cc_final: 0.8360 (m-30) REVERT: B 161 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8662 (mt) REVERT: B 270 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8163 (t) REVERT: B 435 SER cc_start: 0.6781 (p) cc_final: 0.6439 (t) outliers start: 21 outliers final: 11 residues processed: 71 average time/residue: 1.1310 time to fit residues: 87.0653 Evaluate side-chains 60 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 577 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 627 GLN A 789 ASN B 203 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.089954 restraints weight = 13757.399| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.17 r_work: 0.3027 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8811 Z= 0.193 Angle : 0.625 7.766 12043 Z= 0.313 Chirality : 0.042 0.176 1466 Planarity : 0.005 0.058 1537 Dihedral : 5.496 45.378 1281 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.83 % Rotamer: Outliers : 2.61 % Allowed : 15.00 % Favored : 82.39 % 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: -0.71 (0.26), residues: 1143 helix: 0.55 (0.20), residues: 712 sheet: -1.74 (0.59), residues: 70 loop : -2.22 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 323 HIS 0.005 0.001 HIS A 818 PHE 0.011 0.001 PHE B 244 TYR 0.012 0.001 TYR A 568 ARG 0.003 0.000 ARG A 620 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.998 Fit side-chains REVERT: A 392 LYS cc_start: 0.8847 (ttpp) cc_final: 0.8625 (tmtt) REVERT: A 519 ASP cc_start: 0.8822 (t0) cc_final: 0.8470 (t70) REVERT: A 781 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: B 71 ASP cc_start: 0.8630 (m-30) cc_final: 0.8352 (m-30) REVERT: B 161 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8751 (mt) REVERT: B 270 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8155 (t) REVERT: B 435 SER cc_start: 0.6652 (p) cc_final: 0.6309 (t) outliers start: 23 outliers final: 10 residues processed: 74 average time/residue: 1.1310 time to fit residues: 90.5652 Evaluate side-chains 58 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 501 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 84 optimal weight: 0.0570 chunk 37 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 627 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.090427 restraints weight = 13780.956| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.18 r_work: 0.3036 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8811 Z= 0.179 Angle : 0.623 9.264 12043 Z= 0.310 Chirality : 0.042 0.174 1466 Planarity : 0.004 0.058 1537 Dihedral : 5.393 45.242 1281 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.26 % Favored : 92.65 % Rotamer: Outliers : 2.39 % Allowed : 16.59 % Favored : 81.02 % 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: -0.54 (0.26), residues: 1143 helix: 0.69 (0.20), residues: 713 sheet: -1.65 (0.59), residues: 70 loop : -2.17 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 323 HIS 0.004 0.000 HIS A 818 PHE 0.011 0.001 PHE B 244 TYR 0.012 0.001 TYR A 568 ARG 0.011 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.950 Fit side-chains REVERT: A 392 LYS cc_start: 0.8842 (ttpp) cc_final: 0.8636 (tmtt) REVERT: A 519 ASP cc_start: 0.8812 (t0) cc_final: 0.8512 (t70) REVERT: A 781 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: B 71 ASP cc_start: 0.8612 (m-30) cc_final: 0.8346 (m-30) REVERT: B 161 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8692 (mt) outliers start: 21 outliers final: 9 residues processed: 65 average time/residue: 0.9871 time to fit residues: 70.4601 Evaluate side-chains 57 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 501 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 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 463 GLN A 627 GLN A 743 ASN A 789 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.089704 restraints weight = 13816.492| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.20 r_work: 0.3017 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8811 Z= 0.206 Angle : 0.643 9.662 12043 Z= 0.318 Chirality : 0.042 0.174 1466 Planarity : 0.005 0.058 1537 Dihedral : 5.236 37.915 1280 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.17 % Favored : 92.74 % Rotamer: Outliers : 1.93 % Allowed : 16.70 % Favored : 81.36 % 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: -0.43 (0.26), residues: 1143 helix: 0.78 (0.20), residues: 713 sheet: -1.57 (0.59), residues: 70 loop : -2.16 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 323 HIS 0.004 0.001 HIS A 818 PHE 0.011 0.001 PHE B 244 TYR 0.012 0.001 TYR A 568 ARG 0.008 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.974 Fit side-chains REVERT: A 392 LYS cc_start: 0.8832 (ttpp) cc_final: 0.8621 (tmtt) REVERT: A 519 ASP cc_start: 0.8807 (t0) cc_final: 0.8483 (t70) REVERT: A 781 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: B 71 ASP cc_start: 0.8632 (m-30) cc_final: 0.8354 (m-30) REVERT: B 161 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8660 (mt) outliers start: 17 outliers final: 9 residues processed: 61 average time/residue: 1.1066 time to fit residues: 73.5265 Evaluate side-chains 52 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 501 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 101 optimal weight: 0.0010 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 chunk 67 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 627 GLN A 660 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.090559 restraints weight = 13756.730| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.20 r_work: 0.3037 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8811 Z= 0.177 Angle : 0.632 10.662 12043 Z= 0.312 Chirality : 0.042 0.173 1466 Planarity : 0.004 0.058 1537 Dihedral : 5.164 38.156 1280 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.17 % Favored : 92.74 % Rotamer: Outliers : 1.70 % Allowed : 16.93 % Favored : 81.36 % 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: -0.30 (0.26), residues: 1143 helix: 0.88 (0.20), residues: 713 sheet: -1.50 (0.60), residues: 70 loop : -2.11 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 323 HIS 0.004 0.001 HIS A 818 PHE 0.011 0.001 PHE B 244 TYR 0.012 0.001 TYR A 568 ARG 0.007 0.000 ARG B 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.777 Fit side-chains REVERT: A 519 ASP cc_start: 0.8788 (t0) cc_final: 0.8474 (t70) REVERT: A 781 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: B 71 ASP cc_start: 0.8638 (m-30) cc_final: 0.8368 (m-30) REVERT: B 161 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8748 (mt) REVERT: B 231 MET cc_start: 0.7210 (pmm) cc_final: 0.6586 (mmm) outliers start: 15 outliers final: 8 residues processed: 62 average time/residue: 1.0495 time to fit residues: 70.9398 Evaluate side-chains 57 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 448 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 23 optimal weight: 0.0050 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 101 optimal weight: 0.0020 chunk 88 optimal weight: 0.0670 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 0.3540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 627 GLN A 743 ASN A 789 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.091887 restraints weight = 13721.184| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.24 r_work: 0.3058 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8811 Z= 0.160 Angle : 0.626 9.681 12043 Z= 0.309 Chirality : 0.041 0.170 1466 Planarity : 0.004 0.056 1537 Dihedral : 5.040 37.904 1280 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.91 % Favored : 93.00 % Rotamer: Outliers : 1.59 % Allowed : 17.39 % Favored : 81.02 % 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: -0.11 (0.26), residues: 1143 helix: 1.03 (0.20), residues: 716 sheet: -1.41 (0.61), residues: 70 loop : -2.06 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 323 HIS 0.004 0.000 HIS A 818 PHE 0.010 0.001 PHE B 244 TYR 0.011 0.001 TYR A 568 ARG 0.008 0.000 ARG B 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4751.68 seconds wall clock time: 85 minutes 0.62 seconds (5100.62 seconds total)