Starting phenix.real_space_refine on Fri Nov 15 11:01:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wam_37397/11_2024/8wam_37397.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wam_37397/11_2024/8wam_37397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wam_37397/11_2024/8wam_37397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wam_37397/11_2024/8wam_37397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wam_37397/11_2024/8wam_37397.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wam_37397/11_2024/8wam_37397.cif" } resolution = 3.23 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= -0.002 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 5612 2.51 5 N 1448 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8650 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4293 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain breaks: 4 Chain: "B" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4293 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain breaks: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.40, per 1000 atoms: 0.62 Number of scatterers: 8650 At special positions: 0 Unit cell: (97.455, 77.745, 124.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 6 15.00 Mg 2 11.99 O 1528 8.00 N 1448 7.00 C 5612 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 65.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 174 through 189 removed outlier: 3.511A pdb=" N LYS A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.671A pdb=" N LYS A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 255 Processing helix chain 'A' and resid 268 through 274 removed outlier: 3.810A pdb=" N MET A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 4.474A pdb=" N ALA A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 338 through 357 removed outlier: 4.228A pdb=" N ALA A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Proline residue: A 351 - end of helix Processing helix chain 'A' and resid 379 through 402 removed outlier: 3.577A pdb=" N ILE A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 4.106A pdb=" N ILE A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 456 removed outlier: 3.790A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.671A pdb=" N VAL A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 473 removed outlier: 3.551A pdb=" N GLU A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 493 removed outlier: 3.665A pdb=" N TYR A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.844A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 541 removed outlier: 3.593A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 562 removed outlier: 3.945A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 579 removed outlier: 3.973A pdb=" N VAL A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TRP A 575 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N MET A 576 " --> pdb=" O MET A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 595 removed outlier: 4.223A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 removed outlier: 4.004A pdb=" N MET A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 634 through 660 removed outlier: 3.590A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.724A pdb=" N LYS B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 255 Processing helix chain 'B' and resid 268 through 274 removed outlier: 3.854A pdb=" N MET B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.619A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.525A pdb=" N PHE B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 358 removed outlier: 4.391A pdb=" N ALA B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) Proline residue: B 351 - end of helix removed outlier: 3.942A pdb=" N GLU B 358 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 402 removed outlier: 3.656A pdb=" N ILE B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 4.468A pdb=" N ILE B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 455 removed outlier: 3.754A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 457 through 473 removed outlier: 3.854A pdb=" N GLU B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 467 " --> pdb=" O ARG B 463 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 removed outlier: 3.719A pdb=" N TYR B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 489 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 507 removed outlier: 3.838A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 541 removed outlier: 3.513A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 561 removed outlier: 3.717A pdb=" N THR B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 Processing helix chain 'B' and resid 580 through 595 removed outlier: 4.015A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 634 through 660 removed outlier: 3.614A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 91 removed outlier: 3.599A pdb=" N LEU A 84 " --> pdb=" O TYR A 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL A 45 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR A 88 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 43 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET A 90 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS A 41 " --> pdb=" O MET A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.124A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 91 removed outlier: 3.567A pdb=" N LEU B 84 " --> pdb=" O TYR B 47 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 86 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL B 45 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR B 88 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 43 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET B 90 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS B 41 " --> pdb=" O MET B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.271A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N MET B 97 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 278 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL B 289 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 280 " --> pdb=" O LEU B 287 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1410 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: 2.43 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2689 1.34 - 1.46: 1657 1.46 - 1.58: 4386 1.58 - 1.69: 10 1.69 - 1.81: 88 Bond restraints: 8830 Sorted by residual: bond pdb=" CA PHE A 646 " pdb=" C PHE A 646 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.30e-02 5.92e+03 1.13e+00 bond pdb=" CA PHE A 647 " pdb=" C PHE A 647 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.27e-02 6.20e+03 8.79e-01 bond pdb=" C GLU B 599 " pdb=" O GLU B 599 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.26e-02 6.30e+03 7.70e-01 bond pdb=" C ILE B 383 " pdb=" O ILE B 383 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.13e-02 7.83e+03 6.73e-01 bond pdb=" CE1 PHE A 646 " pdb=" CZ PHE A 646 " ideal model delta sigma weight residual 1.382 1.404 -0.022 3.00e-02 1.11e+03 5.17e-01 ... (remaining 8825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 11759 1.28 - 2.55: 155 2.55 - 3.83: 43 3.83 - 5.10: 19 5.10 - 6.38: 4 Bond angle restraints: 11980 Sorted by residual: angle pdb=" CA GLU B 492 " pdb=" CB GLU B 492 " pdb=" CG GLU B 492 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C VAL B 43 " pdb=" N ASP B 44 " pdb=" CA ASP B 44 " ideal model delta sigma weight residual 122.46 125.78 -3.32 1.41e+00 5.03e-01 5.56e+00 angle pdb=" C VAL A 43 " pdb=" N ASP A 44 " pdb=" CA ASP A 44 " ideal model delta sigma weight residual 122.46 125.72 -3.26 1.41e+00 5.03e-01 5.35e+00 angle pdb=" N PHE A 647 " pdb=" CA PHE A 647 " pdb=" C PHE A 647 " ideal model delta sigma weight residual 111.07 112.96 -1.89 1.07e+00 8.73e-01 3.12e+00 angle pdb=" C PHE A 646 " pdb=" CA PHE A 646 " pdb=" CB PHE A 646 " ideal model delta sigma weight residual 110.79 113.68 -2.89 1.66e+00 3.63e-01 3.04e+00 ... (remaining 11975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4369 17.92 - 35.84: 637 35.84 - 53.77: 186 53.77 - 71.69: 25 71.69 - 89.61: 7 Dihedral angle restraints: 5224 sinusoidal: 2072 harmonic: 3152 Sorted by residual: dihedral pdb=" CA TRP B 447 " pdb=" C TRP B 447 " pdb=" N GLY B 448 " pdb=" CA GLY B 448 " ideal model delta harmonic sigma weight residual 180.00 163.29 16.71 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CG ARG A 171 " pdb=" CD ARG A 171 " pdb=" NE ARG A 171 " pdb=" CZ ARG A 171 " ideal model delta sinusoidal sigma weight residual 180.00 135.33 44.67 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA ASP A 44 " pdb=" CB ASP A 44 " pdb=" CG ASP A 44 " pdb=" OD1 ASP A 44 " ideal model delta sinusoidal sigma weight residual -30.00 -85.64 55.64 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 5221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 898 0.026 - 0.052: 303 0.052 - 0.078: 145 0.078 - 0.104: 56 0.104 - 0.130: 18 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA ILE B 129 " pdb=" N ILE B 129 " pdb=" C ILE B 129 " pdb=" CB ILE B 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE A 129 " pdb=" N ILE A 129 " pdb=" C ILE A 129 " pdb=" CB ILE A 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA VAL A 261 " pdb=" N VAL A 261 " pdb=" C VAL A 261 " pdb=" CB VAL A 261 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1417 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 646 " 0.014 2.00e-02 2.50e+03 1.53e-02 4.08e+00 pdb=" CG PHE A 646 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE A 646 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 646 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 646 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 646 " -0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 646 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 492 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C GLU B 492 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU B 492 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 493 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 305 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO A 306 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 306 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 306 " -0.026 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 899 2.75 - 3.29: 8168 3.29 - 3.82: 14286 3.82 - 4.36: 15239 4.36 - 4.90: 27932 Nonbonded interactions: 66524 Sorted by model distance: nonbonded pdb=" OG SER A 108 " pdb=" OD2 ASP A 231 " model vdw 2.211 3.040 nonbonded pdb=" O GLU B 599 " pdb=" NE ARG B 602 " model vdw 2.232 3.120 nonbonded pdb=" O SER B 596 " pdb=" OG SER B 596 " model vdw 2.395 3.040 nonbonded pdb=" OG1 THR A 240 " pdb=" OD1 ASN B 321 " model vdw 2.400 3.040 nonbonded pdb=" O SER B 548 " pdb=" OG1 THR B 552 " model vdw 2.405 3.040 ... (remaining 66519 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.450 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 : 0.002 0.022 8830 Z= 0.114 Angle : 0.450 6.377 11980 Z= 0.230 Chirality : 0.036 0.130 1420 Planarity : 0.003 0.047 1460 Dihedral : 17.901 89.612 3200 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.11 % Allowed : 27.09 % Favored : 72.81 % 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: 1.70 (0.26), residues: 1082 helix: 2.22 (0.21), residues: 638 sheet: 1.47 (0.62), residues: 80 loop : -1.00 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 505 HIS 0.002 0.000 HIS B 219 PHE 0.021 0.001 PHE A 647 TYR 0.004 0.001 TYR A 430 ARG 0.006 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.969 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.2421 time to fit residues: 36.6520 Evaluate side-chains 110 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 0.0980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN B 147 GLN B 484 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8830 Z= 0.277 Angle : 0.544 6.276 11980 Z= 0.275 Chirality : 0.041 0.143 1420 Planarity : 0.004 0.042 1460 Dihedral : 9.927 88.237 1265 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.36 % Allowed : 25.59 % Favored : 72.06 % 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 (0.26), residues: 1082 helix: 1.81 (0.20), residues: 662 sheet: 1.17 (0.59), residues: 80 loop : -0.98 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 447 HIS 0.004 0.001 HIS B 154 PHE 0.019 0.001 PHE A 499 TYR 0.013 0.002 TYR B 594 ARG 0.007 0.001 ARG B 602 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.812 Fit side-chains REVERT: A 573 MET cc_start: 0.7271 (mmt) cc_final: 0.6886 (mmt) REVERT: B 265 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.6657 (t-170) outliers start: 22 outliers final: 13 residues processed: 125 average time/residue: 0.2366 time to fit residues: 39.8902 Evaluate side-chains 118 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 0.0040 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 0.0570 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 overall best weight: 0.3710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 265 HIS A 454 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8830 Z= 0.117 Angle : 0.448 5.333 11980 Z= 0.227 Chirality : 0.037 0.128 1420 Planarity : 0.003 0.037 1460 Dihedral : 9.340 89.400 1262 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.61 % Allowed : 25.59 % Favored : 72.81 % 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 (0.26), residues: 1082 helix: 2.06 (0.21), residues: 660 sheet: 1.22 (0.58), residues: 80 loop : -0.98 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 505 HIS 0.004 0.001 HIS A 265 PHE 0.009 0.001 PHE B 441 TYR 0.004 0.001 TYR A 430 ARG 0.005 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.956 Fit side-chains REVERT: A 310 MET cc_start: 0.4695 (ppp) cc_final: 0.3753 (ppp) REVERT: A 573 MET cc_start: 0.7458 (mmt) cc_final: 0.6963 (mmt) REVERT: A 603 MET cc_start: 0.5036 (mpp) cc_final: 0.3905 (mtt) REVERT: B 265 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.6728 (t-170) REVERT: B 310 MET cc_start: 0.4067 (ppp) cc_final: 0.3125 (ppp) outliers start: 15 outliers final: 9 residues processed: 127 average time/residue: 0.2551 time to fit residues: 43.2372 Evaluate side-chains 114 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.0010 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 484 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8830 Z= 0.248 Angle : 0.514 6.002 11980 Z= 0.259 Chirality : 0.039 0.133 1420 Planarity : 0.003 0.037 1460 Dihedral : 9.212 89.464 1262 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.36 % Allowed : 24.73 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.26), residues: 1082 helix: 1.84 (0.21), residues: 662 sheet: 0.97 (0.57), residues: 80 loop : -0.95 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 505 HIS 0.009 0.001 HIS A 265 PHE 0.017 0.001 PHE A 499 TYR 0.016 0.001 TYR B 594 ARG 0.005 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.051 Fit side-chains REVERT: A 97 MET cc_start: 0.7689 (tpt) cc_final: 0.7281 (tpt) REVERT: A 310 MET cc_start: 0.4767 (ppp) cc_final: 0.3749 (ppp) REVERT: A 573 MET cc_start: 0.7326 (mmt) cc_final: 0.6862 (mmt) REVERT: A 603 MET cc_start: 0.5122 (mpp) cc_final: 0.3965 (mtt) REVERT: B 265 HIS cc_start: 0.7778 (OUTLIER) cc_final: 0.6739 (t-170) REVERT: B 310 MET cc_start: 0.4019 (ppp) cc_final: 0.3278 (ppp) outliers start: 22 outliers final: 16 residues processed: 120 average time/residue: 0.2645 time to fit residues: 42.0875 Evaluate side-chains 116 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8830 Z= 0.380 Angle : 0.619 6.870 11980 Z= 0.311 Chirality : 0.043 0.179 1420 Planarity : 0.004 0.043 1460 Dihedral : 9.346 89.154 1262 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.96 % Allowed : 23.98 % Favored : 72.06 % 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: 0.86 (0.26), residues: 1082 helix: 1.36 (0.20), residues: 662 sheet: 0.56 (0.58), residues: 82 loop : -0.96 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 505 HIS 0.004 0.001 HIS B 154 PHE 0.022 0.002 PHE A 499 TYR 0.027 0.002 TYR B 594 ARG 0.004 0.001 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.935 Fit side-chains REVERT: A 97 MET cc_start: 0.7803 (tpt) cc_final: 0.7512 (ttm) REVERT: A 196 ASN cc_start: 0.8131 (t0) cc_final: 0.7883 (t0) REVERT: A 265 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.6870 (t-170) REVERT: A 310 MET cc_start: 0.4755 (ppp) cc_final: 0.3795 (ppp) REVERT: A 603 MET cc_start: 0.4629 (mpp) cc_final: 0.4212 (tmm) REVERT: B 196 ASN cc_start: 0.8131 (t0) cc_final: 0.7874 (t0) REVERT: B 224 ASN cc_start: 0.7818 (m-40) cc_final: 0.7405 (p0) REVERT: B 265 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.6864 (t-170) REVERT: B 528 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8003 (mp) outliers start: 37 outliers final: 22 residues processed: 148 average time/residue: 0.2873 time to fit residues: 54.4536 Evaluate side-chains 140 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN B 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8830 Z= 0.204 Angle : 0.512 6.058 11980 Z= 0.259 Chirality : 0.039 0.134 1420 Planarity : 0.003 0.039 1460 Dihedral : 9.083 86.063 1262 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.89 % Allowed : 25.48 % Favored : 71.63 % 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: 1.02 (0.26), residues: 1082 helix: 1.57 (0.20), residues: 662 sheet: 0.43 (0.56), residues: 82 loop : -1.04 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 447 HIS 0.003 0.001 HIS B 427 PHE 0.014 0.001 PHE A 499 TYR 0.014 0.001 TYR B 594 ARG 0.008 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.993 Fit side-chains REVERT: A 97 MET cc_start: 0.7827 (tpt) cc_final: 0.7504 (ttm) REVERT: A 196 ASN cc_start: 0.8083 (t0) cc_final: 0.7801 (t0) REVERT: A 265 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.7028 (t-170) REVERT: A 310 MET cc_start: 0.4732 (ppp) cc_final: 0.3755 (ppp) REVERT: A 492 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6980 (tp30) REVERT: A 603 MET cc_start: 0.5419 (mpp) cc_final: 0.4804 (tmm) REVERT: B 196 ASN cc_start: 0.8081 (t0) cc_final: 0.7783 (t0) REVERT: B 224 ASN cc_start: 0.7833 (m-40) cc_final: 0.7380 (p0) REVERT: B 265 HIS cc_start: 0.7787 (OUTLIER) cc_final: 0.6673 (t-170) REVERT: B 310 MET cc_start: 0.4465 (ppp) cc_final: 0.3696 (ppp) REVERT: B 528 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7988 (mp) outliers start: 27 outliers final: 17 residues processed: 139 average time/residue: 0.2718 time to fit residues: 49.2622 Evaluate side-chains 135 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8830 Z= 0.361 Angle : 0.610 7.332 11980 Z= 0.308 Chirality : 0.043 0.155 1420 Planarity : 0.004 0.044 1460 Dihedral : 9.192 87.231 1262 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.32 % Allowed : 24.52 % Favored : 72.16 % 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: 0.72 (0.25), residues: 1082 helix: 1.32 (0.20), residues: 660 sheet: 0.27 (0.56), residues: 82 loop : -1.08 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 447 HIS 0.004 0.001 HIS B 427 PHE 0.021 0.002 PHE A 499 TYR 0.020 0.002 TYR B 594 ARG 0.008 0.001 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.858 Fit side-chains REVERT: A 97 MET cc_start: 0.7743 (tpt) cc_final: 0.7428 (ttm) REVERT: A 196 ASN cc_start: 0.8056 (t0) cc_final: 0.7752 (t0) REVERT: A 265 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.6944 (t-170) REVERT: A 310 MET cc_start: 0.4954 (ppp) cc_final: 0.3970 (ppp) REVERT: A 397 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7366 (mp) REVERT: A 492 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6810 (tp30) REVERT: A 573 MET cc_start: 0.7306 (mmt) cc_final: 0.6835 (mmt) REVERT: A 603 MET cc_start: 0.4949 (mpp) cc_final: 0.4438 (tmm) REVERT: B 168 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7924 (tpp80) REVERT: B 196 ASN cc_start: 0.8100 (t0) cc_final: 0.7776 (t0) REVERT: B 224 ASN cc_start: 0.7789 (m-40) cc_final: 0.7335 (p0) REVERT: B 265 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.6814 (t-170) REVERT: B 462 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: B 528 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8007 (mp) outliers start: 31 outliers final: 22 residues processed: 140 average time/residue: 0.2643 time to fit residues: 48.1615 Evaluate side-chains 141 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 96 optimal weight: 0.0870 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8830 Z= 0.158 Angle : 0.493 6.005 11980 Z= 0.249 Chirality : 0.038 0.126 1420 Planarity : 0.003 0.043 1460 Dihedral : 8.907 84.309 1262 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.25 % Allowed : 25.80 % Favored : 71.95 % 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: 1.14 (0.26), residues: 1082 helix: 1.72 (0.20), residues: 660 sheet: 0.35 (0.56), residues: 82 loop : -1.05 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 505 HIS 0.003 0.001 HIS B 219 PHE 0.012 0.001 PHE A 441 TYR 0.010 0.001 TYR B 594 ARG 0.007 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 1.006 Fit side-chains REVERT: A 97 MET cc_start: 0.7895 (tpt) cc_final: 0.7527 (ttm) REVERT: A 171 ARG cc_start: 0.5723 (mmm160) cc_final: 0.5476 (mmm160) REVERT: A 196 ASN cc_start: 0.8115 (t0) cc_final: 0.7836 (t0) REVERT: A 310 MET cc_start: 0.4927 (ppp) cc_final: 0.3934 (ppp) REVERT: A 492 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6818 (tp30) REVERT: A 603 MET cc_start: 0.5550 (mpp) cc_final: 0.4976 (tmm) REVERT: B 168 ARG cc_start: 0.8161 (tpp80) cc_final: 0.7888 (tpp80) REVERT: B 196 ASN cc_start: 0.8148 (t0) cc_final: 0.7855 (t0) REVERT: B 265 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.6641 (t-170) REVERT: B 310 MET cc_start: 0.4621 (ppp) cc_final: 0.3792 (ppp) REVERT: B 462 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: B 528 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7952 (mp) outliers start: 21 outliers final: 14 residues processed: 136 average time/residue: 0.2640 time to fit residues: 47.2296 Evaluate side-chains 131 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 0.0670 chunk 63 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8830 Z= 0.193 Angle : 0.508 5.884 11980 Z= 0.256 Chirality : 0.038 0.142 1420 Planarity : 0.004 0.045 1460 Dihedral : 8.855 85.518 1262 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.14 % Allowed : 25.80 % Favored : 72.06 % 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: 1.16 (0.26), residues: 1082 helix: 1.73 (0.20), residues: 662 sheet: 0.34 (0.56), residues: 82 loop : -1.06 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 505 HIS 0.003 0.001 HIS A 265 PHE 0.013 0.001 PHE B 275 TYR 0.011 0.001 TYR B 594 ARG 0.007 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.994 Fit side-chains REVERT: A 90 MET cc_start: 0.6662 (ptp) cc_final: 0.6421 (ptp) REVERT: A 97 MET cc_start: 0.7909 (tpt) cc_final: 0.7578 (ttm) REVERT: A 171 ARG cc_start: 0.5790 (mmm160) cc_final: 0.5506 (mmm160) REVERT: A 196 ASN cc_start: 0.8187 (t0) cc_final: 0.7770 (t0) REVERT: A 265 HIS cc_start: 0.7484 (OUTLIER) cc_final: 0.7015 (t-170) REVERT: A 270 ARG cc_start: 0.7466 (mmm160) cc_final: 0.7256 (mmp80) REVERT: A 310 MET cc_start: 0.4955 (ppp) cc_final: 0.3984 (ppp) REVERT: A 492 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6817 (tp30) REVERT: A 603 MET cc_start: 0.5760 (mpp) cc_final: 0.5052 (tmm) REVERT: B 168 ARG cc_start: 0.8194 (tpp80) cc_final: 0.7934 (tpp80) REVERT: B 196 ASN cc_start: 0.8181 (t0) cc_final: 0.7909 (t0) REVERT: B 265 HIS cc_start: 0.7728 (OUTLIER) cc_final: 0.6777 (t-170) REVERT: B 310 MET cc_start: 0.4649 (ppp) cc_final: 0.3796 (ppp) REVERT: B 462 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: B 528 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7965 (mp) outliers start: 20 outliers final: 15 residues processed: 132 average time/residue: 0.2719 time to fit residues: 47.2235 Evaluate side-chains 134 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8830 Z= 0.168 Angle : 0.494 6.092 11980 Z= 0.249 Chirality : 0.038 0.136 1420 Planarity : 0.003 0.044 1460 Dihedral : 8.776 85.272 1262 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.14 % Allowed : 26.45 % Favored : 71.41 % 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: 1.23 (0.26), residues: 1082 helix: 1.84 (0.20), residues: 660 sheet: 0.14 (0.56), residues: 80 loop : -1.05 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 505 HIS 0.002 0.001 HIS B 265 PHE 0.012 0.001 PHE B 275 TYR 0.010 0.001 TYR B 594 ARG 0.007 0.000 ARG B 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.948 Fit side-chains REVERT: A 90 MET cc_start: 0.6649 (ptp) cc_final: 0.6357 (ptp) REVERT: A 97 MET cc_start: 0.7898 (tpt) cc_final: 0.7567 (ttm) REVERT: A 171 ARG cc_start: 0.5768 (mmm160) cc_final: 0.5554 (mmm160) REVERT: A 196 ASN cc_start: 0.8096 (t0) cc_final: 0.7804 (t0) REVERT: A 270 ARG cc_start: 0.7458 (mmm160) cc_final: 0.7230 (mmp80) REVERT: A 310 MET cc_start: 0.4965 (ppp) cc_final: 0.3987 (ppp) REVERT: A 492 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: A 603 MET cc_start: 0.5764 (mpp) cc_final: 0.5126 (tmm) REVERT: B 168 ARG cc_start: 0.8174 (tpp80) cc_final: 0.7968 (tpp80) REVERT: B 196 ASN cc_start: 0.8182 (t0) cc_final: 0.7920 (t0) REVERT: B 265 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.6635 (t-170) REVERT: B 310 MET cc_start: 0.4584 (ppp) cc_final: 0.3702 (ppp) REVERT: B 462 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: B 528 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8008 (mp) outliers start: 20 outliers final: 15 residues processed: 131 average time/residue: 0.2676 time to fit residues: 45.8118 Evaluate side-chains 128 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.0270 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.187415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.149658 restraints weight = 10612.645| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.38 r_work: 0.3602 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8830 Z= 0.168 Angle : 0.491 5.896 11980 Z= 0.247 Chirality : 0.038 0.133 1420 Planarity : 0.003 0.044 1460 Dihedral : 8.723 85.992 1262 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.14 % Allowed : 26.55 % Favored : 71.31 % 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: 1.26 (0.26), residues: 1082 helix: 1.88 (0.21), residues: 660 sheet: 0.12 (0.55), residues: 80 loop : -1.06 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 505 HIS 0.002 0.001 HIS A 265 PHE 0.013 0.001 PHE B 275 TYR 0.010 0.001 TYR B 594 ARG 0.008 0.000 ARG A 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.08 seconds wall clock time: 34 minutes 39.33 seconds (2079.33 seconds total)