Starting phenix.real_space_refine on Fri Nov 15 07:27:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i39_35146/11_2024/8i39_35146_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i39_35146/11_2024/8i39_35146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i39_35146/11_2024/8i39_35146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i39_35146/11_2024/8i39_35146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i39_35146/11_2024/8i39_35146_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i39_35146/11_2024/8i39_35146_trim.cif" } resolution = 2.85 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= 0.000 sd= 0.184 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 5495 2.51 5 N 1398 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8413 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4197 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 17, 'TRANS': 520} Chain breaks: 4 Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'A8S': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 7.73, per 1000 atoms: 0.92 Number of scatterers: 8413 At special positions: 0 Unit cell: (77.35, 103.53, 119, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1470 8.00 N 1398 7.00 C 5495 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: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 50.2% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 106 through 115 removed outlier: 3.541A pdb=" N LEU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.595A pdb=" N LEU A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 189 Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.986A pdb=" N GLU A 195 " --> pdb=" O THR A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.618A pdb=" N SER A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.809A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 274 removed outlier: 3.543A pdb=" N GLN A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 300 removed outlier: 4.728A pdb=" N MET A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.634A pdb=" N THR A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 397 removed outlier: 3.961A pdb=" N PHE A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 removed outlier: 3.585A pdb=" N ARG A 402 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS A 403 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 438 through 455 removed outlier: 3.914A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.745A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 492 removed outlier: 4.031A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.524A pdb=" N SER A 498 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 541 removed outlier: 3.874A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 551 removed outlier: 3.766A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 561 removed outlier: 3.581A pdb=" N ALA A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.547A pdb=" N LYS A 577 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 594 removed outlier: 3.538A pdb=" N CYS A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 658 removed outlier: 3.576A pdb=" N ALA A 653 " --> pdb=" O TYR A 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 removed outlier: 3.541A pdb=" N LEU B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 169 removed outlier: 3.595A pdb=" N LEU B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.986A pdb=" N GLU B 195 " --> pdb=" O THR B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.618A pdb=" N SER B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 255 removed outlier: 3.809A pdb=" N VAL B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 274 removed outlier: 3.542A pdb=" N GLN B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 removed outlier: 4.728A pdb=" N MET B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU B 300 " --> pdb=" O MET B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 322 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.634A pdb=" N THR B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 397 removed outlier: 3.961A pdb=" N PHE B 387 " --> pdb=" O ILE B 383 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS B 391 " --> pdb=" O PHE B 387 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 removed outlier: 3.586A pdb=" N ARG B 402 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS B 403 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 438 through 455 removed outlier: 3.914A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 472 removed outlier: 3.745A pdb=" N SER B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 492 removed outlier: 4.031A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 500 removed outlier: 3.524A pdb=" N SER B 498 " --> pdb=" O VAL B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 541 removed outlier: 3.875A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.766A pdb=" N ILE B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 561 removed outlier: 3.581A pdb=" N ALA B 557 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 578 removed outlier: 3.547A pdb=" N LYS B 577 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 594 removed outlier: 3.538A pdb=" N CYS B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 658 removed outlier: 3.576A pdb=" N ALA B 653 " --> pdb=" O TYR B 649 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 88 removed outlier: 5.317A pdb=" N SER A 85 " --> pdb=" O TYR A 47 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR A 47 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP A 44 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LYS A 126 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.141A pdb=" N GLY A 143 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASP A 231 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL A 145 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N SER A 263 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU A 230 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 88 removed outlier: 5.316A pdb=" N SER B 85 " --> pdb=" O TYR B 47 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR B 47 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP B 44 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LYS B 126 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.140A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASP B 231 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 145 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N SER B 263 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU B 230 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N MET B 97 " --> pdb=" O THR B 262 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 840 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: 2.32 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1279 1.30 - 1.42: 2251 1.42 - 1.55: 4961 1.55 - 1.68: 12 1.68 - 1.81: 84 Bond restraints: 8587 Sorted by residual: bond pdb=" C1 A8S B 701 " pdb=" O11 A8S B 701 " ideal model delta sigma weight residual 1.250 1.167 0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C3 A8S B 701 " pdb=" C4 A8S B 701 " ideal model delta sigma weight residual 1.463 1.381 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C1 A8S B 701 " pdb=" O12 A8S B 701 " ideal model delta sigma weight residual 1.249 1.173 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C1 A8S B 701 " pdb=" C2 A8S B 701 " ideal model delta sigma weight residual 1.512 1.457 0.055 2.00e-02 2.50e+03 7.63e+00 bond pdb=" CB GLU A 183 " pdb=" CG GLU A 183 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.29e+00 ... (remaining 8582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 11506 2.94 - 5.87: 108 5.87 - 8.81: 16 8.81 - 11.75: 5 11.75 - 14.68: 6 Bond angle restraints: 11641 Sorted by residual: angle pdb=" CA GLU B 183 " pdb=" CB GLU B 183 " pdb=" CG GLU B 183 " ideal model delta sigma weight residual 114.10 128.78 -14.68 2.00e+00 2.50e-01 5.39e+01 angle pdb=" CA GLU A 183 " pdb=" CB GLU A 183 " pdb=" CG GLU A 183 " ideal model delta sigma weight residual 114.10 128.74 -14.64 2.00e+00 2.50e-01 5.36e+01 angle pdb=" CA GLU A 188 " pdb=" CB GLU A 188 " pdb=" CG GLU A 188 " ideal model delta sigma weight residual 114.10 127.95 -13.85 2.00e+00 2.50e-01 4.79e+01 angle pdb=" CA GLU B 188 " pdb=" CB GLU B 188 " pdb=" CG GLU B 188 " ideal model delta sigma weight residual 114.10 127.94 -13.84 2.00e+00 2.50e-01 4.79e+01 angle pdb=" N HIS A 403 " pdb=" CA HIS A 403 " pdb=" C HIS A 403 " ideal model delta sigma weight residual 114.04 105.48 8.56 1.24e+00 6.50e-01 4.77e+01 ... (remaining 11636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.95: 4722 19.95 - 39.91: 275 39.91 - 59.86: 40 59.86 - 79.81: 9 79.81 - 99.76: 12 Dihedral angle restraints: 5058 sinusoidal: 1976 harmonic: 3082 Sorted by residual: dihedral pdb=" CA MET B 310 " pdb=" C MET B 310 " pdb=" N ASN B 311 " pdb=" CA ASN B 311 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA MET A 310 " pdb=" C MET A 310 " pdb=" N ASN A 311 " pdb=" CA ASN A 311 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LYS A 133 " pdb=" C LYS A 133 " pdb=" N ILE A 134 " pdb=" CA ILE A 134 " ideal model delta harmonic sigma weight residual -180.00 -157.72 -22.28 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 5055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1222 0.073 - 0.146: 156 0.146 - 0.219: 8 0.219 - 0.292: 0 0.292 - 0.364: 1 Chirality restraints: 1387 Sorted by residual: chirality pdb=" C7 A8S B 701 " pdb=" C12 A8S B 701 " pdb=" C8 A8S B 701 " pdb=" O7 A8S B 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.32 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA GLU A 188 " pdb=" N GLU A 188 " pdb=" C GLU A 188 " pdb=" CB GLU A 188 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA GLU B 188 " pdb=" N GLU B 188 " pdb=" C GLU B 188 " pdb=" CB GLU B 188 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 1384 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 A8S B 701 " -0.244 2.00e-02 2.50e+03 2.51e-01 6.31e+02 pdb=" C4 A8S B 701 " 0.202 2.00e-02 2.50e+03 pdb=" C5 A8S B 701 " 0.296 2.00e-02 2.50e+03 pdb=" C7 A8S B 701 " -0.254 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 A8S B 701 " -0.128 2.00e-02 2.50e+03 1.07e-01 1.42e+02 pdb=" C2 A8S B 701 " 0.175 2.00e-02 2.50e+03 pdb=" C3 A8S B 701 " 0.030 2.00e-02 2.50e+03 pdb=" C4 A8S B 701 " 0.016 2.00e-02 2.50e+03 pdb=" C6 A8S B 701 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 450 " 0.045 5.00e-02 4.00e+02 6.74e-02 7.26e+00 pdb=" N PRO B 451 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 451 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 451 " 0.037 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 138 2.67 - 3.23: 8252 3.23 - 3.79: 11946 3.79 - 4.34: 19065 4.34 - 4.90: 29642 Nonbonded interactions: 69043 Sorted by model distance: nonbonded pdb=" O TYR B 298 " pdb=" OG SER B 301 " model vdw 2.116 3.040 nonbonded pdb=" O TYR A 298 " pdb=" OG SER A 301 " model vdw 2.117 3.040 nonbonded pdb=" O PRO A 102 " pdb=" OG SER A 105 " model vdw 2.136 3.040 nonbonded pdb=" O PRO B 102 " pdb=" OG SER B 105 " model vdw 2.137 3.040 nonbonded pdb=" OE2 GLU B 300 " pdb=" OG SER B 305 " model vdw 2.209 3.040 ... (remaining 69038 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' and resid 36 through 660) } 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.210 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 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:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 : 0.009 0.083 8587 Z= 0.550 Angle : 0.901 14.682 11641 Z= 0.504 Chirality : 0.050 0.364 1387 Planarity : 0.009 0.251 1424 Dihedral : 14.167 99.764 3078 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.22 % Allowed : 4.81 % Favored : 94.97 % 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: -5.71 (0.19), residues: 1056 helix: -4.67 (0.10), residues: 572 sheet: -2.41 (0.57), residues: 56 loop : -2.36 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 426 HIS 0.011 0.003 HIS B 427 PHE 0.028 0.002 PHE B 499 TYR 0.027 0.003 TYR A 475 ARG 0.008 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7579 (ttm) cc_final: 0.7282 (ttm) REVERT: A 148 ASP cc_start: 0.7773 (m-30) cc_final: 0.7547 (m-30) REVERT: A 180 ARG cc_start: 0.7258 (mtp180) cc_final: 0.6950 (mtm180) REVERT: A 224 ASN cc_start: 0.7914 (t0) cc_final: 0.7490 (t0) REVERT: A 227 LEU cc_start: 0.8199 (tp) cc_final: 0.7943 (tp) REVERT: A 424 MET cc_start: 0.7713 (mmm) cc_final: 0.7447 (mmm) REVERT: A 430 TYR cc_start: 0.7900 (p90) cc_final: 0.7597 (p90) REVERT: A 469 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7494 (mt-10) REVERT: A 474 MET cc_start: 0.8257 (ttt) cc_final: 0.7957 (ttt) REVERT: A 475 TYR cc_start: 0.8743 (p90) cc_final: 0.8529 (p90) REVERT: A 555 MET cc_start: 0.8615 (mmm) cc_final: 0.8270 (mmm) REVERT: A 568 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7568 (mmmt) REVERT: B 97 MET cc_start: 0.7163 (ttm) cc_final: 0.6756 (ttm) REVERT: B 139 LEU cc_start: 0.8547 (mt) cc_final: 0.8343 (tp) REVERT: B 180 ARG cc_start: 0.7293 (mtp180) cc_final: 0.7017 (mtm180) REVERT: B 270 ARG cc_start: 0.6542 (mtt180) cc_final: 0.6310 (mtt180) REVERT: B 291 LYS cc_start: 0.7537 (mmmt) cc_final: 0.7067 (tptp) REVERT: B 430 TYR cc_start: 0.7819 (p90) cc_final: 0.7342 (p90) REVERT: B 474 MET cc_start: 0.8242 (ttt) cc_final: 0.7924 (ttt) REVERT: B 506 MET cc_start: 0.7258 (mtp) cc_final: 0.7027 (mtp) REVERT: B 545 LYS cc_start: 0.7742 (mptt) cc_final: 0.7504 (pttm) REVERT: B 555 MET cc_start: 0.8237 (mmm) cc_final: 0.7888 (mmm) REVERT: B 568 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7812 (mmmt) outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 1.3539 time to fit residues: 213.0338 Evaluate side-chains 114 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 321 ASN A 454 ASN B 130 ASN B 321 ASN B 325 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8587 Z= 0.203 Angle : 0.622 5.294 11641 Z= 0.322 Chirality : 0.042 0.143 1387 Planarity : 0.005 0.038 1424 Dihedral : 6.759 44.626 1188 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.30 % Allowed : 9.08 % Favored : 88.62 % 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: -4.47 (0.22), residues: 1056 helix: -3.28 (0.15), residues: 634 sheet: -2.10 (0.55), residues: 76 loop : -2.02 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 447 HIS 0.005 0.001 HIS B 427 PHE 0.021 0.001 PHE A 144 TYR 0.021 0.001 TYR B 475 ARG 0.007 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6966 (tmm) REVERT: A 97 MET cc_start: 0.7415 (ttm) cc_final: 0.7194 (ttm) REVERT: A 232 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: A 291 LYS cc_start: 0.7428 (mmmt) cc_final: 0.6158 (ttpp) REVERT: A 469 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7123 (mt-10) REVERT: A 474 MET cc_start: 0.8013 (ttt) cc_final: 0.7676 (ttt) REVERT: A 475 TYR cc_start: 0.8414 (p90) cc_final: 0.8060 (p90) REVERT: A 555 MET cc_start: 0.8411 (mmm) cc_final: 0.8077 (mmm) REVERT: A 576 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6921 (ttm) REVERT: B 97 MET cc_start: 0.7017 (ttm) cc_final: 0.6716 (ttm) REVERT: B 139 LEU cc_start: 0.8708 (mt) cc_final: 0.8466 (tp) REVERT: B 158 ARG cc_start: 0.7403 (ttp80) cc_final: 0.7070 (ttp80) REVERT: B 180 ARG cc_start: 0.7101 (mtp180) cc_final: 0.6856 (mtm180) REVERT: B 291 LYS cc_start: 0.7569 (mmmt) cc_final: 0.7151 (tptp) REVERT: B 395 HIS cc_start: 0.7548 (t-170) cc_final: 0.6799 (m90) REVERT: B 430 TYR cc_start: 0.7674 (p90) cc_final: 0.7416 (p90) REVERT: B 474 MET cc_start: 0.7743 (ttt) cc_final: 0.7536 (ttt) REVERT: B 545 LYS cc_start: 0.7705 (mptt) cc_final: 0.7491 (pttm) REVERT: B 555 MET cc_start: 0.8172 (mmm) cc_final: 0.7907 (mmm) REVERT: B 658 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7212 (mtm180) outliers start: 21 outliers final: 6 residues processed: 151 average time/residue: 1.2947 time to fit residues: 207.7855 Evaluate side-chains 129 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 658 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 65 optimal weight: 0.1980 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.7455 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8587 Z= 0.319 Angle : 0.640 7.189 11641 Z= 0.326 Chirality : 0.044 0.147 1387 Planarity : 0.005 0.039 1424 Dihedral : 5.636 36.712 1188 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.83 % Allowed : 11.38 % Favored : 84.79 % 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: -3.56 (0.23), residues: 1056 helix: -2.44 (0.18), residues: 624 sheet: -1.90 (0.52), residues: 82 loop : -1.87 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 426 HIS 0.006 0.002 HIS A 403 PHE 0.021 0.002 PHE B 42 TYR 0.041 0.002 TYR B 475 ARG 0.007 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7313 (ttm) cc_final: 0.7085 (ttm) REVERT: A 188 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7814 (pp20) REVERT: A 280 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6602 (mm) REVERT: A 291 LYS cc_start: 0.7681 (mmmt) cc_final: 0.7413 (tptp) REVERT: A 430 TYR cc_start: 0.7753 (p90) cc_final: 0.7380 (p90) REVERT: A 474 MET cc_start: 0.8112 (ttt) cc_final: 0.7869 (ttt) REVERT: A 555 MET cc_start: 0.8388 (mmm) cc_final: 0.8110 (mmp) REVERT: A 576 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.7011 (ttm) REVERT: B 139 LEU cc_start: 0.8781 (mt) cc_final: 0.8529 (tp) REVERT: B 180 ARG cc_start: 0.7120 (mtp180) cc_final: 0.6918 (mtm180) REVERT: B 276 ASP cc_start: 0.7497 (m-30) cc_final: 0.7297 (m-30) REVERT: B 279 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7924 (tp) REVERT: B 291 LYS cc_start: 0.7563 (mmmt) cc_final: 0.7126 (tptp) REVERT: B 395 HIS cc_start: 0.7656 (t-170) cc_final: 0.6935 (m90) REVERT: B 474 MET cc_start: 0.8076 (ttt) cc_final: 0.7837 (ttt) REVERT: B 545 LYS cc_start: 0.7815 (mptt) cc_final: 0.7499 (pttm) REVERT: B 555 MET cc_start: 0.8362 (mmm) cc_final: 0.8093 (mmp) outliers start: 35 outliers final: 12 residues processed: 164 average time/residue: 1.2516 time to fit residues: 218.9417 Evaluate side-chains 139 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 27 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8587 Z= 0.227 Angle : 0.574 5.958 11641 Z= 0.294 Chirality : 0.042 0.142 1387 Planarity : 0.004 0.038 1424 Dihedral : 5.194 32.459 1188 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.94 % Allowed : 12.69 % Favored : 83.37 % 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: -2.81 (0.24), residues: 1056 helix: -1.80 (0.19), residues: 616 sheet: -1.45 (0.54), residues: 78 loop : -1.72 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 447 HIS 0.004 0.001 HIS A 434 PHE 0.013 0.001 PHE A 499 TYR 0.030 0.001 TYR B 475 ARG 0.006 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 176 ASP cc_start: 0.7672 (t0) cc_final: 0.6516 (p0) REVERT: A 280 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6572 (mm) REVERT: A 291 LYS cc_start: 0.7614 (mmmt) cc_final: 0.7266 (tptp) REVERT: A 310 MET cc_start: 0.7232 (ttm) cc_final: 0.7004 (ttp) REVERT: A 315 PHE cc_start: 0.8259 (t80) cc_final: 0.7997 (t80) REVERT: A 430 TYR cc_start: 0.7819 (p90) cc_final: 0.7357 (p90) REVERT: A 474 MET cc_start: 0.7919 (ttt) cc_final: 0.7654 (ttt) REVERT: A 555 MET cc_start: 0.8326 (mmm) cc_final: 0.8076 (mmp) REVERT: A 587 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7320 (mmp-170) REVERT: B 139 LEU cc_start: 0.8658 (mt) cc_final: 0.8443 (tp) REVERT: B 180 ARG cc_start: 0.7175 (mtp180) cc_final: 0.6910 (mtm180) REVERT: B 276 ASP cc_start: 0.7428 (m-30) cc_final: 0.7221 (m-30) REVERT: B 279 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7897 (tp) REVERT: B 291 LYS cc_start: 0.7472 (mmmt) cc_final: 0.7040 (tptp) REVERT: B 395 HIS cc_start: 0.7613 (t-170) cc_final: 0.6914 (m90) REVERT: B 474 MET cc_start: 0.7866 (ttt) cc_final: 0.7642 (ttt) REVERT: B 545 LYS cc_start: 0.7786 (mptt) cc_final: 0.7508 (pttm) REVERT: B 555 MET cc_start: 0.8273 (mmm) cc_final: 0.8044 (mmp) outliers start: 36 outliers final: 15 residues processed: 161 average time/residue: 1.2628 time to fit residues: 217.3183 Evaluate side-chains 145 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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: 0.7440 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8587 Z= 0.289 Angle : 0.611 6.784 11641 Z= 0.309 Chirality : 0.043 0.140 1387 Planarity : 0.005 0.052 1424 Dihedral : 5.171 33.318 1188 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.81 % Allowed : 13.35 % Favored : 81.84 % 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: -2.50 (0.25), residues: 1056 helix: -1.56 (0.20), residues: 612 sheet: -0.93 (0.58), residues: 66 loop : -1.67 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 426 HIS 0.005 0.001 HIS B 403 PHE 0.024 0.002 PHE B 42 TYR 0.042 0.002 TYR B 475 ARG 0.015 0.001 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 158 ARG cc_start: 0.7423 (ttp80) cc_final: 0.7075 (ttp80) REVERT: A 280 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6591 (mm) REVERT: A 291 LYS cc_start: 0.7569 (mmmt) cc_final: 0.7278 (tptp) REVERT: A 474 MET cc_start: 0.8014 (ttt) cc_final: 0.7778 (ttt) REVERT: A 576 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.7085 (ttt) REVERT: A 654 TYR cc_start: 0.8124 (t80) cc_final: 0.7897 (t80) REVERT: B 90 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7963 (tmt) REVERT: B 139 LEU cc_start: 0.8571 (mt) cc_final: 0.8364 (tp) REVERT: B 180 ARG cc_start: 0.7174 (mtp180) cc_final: 0.6906 (mtm180) REVERT: B 279 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7879 (tp) REVERT: B 280 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6485 (mt) REVERT: B 291 LYS cc_start: 0.7537 (mmmt) cc_final: 0.7100 (tptp) REVERT: B 395 HIS cc_start: 0.7636 (t-170) cc_final: 0.6921 (m90) REVERT: B 474 MET cc_start: 0.8017 (ttt) cc_final: 0.7783 (ttt) REVERT: B 545 LYS cc_start: 0.7813 (mptt) cc_final: 0.7453 (pttm) outliers start: 44 outliers final: 20 residues processed: 156 average time/residue: 1.1547 time to fit residues: 192.5413 Evaluate side-chains 142 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7375 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8587 Z= 0.158 Angle : 0.532 6.543 11641 Z= 0.269 Chirality : 0.040 0.141 1387 Planarity : 0.004 0.043 1424 Dihedral : 4.565 23.592 1188 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.39 % Allowed : 15.43 % Favored : 81.18 % 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: -1.93 (0.25), residues: 1056 helix: -1.10 (0.20), residues: 616 sheet: -0.67 (0.59), residues: 66 loop : -1.42 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.003 0.001 HIS A 434 PHE 0.011 0.001 PHE A 499 TYR 0.035 0.001 TYR B 475 ARG 0.010 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 280 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6548 (mm) REVERT: A 291 LYS cc_start: 0.7563 (mmmt) cc_final: 0.7251 (tptp) REVERT: A 505 TRP cc_start: 0.8041 (m100) cc_final: 0.7722 (m100) REVERT: A 555 MET cc_start: 0.8172 (mmm) cc_final: 0.7943 (mmm) REVERT: A 576 MET cc_start: 0.7192 (ttm) cc_final: 0.6984 (ttt) REVERT: A 587 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7287 (mmp-170) REVERT: B 90 MET cc_start: 0.8333 (tmm) cc_final: 0.7839 (tmt) REVERT: B 139 LEU cc_start: 0.8494 (mt) cc_final: 0.8251 (tp) REVERT: B 158 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7096 (ttp80) REVERT: B 279 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7928 (tp) REVERT: B 280 LEU cc_start: 0.7169 (tp) cc_final: 0.6691 (mt) REVERT: B 291 LYS cc_start: 0.7388 (mmmt) cc_final: 0.6963 (tptp) REVERT: B 395 HIS cc_start: 0.7601 (t-170) cc_final: 0.6894 (m90) REVERT: B 505 TRP cc_start: 0.8035 (m100) cc_final: 0.7715 (m100) REVERT: B 555 MET cc_start: 0.8128 (mmm) cc_final: 0.7920 (mmm) outliers start: 31 outliers final: 14 residues processed: 149 average time/residue: 1.1862 time to fit residues: 188.7704 Evaluate side-chains 137 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 102 optimal weight: 0.0050 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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: 0.7400 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8587 Z= 0.216 Angle : 0.564 8.758 11641 Z= 0.283 Chirality : 0.041 0.147 1387 Planarity : 0.004 0.050 1424 Dihedral : 4.599 27.046 1188 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.38 % Allowed : 15.43 % Favored : 80.20 % 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: 1056 helix: -0.92 (0.21), residues: 616 sheet: -0.51 (0.60), residues: 66 loop : -1.35 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.004 0.001 HIS A 434 PHE 0.022 0.001 PHE B 42 TYR 0.040 0.002 TYR A 475 ARG 0.012 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 158 ARG cc_start: 0.7417 (ttp80) cc_final: 0.7089 (ttp80) REVERT: A 280 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6606 (mm) REVERT: A 291 LYS cc_start: 0.7573 (mmmt) cc_final: 0.7250 (tptp) REVERT: A 505 TRP cc_start: 0.8081 (m100) cc_final: 0.7738 (m100) REVERT: A 555 MET cc_start: 0.8239 (mmm) cc_final: 0.8010 (mmm) REVERT: A 576 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.7043 (ttt) REVERT: B 90 MET cc_start: 0.8307 (tmm) cc_final: 0.7853 (tmt) REVERT: B 139 LEU cc_start: 0.8518 (mt) cc_final: 0.8296 (tp) REVERT: B 158 ARG cc_start: 0.7478 (ttp80) cc_final: 0.7000 (ttp80) REVERT: B 279 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7897 (tp) REVERT: B 280 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6619 (mt) REVERT: B 291 LYS cc_start: 0.7533 (mmmt) cc_final: 0.7192 (tptp) REVERT: B 395 HIS cc_start: 0.7598 (t-170) cc_final: 0.6893 (m90) REVERT: B 505 TRP cc_start: 0.8082 (m100) cc_final: 0.7746 (m100) REVERT: B 555 MET cc_start: 0.8153 (mmm) cc_final: 0.7943 (mmm) outliers start: 40 outliers final: 20 residues processed: 146 average time/residue: 1.1757 time to fit residues: 183.3835 Evaluate side-chains 142 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.7401 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8587 Z= 0.227 Angle : 0.578 8.524 11641 Z= 0.288 Chirality : 0.042 0.139 1387 Planarity : 0.004 0.051 1424 Dihedral : 4.599 35.264 1188 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.27 % Allowed : 15.65 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.26), residues: 1056 helix: -0.80 (0.21), residues: 616 sheet: -0.62 (0.56), residues: 76 loop : -1.28 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 447 HIS 0.004 0.001 HIS A 434 PHE 0.018 0.001 PHE A 275 TYR 0.040 0.002 TYR A 475 ARG 0.012 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8075 (tmm) REVERT: A 158 ARG cc_start: 0.7426 (ttp80) cc_final: 0.7085 (ttp80) REVERT: A 280 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6664 (mm) REVERT: A 291 LYS cc_start: 0.7566 (mmmt) cc_final: 0.7255 (tptp) REVERT: A 505 TRP cc_start: 0.8076 (m100) cc_final: 0.7739 (m100) REVERT: A 555 MET cc_start: 0.8218 (mmm) cc_final: 0.7967 (mmm) REVERT: A 576 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.7041 (ttt) REVERT: A 587 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7351 (mmp-170) REVERT: B 90 MET cc_start: 0.8357 (tmm) cc_final: 0.7909 (tmt) REVERT: B 139 LEU cc_start: 0.8504 (mt) cc_final: 0.8272 (tp) REVERT: B 158 ARG cc_start: 0.7488 (ttp80) cc_final: 0.7226 (ttp80) REVERT: B 279 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7850 (tp) REVERT: B 280 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6642 (mt) REVERT: B 291 LYS cc_start: 0.7477 (mmmt) cc_final: 0.7111 (tptp) REVERT: B 395 HIS cc_start: 0.7611 (t-170) cc_final: 0.6899 (m90) REVERT: B 505 TRP cc_start: 0.8070 (m100) cc_final: 0.7772 (m100) REVERT: B 555 MET cc_start: 0.8170 (mmm) cc_final: 0.7942 (mmm) outliers start: 39 outliers final: 22 residues processed: 144 average time/residue: 1.1652 time to fit residues: 179.1245 Evaluate side-chains 143 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7366 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8587 Z= 0.167 Angle : 0.554 10.157 11641 Z= 0.273 Chirality : 0.040 0.141 1387 Planarity : 0.004 0.054 1424 Dihedral : 4.351 29.912 1188 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.72 % Allowed : 16.41 % Favored : 79.87 % 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: -1.21 (0.26), residues: 1056 helix: -0.48 (0.21), residues: 616 sheet: -0.52 (0.57), residues: 76 loop : -1.17 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.003 0.001 HIS A 434 PHE 0.020 0.001 PHE A 275 TYR 0.038 0.001 TYR A 475 ARG 0.013 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.7422 (ttp80) cc_final: 0.7085 (ttp80) REVERT: A 237 LEU cc_start: 0.8613 (mt) cc_final: 0.8291 (tp) REVERT: A 280 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6635 (mm) REVERT: A 291 LYS cc_start: 0.7481 (mmmt) cc_final: 0.7160 (tptp) REVERT: A 505 TRP cc_start: 0.8090 (m100) cc_final: 0.7784 (m100) REVERT: A 555 MET cc_start: 0.8199 (mmm) cc_final: 0.7932 (mmm) REVERT: A 576 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6987 (ttt) REVERT: A 587 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7256 (mmp-170) REVERT: B 90 MET cc_start: 0.8393 (tmm) cc_final: 0.7928 (tmt) REVERT: B 158 ARG cc_start: 0.7468 (ttp80) cc_final: 0.7197 (ttp80) REVERT: B 280 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6693 (mt) REVERT: B 291 LYS cc_start: 0.7407 (mmmt) cc_final: 0.7036 (tptp) REVERT: B 395 HIS cc_start: 0.7594 (t-170) cc_final: 0.6891 (m90) REVERT: B 474 MET cc_start: 0.7386 (ttp) cc_final: 0.7021 (ttm) REVERT: B 505 TRP cc_start: 0.8083 (m100) cc_final: 0.7773 (m100) REVERT: B 555 MET cc_start: 0.8194 (mmm) cc_final: 0.7960 (mmm) outliers start: 34 outliers final: 19 residues processed: 149 average time/residue: 1.1087 time to fit residues: 177.1117 Evaluate side-chains 141 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.0000 chunk 89 optimal weight: 3.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- 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: 0.7364 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8587 Z= 0.174 Angle : 0.570 10.658 11641 Z= 0.279 Chirality : 0.040 0.168 1387 Planarity : 0.004 0.058 1424 Dihedral : 4.267 26.213 1188 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.74 % Allowed : 18.05 % Favored : 79.21 % 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: -1.05 (0.26), residues: 1056 helix: -0.34 (0.21), residues: 616 sheet: -0.52 (0.57), residues: 76 loop : -1.14 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.003 0.001 HIS A 434 PHE 0.025 0.001 PHE B 42 TYR 0.038 0.001 TYR B 475 ARG 0.014 0.001 ARG B 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8294 (tmm) cc_final: 0.8077 (tmt) REVERT: A 97 MET cc_start: 0.7612 (ttp) cc_final: 0.7259 (tmm) REVERT: A 158 ARG cc_start: 0.7423 (ttp80) cc_final: 0.7083 (ttp80) REVERT: A 237 LEU cc_start: 0.8638 (mt) cc_final: 0.8255 (tp) REVERT: A 280 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6645 (mm) REVERT: A 291 LYS cc_start: 0.7481 (mmmt) cc_final: 0.7154 (tptp) REVERT: A 474 MET cc_start: 0.7425 (ttp) cc_final: 0.7051 (ttm) REVERT: A 505 TRP cc_start: 0.8084 (m100) cc_final: 0.7785 (m100) REVERT: A 555 MET cc_start: 0.8188 (mmm) cc_final: 0.7983 (mmp) REVERT: A 576 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6992 (ttt) REVERT: A 587 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7282 (mmp-170) REVERT: B 90 MET cc_start: 0.8460 (tmm) cc_final: 0.7934 (tmt) REVERT: B 158 ARG cc_start: 0.7433 (ttp80) cc_final: 0.7149 (ttp80) REVERT: B 291 LYS cc_start: 0.7518 (mmmt) cc_final: 0.7153 (tptp) REVERT: B 395 HIS cc_start: 0.7590 (t-170) cc_final: 0.6889 (m90) REVERT: B 430 TYR cc_start: 0.7729 (p90) cc_final: 0.7522 (p90) REVERT: B 474 MET cc_start: 0.7419 (ttp) cc_final: 0.7048 (ttm) REVERT: B 505 TRP cc_start: 0.8078 (m100) cc_final: 0.7776 (m100) REVERT: B 555 MET cc_start: 0.8189 (mmm) cc_final: 0.7951 (mmm) outliers start: 25 outliers final: 19 residues processed: 142 average time/residue: 1.1189 time to fit residues: 170.2495 Evaluate side-chains 141 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.182853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120955 restraints weight = 8215.230| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.79 r_work: 0.3395 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8587 Z= 0.186 Angle : 0.585 11.326 11641 Z= 0.284 Chirality : 0.041 0.163 1387 Planarity : 0.005 0.059 1424 Dihedral : 4.248 24.604 1188 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.84 % Allowed : 18.05 % Favored : 79.10 % 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: -0.76 (0.27), residues: 1056 helix: -0.12 (0.21), residues: 604 sheet: -0.40 (0.56), residues: 78 loop : -0.94 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.003 0.001 HIS A 434 PHE 0.017 0.001 PHE B 275 TYR 0.038 0.001 TYR B 475 ARG 0.014 0.001 ARG B 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3524.06 seconds wall clock time: 63 minutes 54.31 seconds (3834.31 seconds total)