Starting phenix.real_space_refine on Fri Oct 11 03:23:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y8z_39064/10_2024/8y8z_39064.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y8z_39064/10_2024/8y8z_39064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y8z_39064/10_2024/8y8z_39064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y8z_39064/10_2024/8y8z_39064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y8z_39064/10_2024/8y8z_39064.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y8z_39064/10_2024/8y8z_39064.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.047 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 S 40 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 6092 2.51 5 N 1414 2.21 5 O 1532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 9082 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "E" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {' CL': 1, ' NA': 1, 'A1LX3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {' CL': 1, ' NA': 1, 'A1LX3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.72, per 1000 atoms: 0.63 Number of scatterers: 9082 At special positions: 0 Unit cell: (97.09, 113.15, 91.98, 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) Cl 2 17.00 S 40 16.00 Na 2 11.00 O 1532 8.00 N 1414 7.00 C 6092 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: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 0 sheets defined 74.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 61 through 74 removed outlier: 4.112A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 81 Processing helix chain 'A' and resid 81 through 90 Processing helix chain 'A' and resid 91 through 104 removed outlier: 4.250A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 106 through 120 Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.716A pdb=" N VAL A 127 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 128' Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.732A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 162 " --> pdb=" O TRP A 158 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.584A pdb=" N GLU A 223 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 252 removed outlier: 3.717A pdb=" N CYS A 240 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 244 " --> pdb=" O CYS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.734A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 removed outlier: 4.289A pdb=" N TYR A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 308 through 320 removed outlier: 4.037A pdb=" N PHE A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 332 removed outlier: 3.587A pdb=" N ILE A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 373 removed outlier: 3.608A pdb=" N SER A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 389 through 398 removed outlier: 4.248A pdb=" N GLU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.676A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 4.372A pdb=" N ARG A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 436 through 441' Processing helix chain 'A' and resid 441 through 457 Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 471 through 477 removed outlier: 3.998A pdb=" N ALA A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 Processing helix chain 'A' and resid 497 through 509 Processing helix chain 'A' and resid 514 through 523 removed outlier: 3.874A pdb=" N LYS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.969A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.765A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.951A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 598 through 603' Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.147A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 74 removed outlier: 3.916A pdb=" N LEU E 66 " --> pdb=" O LYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 81 removed outlier: 3.503A pdb=" N VAL E 79 " --> pdb=" O ASP E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 90 Processing helix chain 'E' and resid 91 through 104 removed outlier: 4.182A pdb=" N ILE E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Proline residue: E 97 - end of helix Processing helix chain 'E' and resid 106 through 120 Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.624A pdb=" N VAL E 127 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TRP E 128 " --> pdb=" O ALA E 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 124 through 128' Processing helix chain 'E' and resid 131 through 133 No H-bonds generated for 'chain 'E' and resid 131 through 133' Processing helix chain 'E' and resid 134 through 166 removed outlier: 3.677A pdb=" N GLY E 138 " --> pdb=" O PHE E 134 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY E 149 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR E 151 " --> pdb=" O TYR E 147 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL E 154 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR E 162 " --> pdb=" O TRP E 158 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.612A pdb=" N GLU E 223 " --> pdb=" O HIS E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 252 removed outlier: 3.676A pdb=" N CYS E 240 " --> pdb=" O GLN E 236 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL E 244 " --> pdb=" O CYS E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.820A pdb=" N SER E 259 " --> pdb=" O GLY E 255 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE E 265 " --> pdb=" O LYS E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 removed outlier: 4.248A pdb=" N TYR E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE E 272 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR E 283 " --> pdb=" O VAL E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 295 Processing helix chain 'E' and resid 306 through 320 removed outlier: 4.978A pdb=" N ALA E 312 " --> pdb=" O TRP E 308 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN E 314 " --> pdb=" O ASP E 310 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE E 316 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 332 removed outlier: 3.544A pdb=" N ILE E 327 " --> pdb=" O PHE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 373 removed outlier: 3.591A pdb=" N SER E 347 " --> pdb=" O ALA E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 380 removed outlier: 3.510A pdb=" N ALA E 380 " --> pdb=" O ILE E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 398 removed outlier: 4.272A pdb=" N GLU E 393 " --> pdb=" O ILE E 389 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 398 " --> pdb=" O ALA E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 432 removed outlier: 3.650A pdb=" N TRP E 404 " --> pdb=" O GLY E 400 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL E 427 " --> pdb=" O GLY E 423 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLY E 430 " --> pdb=" O ALA E 426 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 431 " --> pdb=" O VAL E 427 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA E 432 " --> pdb=" O ILE E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 441 removed outlier: 4.298A pdb=" N ARG E 440 " --> pdb=" O GLN E 436 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS E 441 " --> pdb=" O VAL E 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 436 through 441' Processing helix chain 'E' and resid 441 through 457 Processing helix chain 'E' and resid 471 through 476 removed outlier: 3.501A pdb=" N PHE E 475 " --> pdb=" O LEU E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 494 removed outlier: 3.687A pdb=" N VAL E 485 " --> pdb=" O ILE E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 509 Processing helix chain 'E' and resid 514 through 523 removed outlier: 3.886A pdb=" N LYS E 522 " --> pdb=" O ARG E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 539 Processing helix chain 'E' and resid 551 through 567 removed outlier: 3.991A pdb=" N ASN E 555 " --> pdb=" O PRO E 551 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP E 556 " --> pdb=" O PRO E 552 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E 565 " --> pdb=" O ILE E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 579 Processing helix chain 'E' and resid 583 through 588 removed outlier: 3.839A pdb=" N LEU E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 597 Processing helix chain 'E' and resid 598 through 603 removed outlier: 4.104A pdb=" N ALA E 602 " --> pdb=" O HIS E 598 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN E 603 " --> pdb=" O HIS E 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 598 through 603' Processing helix chain 'E' and resid 610 through 615 removed outlier: 4.130A pdb=" N TRP E 614 " --> pdb=" O GLN E 610 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1467 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: 2.54 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2708 1.36 - 1.49: 2824 1.49 - 1.62: 3778 1.62 - 1.75: 0 1.75 - 1.88: 64 Bond restraints: 9374 Sorted by residual: bond pdb=" C07 A1LX3 A 701 " pdb=" C08 A1LX3 A 701 " ideal model delta sigma weight residual 1.539 1.884 -0.345 2.00e-02 2.50e+03 2.97e+02 bond pdb=" C07 A1LX3 E 701 " pdb=" C08 A1LX3 E 701 " ideal model delta sigma weight residual 1.539 1.874 -0.335 2.00e-02 2.50e+03 2.81e+02 bond pdb=" C16 A1LX3 E 701 " pdb=" C21 A1LX3 E 701 " ideal model delta sigma weight residual 1.399 1.257 0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C16 A1LX3 A 701 " pdb=" C21 A1LX3 A 701 " ideal model delta sigma weight residual 1.399 1.268 0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" C12 A1LX3 E 701 " pdb=" C13 A1LX3 E 701 " ideal model delta sigma weight residual 1.387 1.261 0.126 2.00e-02 2.50e+03 3.94e+01 ... (remaining 9369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 12543 1.85 - 3.70: 201 3.70 - 5.55: 40 5.55 - 7.40: 7 7.40 - 9.25: 5 Bond angle restraints: 12796 Sorted by residual: angle pdb=" N VAL E 468 " pdb=" CA VAL E 468 " pdb=" C VAL E 468 " ideal model delta sigma weight residual 112.43 107.98 4.45 9.20e-01 1.18e+00 2.34e+01 angle pdb=" N VAL A 468 " pdb=" CA VAL A 468 " pdb=" C VAL A 468 " ideal model delta sigma weight residual 112.17 107.94 4.23 9.50e-01 1.11e+00 1.98e+01 angle pdb=" N VAL A 127 " pdb=" CA VAL A 127 " pdb=" C VAL A 127 " ideal model delta sigma weight residual 113.07 108.15 4.92 1.37e+00 5.33e-01 1.29e+01 angle pdb=" N VAL E 127 " pdb=" CA VAL E 127 " pdb=" C VAL E 127 " ideal model delta sigma weight residual 113.07 108.20 4.87 1.37e+00 5.33e-01 1.26e+01 angle pdb=" C06 A1LX3 E 701 " pdb=" C07 A1LX3 E 701 " pdb=" C08 A1LX3 E 701 " ideal model delta sigma weight residual 111.38 102.13 9.25 3.00e+00 1.11e-01 9.50e+00 ... (remaining 12791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 4926 17.32 - 34.63: 254 34.63 - 51.95: 66 51.95 - 69.26: 12 69.26 - 86.58: 4 Dihedral angle restraints: 5262 sinusoidal: 1998 harmonic: 3264 Sorted by residual: dihedral pdb=" CA ALA E 305 " pdb=" C ALA E 305 " pdb=" N THR E 306 " pdb=" CA THR E 306 " ideal model delta harmonic sigma weight residual 180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA THR E 179 " pdb=" C THR E 179 " pdb=" N TRP E 180 " pdb=" CA TRP E 180 " ideal model delta harmonic sigma weight residual -180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR A 179 " pdb=" C THR A 179 " pdb=" N TRP A 180 " pdb=" CA TRP A 180 " ideal model delta harmonic sigma weight residual -180.00 -164.33 -15.67 0 5.00e+00 4.00e-02 9.82e+00 ... (remaining 5259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1264 0.055 - 0.110: 155 0.110 - 0.166: 1 0.166 - 0.221: 0 0.221 - 0.276: 2 Chirality restraints: 1422 Sorted by residual: chirality pdb=" C06 A1LX3 E 701 " pdb=" C07 A1LX3 E 701 " pdb=" C15 A1LX3 E 701 " pdb=" C21 A1LX3 E 701 " both_signs ideal model delta sigma weight residual False 3.11 2.84 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C06 A1LX3 A 701 " pdb=" C07 A1LX3 A 701 " pdb=" C15 A1LX3 A 701 " pdb=" C21 A1LX3 A 701 " both_signs ideal model delta sigma weight residual False 3.11 2.87 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ILE E 549 " pdb=" N ILE E 549 " pdb=" C ILE E 549 " pdb=" CB ILE E 549 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.43e-01 ... (remaining 1419 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 54 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 55 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 54 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO E 55 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 55 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 55 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 525 " 0.019 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO E 526 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO E 526 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 526 " 0.016 5.00e-02 4.00e+02 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 31 2.39 - 3.02: 5145 3.02 - 3.64: 14176 3.64 - 4.27: 21382 4.27 - 4.90: 35510 Nonbonded interactions: 76244 Sorted by model distance: nonbonded pdb=" O GLY E 71 " pdb="NA NA E 702 " model vdw 1.761 2.470 nonbonded pdb=" OG SER E 318 " pdb="CL CL E 703 " model vdw 1.845 3.190 nonbonded pdb=" OH TYR E 98 " pdb="CL CL E 703 " model vdw 1.868 3.190 nonbonded pdb=" OH TYR A 98 " pdb="CL CL A 703 " model vdw 1.982 3.190 nonbonded pdb=" O VAL E 74 " pdb="NA NA E 702 " model vdw 2.177 2.470 ... (remaining 76239 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 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.730 Find NCS groups from input model: 0.260 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 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 : 0.007 0.345 9374 Z= 0.531 Angle : 0.630 9.247 12796 Z= 0.361 Chirality : 0.036 0.276 1422 Planarity : 0.003 0.037 1556 Dihedral : 11.548 86.575 3186 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 6.41 % Allowed : 8.93 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.23), residues: 1126 helix: -1.02 (0.18), residues: 732 sheet: None (None), residues: 0 loop : -1.70 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 308 HIS 0.001 0.000 HIS E 228 PHE 0.008 0.001 PHE E 362 TYR 0.010 0.001 TYR A 151 ARG 0.002 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 242 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.8477 (mttm) cc_final: 0.8035 (mtmt) REVERT: A 386 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6924 (tt) REVERT: A 389 ILE cc_start: 0.8099 (mm) cc_final: 0.7815 (mm) REVERT: A 600 LEU cc_start: 0.8499 (mt) cc_final: 0.8194 (mt) REVERT: E 191 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6437 (mt) REVERT: E 349 ILE cc_start: 0.6118 (mt) cc_final: 0.5886 (mm) REVERT: E 386 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7347 (tt) REVERT: E 389 ILE cc_start: 0.8076 (mm) cc_final: 0.7856 (mm) outliers start: 61 outliers final: 9 residues processed: 283 average time/residue: 0.1932 time to fit residues: 77.8136 Evaluate side-chains 168 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 462 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.6392 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9374 Z= 0.191 Angle : 0.579 8.629 12796 Z= 0.294 Chirality : 0.040 0.168 1422 Planarity : 0.004 0.039 1556 Dihedral : 6.822 69.288 1286 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.41 % Allowed : 14.60 % Favored : 80.99 % 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: 1126 helix: 0.17 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -1.67 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 585 HIS 0.003 0.001 HIS A 222 PHE 0.022 0.001 PHE A 403 TYR 0.012 0.001 TYR E 294 ARG 0.002 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 159 time to evaluate : 1.026 Fit side-chains REVERT: A 254 LYS cc_start: 0.8406 (mttm) cc_final: 0.8028 (mtmt) REVERT: E 63 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6265 (tp) REVERT: E 254 LYS cc_start: 0.8438 (mttm) cc_final: 0.8053 (mtmt) REVERT: E 332 TYR cc_start: 0.7358 (m-10) cc_final: 0.7008 (m-10) REVERT: E 481 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7368 (tp) REVERT: E 504 ASP cc_start: 0.6815 (m-30) cc_final: 0.6534 (m-30) outliers start: 42 outliers final: 23 residues processed: 189 average time/residue: 0.1847 time to fit residues: 52.0136 Evaluate side-chains 164 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 391 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 611 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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: 0.6518 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9374 Z= 0.237 Angle : 0.599 7.703 12796 Z= 0.303 Chirality : 0.041 0.170 1422 Planarity : 0.004 0.037 1556 Dihedral : 6.235 76.346 1273 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.46 % Allowed : 14.60 % Favored : 79.94 % 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: -0.39 (0.25), residues: 1126 helix: 0.50 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -1.83 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 585 HIS 0.007 0.001 HIS A 599 PHE 0.021 0.001 PHE A 403 TYR 0.021 0.002 TYR E 294 ARG 0.005 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 149 time to evaluate : 0.960 Fit side-chains REVERT: A 133 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8083 (m-10) REVERT: A 230 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6758 (mt) REVERT: A 254 LYS cc_start: 0.8499 (mttm) cc_final: 0.8100 (mtmt) REVERT: E 133 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8082 (m-10) REVERT: E 254 LYS cc_start: 0.8529 (mttm) cc_final: 0.8143 (mtmt) REVERT: E 368 MET cc_start: 0.6522 (tpp) cc_final: 0.6190 (tmm) REVERT: E 481 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7610 (tp) REVERT: E 504 ASP cc_start: 0.6872 (m-30) cc_final: 0.6630 (m-30) outliers start: 52 outliers final: 35 residues processed: 183 average time/residue: 0.1812 time to fit residues: 48.7878 Evaluate side-chains 171 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 544 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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: 0.6730 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 9374 Z= 0.525 Angle : 0.807 9.123 12796 Z= 0.413 Chirality : 0.049 0.182 1422 Planarity : 0.005 0.049 1556 Dihedral : 6.956 79.542 1271 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 7.35 % Allowed : 13.34 % Favored : 79.31 % 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: -0.82 (0.25), residues: 1126 helix: 0.05 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.60 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 128 HIS 0.005 0.001 HIS E 228 PHE 0.032 0.003 PHE A 316 TYR 0.025 0.003 TYR A 294 ARG 0.005 0.001 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 131 time to evaluate : 0.985 Fit side-chains REVERT: A 119 TYR cc_start: 0.7355 (t80) cc_final: 0.7139 (t80) REVERT: A 234 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: A 254 LYS cc_start: 0.8713 (mttm) cc_final: 0.8273 (mtmt) REVERT: E 122 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7556 (tp30) REVERT: E 234 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7572 (tp40) REVERT: E 254 LYS cc_start: 0.8724 (mttm) cc_final: 0.8275 (mtmt) REVERT: E 332 TYR cc_start: 0.7691 (m-10) cc_final: 0.7481 (m-10) REVERT: E 367 TYR cc_start: 0.6569 (t80) cc_final: 0.6255 (t80) REVERT: E 408 PHE cc_start: 0.7904 (t80) cc_final: 0.7564 (t80) REVERT: E 481 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7885 (tp) REVERT: E 610 GLN cc_start: 0.7538 (mm110) cc_final: 0.7326 (mt0) outliers start: 70 outliers final: 48 residues processed: 181 average time/residue: 0.1735 time to fit residues: 46.4196 Evaluate side-chains 173 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 121 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 351 CYS Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 509 MET Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 611 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.6596 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9374 Z= 0.198 Angle : 0.600 8.722 12796 Z= 0.303 Chirality : 0.039 0.177 1422 Planarity : 0.004 0.038 1556 Dihedral : 6.403 78.802 1271 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.83 % Allowed : 17.02 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1126 helix: 0.63 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.72 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 585 HIS 0.008 0.001 HIS A 598 PHE 0.018 0.001 PHE A 316 TYR 0.020 0.001 TYR A 294 ARG 0.004 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 127 time to evaluate : 1.024 Fit side-chains REVERT: A 122 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7213 (tp30) REVERT: A 230 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6827 (mt) REVERT: A 254 LYS cc_start: 0.8607 (mttm) cc_final: 0.8219 (mtmt) REVERT: E 254 LYS cc_start: 0.8668 (mttm) cc_final: 0.8259 (mtmt) REVERT: E 368 MET cc_start: 0.6737 (tmm) cc_final: 0.6459 (tpp) outliers start: 46 outliers final: 32 residues processed: 163 average time/residue: 0.1669 time to fit residues: 40.9257 Evaluate side-chains 147 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 113 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 391 TYR Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 509 MET Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 595 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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: 0.6653 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9374 Z= 0.296 Angle : 0.644 9.783 12796 Z= 0.324 Chirality : 0.041 0.177 1422 Planarity : 0.004 0.038 1556 Dihedral : 6.536 83.925 1271 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.67 % Allowed : 17.33 % Favored : 77.00 % 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: -0.28 (0.25), residues: 1126 helix: 0.62 (0.19), residues: 742 sheet: None (None), residues: 0 loop : -1.75 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 585 HIS 0.006 0.001 HIS A 598 PHE 0.022 0.002 PHE A 72 TYR 0.020 0.002 TYR A 294 ARG 0.004 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 119 time to evaluate : 1.017 Fit side-chains REVERT: A 122 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7469 (tp30) REVERT: A 230 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6960 (mt) REVERT: A 234 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7448 (tp40) REVERT: A 254 LYS cc_start: 0.8645 (mttm) cc_final: 0.8251 (mtmt) REVERT: E 63 ILE cc_start: 0.6568 (OUTLIER) cc_final: 0.6156 (tp) REVERT: E 122 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7235 (tp30) REVERT: E 254 LYS cc_start: 0.8731 (mttm) cc_final: 0.8290 (mtmt) REVERT: E 408 PHE cc_start: 0.7881 (t80) cc_final: 0.7609 (t80) outliers start: 54 outliers final: 40 residues processed: 158 average time/residue: 0.1638 time to fit residues: 39.2644 Evaluate side-chains 161 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 116 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 351 CYS Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 391 TYR Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 509 MET Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 595 GLU Chi-restraints excluded: chain E residue 611 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 0.3980 chunk 79 optimal weight: 0.0770 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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: 0.6536 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 9374 Z= 0.163 Angle : 0.568 10.285 12796 Z= 0.282 Chirality : 0.038 0.181 1422 Planarity : 0.004 0.040 1556 Dihedral : 6.189 87.693 1271 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.20 % Allowed : 19.22 % Favored : 76.58 % 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: 0.23 (0.25), residues: 1126 helix: 1.06 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.68 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 585 HIS 0.005 0.001 HIS A 598 PHE 0.017 0.001 PHE A 72 TYR 0.023 0.001 TYR A 294 ARG 0.004 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 1.060 Fit side-chains REVERT: A 122 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6747 (tp30) REVERT: A 234 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7273 (tp40) REVERT: A 254 LYS cc_start: 0.8561 (mttm) cc_final: 0.8203 (mtmt) REVERT: A 332 TYR cc_start: 0.7292 (m-10) cc_final: 0.6974 (m-10) REVERT: E 63 ILE cc_start: 0.6433 (OUTLIER) cc_final: 0.6044 (tp) REVERT: E 122 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6171 (tp30) REVERT: E 254 LYS cc_start: 0.8623 (mttm) cc_final: 0.8244 (mtmt) REVERT: E 368 MET cc_start: 0.7025 (tmm) cc_final: 0.6525 (tpp) outliers start: 40 outliers final: 27 residues processed: 163 average time/residue: 0.1721 time to fit residues: 42.1826 Evaluate side-chains 145 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 391 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 509 MET Chi-restraints excluded: chain E residue 529 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.6543 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 9374 Z= 0.188 Angle : 0.586 9.746 12796 Z= 0.288 Chirality : 0.038 0.183 1422 Planarity : 0.004 0.039 1556 Dihedral : 5.749 73.843 1269 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.89 % Allowed : 18.80 % Favored : 77.31 % 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: 0.35 (0.25), residues: 1126 helix: 1.20 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.73 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 585 HIS 0.004 0.001 HIS A 598 PHE 0.027 0.001 PHE A 72 TYR 0.030 0.002 TYR E 119 ARG 0.003 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 1.043 Fit side-chains REVERT: A 122 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6495 (tp30) REVERT: A 234 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7308 (tp40) REVERT: A 254 LYS cc_start: 0.8557 (mttm) cc_final: 0.8210 (mtmt) REVERT: A 332 TYR cc_start: 0.7298 (m-10) cc_final: 0.6912 (m-10) REVERT: E 63 ILE cc_start: 0.6349 (OUTLIER) cc_final: 0.5995 (tp) REVERT: E 122 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.6277 (tp30) REVERT: E 254 LYS cc_start: 0.8622 (mttm) cc_final: 0.8264 (mtmt) outliers start: 37 outliers final: 27 residues processed: 148 average time/residue: 0.1884 time to fit residues: 41.1327 Evaluate side-chains 148 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 391 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 509 MET Chi-restraints excluded: chain E residue 529 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.6546 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9374 Z= 0.196 Angle : 0.601 11.481 12796 Z= 0.294 Chirality : 0.039 0.182 1422 Planarity : 0.004 0.039 1556 Dihedral : 5.420 54.840 1269 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.57 % Allowed : 19.01 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.26), residues: 1126 helix: 1.33 (0.19), residues: 734 sheet: None (None), residues: 0 loop : -1.45 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 585 HIS 0.004 0.001 HIS A 598 PHE 0.024 0.001 PHE A 72 TYR 0.025 0.002 TYR E 119 ARG 0.004 0.000 ARG E 442 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 122 time to evaluate : 0.996 Fit side-chains REVERT: A 234 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7356 (tp40) REVERT: A 254 LYS cc_start: 0.8574 (mttm) cc_final: 0.8234 (mtmt) REVERT: E 63 ILE cc_start: 0.6333 (OUTLIER) cc_final: 0.5989 (tp) REVERT: E 122 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.6112 (tp30) REVERT: E 234 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7284 (tt0) REVERT: E 254 LYS cc_start: 0.8512 (mttm) cc_final: 0.8190 (mtmt) REVERT: E 332 TYR cc_start: 0.6835 (m-10) cc_final: 0.6612 (m-10) REVERT: E 518 ARG cc_start: 0.7247 (mtm180) cc_final: 0.6764 (mtm110) outliers start: 34 outliers final: 29 residues processed: 148 average time/residue: 0.1808 time to fit residues: 39.5053 Evaluate side-chains 149 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 391 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 509 MET Chi-restraints excluded: chain E residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 111 optimal weight: 0.0370 chunk 102 optimal weight: 0.2980 chunk 88 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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: 0.6485 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.093 9374 Z= 0.169 Angle : 0.578 10.586 12796 Z= 0.281 Chirality : 0.038 0.183 1422 Planarity : 0.004 0.040 1556 Dihedral : 4.978 37.024 1269 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.47 % Allowed : 19.33 % Favored : 77.21 % 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: 0.75 (0.25), residues: 1126 helix: 1.43 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -1.35 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 585 HIS 0.004 0.000 HIS E 599 PHE 0.021 0.001 PHE A 72 TYR 0.022 0.001 TYR E 119 ARG 0.003 0.000 ARG A 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 1.056 Fit side-chains REVERT: A 212 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7091 (mm-30) REVERT: A 234 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: A 254 LYS cc_start: 0.8512 (mttm) cc_final: 0.8206 (mtmt) REVERT: E 63 ILE cc_start: 0.6233 (OUTLIER) cc_final: 0.5943 (tp) REVERT: E 122 GLU cc_start: 0.5656 (OUTLIER) cc_final: 0.5368 (tp30) REVERT: E 128 TRP cc_start: 0.8031 (m100) cc_final: 0.7743 (m100) REVERT: E 254 LYS cc_start: 0.8434 (mttm) cc_final: 0.8182 (mtmt) REVERT: E 332 TYR cc_start: 0.6766 (m-10) cc_final: 0.6496 (m-10) outliers start: 33 outliers final: 28 residues processed: 155 average time/residue: 0.1640 time to fit residues: 38.7758 Evaluate side-chains 154 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 391 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 509 MET Chi-restraints excluded: chain E residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.4279 r_free = 0.4279 target = 0.196056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.166550 restraints weight = 11421.761| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.18 r_work: 0.3785 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 9374 Z= 0.256 Angle : 0.641 11.072 12796 Z= 0.316 Chirality : 0.040 0.187 1422 Planarity : 0.004 0.040 1556 Dihedral : 5.201 39.578 1269 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.47 % Allowed : 19.54 % Favored : 77.00 % 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: 0.63 (0.25), residues: 1126 helix: 1.37 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -1.42 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 585 HIS 0.003 0.001 HIS E 599 PHE 0.021 0.002 PHE A 72 TYR 0.018 0.002 TYR E 294 ARG 0.004 0.000 ARG E 442 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1999.30 seconds wall clock time: 36 minutes 53.40 seconds (2213.40 seconds total)