Starting phenix.real_space_refine on Sun Feb 18 07:58:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yie_33856/02_2024/7yie_33856.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yie_33856/02_2024/7yie_33856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yie_33856/02_2024/7yie_33856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yie_33856/02_2024/7yie_33856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yie_33856/02_2024/7yie_33856.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yie_33856/02_2024/7yie_33856.pdb" } resolution = 3.4 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= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 6 8.98 5 S 128 5.16 5 C 13796 2.51 5 N 3544 2.21 5 O 3852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 377": "OD1" <-> "OD2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 637": "OD1" <-> "OD2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 377": "OD1" <-> "OD2" Residue "B ASP 443": "OD1" <-> "OD2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "B TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 637": "OD1" <-> "OD2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 377": "OD1" <-> "OD2" Residue "C ASP 443": "OD1" <-> "OD2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 637": "OD1" <-> "OD2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 377": "OD1" <-> "OD2" Residue "D ASP 443": "OD1" <-> "OD2" Residue "D GLU 565": "OE1" <-> "OE2" Residue "D TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 637": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21326 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "B" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "C" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "D" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' K': 6} Classifications: {'undetermined': 6, 'water': 2} Link IDs: {None: 7} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" 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: 11.45, per 1000 atoms: 0.54 Number of scatterers: 21326 At special positions: 0 Unit cell: (157.065, 157.065, 131.595, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 6 19.00 S 128 16.00 O 3852 8.00 N 3544 7.00 C 13796 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 - 3.50 Amino acid : False - 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: 8.56 Conformation dependent library (CDL) restraints added in 3.8 seconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 20 sheets defined 54.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 15 through 24 removed outlier: 3.960A pdb=" N SER A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.501A pdb=" N SER A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.182A pdb=" N ARG A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.735A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 247 through 265 removed outlier: 3.739A pdb=" N ASP A 251 " --> pdb=" O TRP A 247 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 280 through 293 removed outlier: 3.587A pdb=" N ARG A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.949A pdb=" N VAL A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 345 through 375 Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 414 through 429 removed outlier: 3.585A pdb=" N TYR A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 495 removed outlier: 4.018A pdb=" N ALA A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 458 " --> pdb=" O MET A 454 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN A 477 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.938A pdb=" N ILE A 527 " --> pdb=" O LYS A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 541 removed outlier: 4.244A pdb=" N ASP A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 removed outlier: 3.620A pdb=" N PHE A 545 " --> pdb=" O ASN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.955A pdb=" N LYS A 619 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 620 " --> pdb=" O PHE A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 616 through 620' Processing helix chain 'A' and resid 643 through 653 Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 678 through 692 removed outlier: 3.565A pdb=" N GLU A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 removed outlier: 3.960A pdb=" N SER B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.501A pdb=" N SER B 51 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 146 through 156 removed outlier: 4.182A pdb=" N ARG B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 153 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.735A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 247 through 265 removed outlier: 3.739A pdb=" N ASP B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 280 through 293 removed outlier: 3.587A pdb=" N ARG B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET B 286 " --> pdb=" O LYS B 282 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.949A pdb=" N VAL B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 345 through 375 Processing helix chain 'B' and resid 387 through 397 Processing helix chain 'B' and resid 414 through 429 removed outlier: 3.594A pdb=" N TYR B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 495 removed outlier: 4.019A pdb=" N ALA B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 458 " --> pdb=" O MET B 454 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN B 477 " --> pdb=" O GLN B 473 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET B 484 " --> pdb=" O ARG B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 517 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.938A pdb=" N ILE B 527 " --> pdb=" O LYS B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 541 removed outlier: 4.244A pdb=" N ASP B 535 " --> pdb=" O ASP B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 removed outlier: 3.620A pdb=" N PHE B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.955A pdb=" N LYS B 619 " --> pdb=" O ILE B 616 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 620 " --> pdb=" O PHE B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 620' Processing helix chain 'B' and resid 643 through 653 Processing helix chain 'B' and resid 654 through 664 Processing helix chain 'B' and resid 678 through 692 removed outlier: 3.565A pdb=" N GLU B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 688 " --> pdb=" O LYS B 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 24 removed outlier: 3.960A pdb=" N SER C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 removed outlier: 3.501A pdb=" N SER C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.182A pdb=" N ARG C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 153 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 186 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.735A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 247 through 265 removed outlier: 3.739A pdb=" N ASP C 251 " --> pdb=" O TRP C 247 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 280 through 293 removed outlier: 3.587A pdb=" N ARG C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 300 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 327 through 329 No H-bonds generated for 'chain 'C' and resid 327 through 329' Processing helix chain 'C' and resid 330 through 338 removed outlier: 3.949A pdb=" N VAL C 334 " --> pdb=" O ARG C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 345 through 375 Processing helix chain 'C' and resid 387 through 397 Processing helix chain 'C' and resid 414 through 429 removed outlier: 3.594A pdb=" N TYR C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 495 removed outlier: 4.019A pdb=" N ALA C 451 " --> pdb=" O MET C 447 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 458 " --> pdb=" O MET C 454 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET C 474 " --> pdb=" O ILE C 470 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN C 477 " --> pdb=" O GLN C 473 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET C 484 " --> pdb=" O ARG C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 517 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.938A pdb=" N ILE C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 541 removed outlier: 4.244A pdb=" N ASP C 535 " --> pdb=" O ASP C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 removed outlier: 3.620A pdb=" N PHE C 545 " --> pdb=" O ASN C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.955A pdb=" N LYS C 619 " --> pdb=" O ILE C 616 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 620 " --> pdb=" O PHE C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 643 through 653 Processing helix chain 'C' and resid 654 through 664 Processing helix chain 'C' and resid 678 through 692 removed outlier: 3.565A pdb=" N GLU C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 688 " --> pdb=" O LYS C 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 24 removed outlier: 3.960A pdb=" N SER D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.502A pdb=" N SER D 51 " --> pdb=" O PHE D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.182A pdb=" N ARG D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 153 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 186 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.735A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 247 through 265 removed outlier: 3.739A pdb=" N ASP D 251 " --> pdb=" O TRP D 247 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.587A pdb=" N ARG D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET D 286 " --> pdb=" O LYS D 282 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 330 through 338 removed outlier: 3.949A pdb=" N VAL D 334 " --> pdb=" O ARG D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 345 through 375 Processing helix chain 'D' and resid 387 through 397 Processing helix chain 'D' and resid 414 through 429 removed outlier: 3.594A pdb=" N TYR D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 495 removed outlier: 4.019A pdb=" N ALA D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 458 " --> pdb=" O MET D 454 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET D 474 " --> pdb=" O ILE D 470 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN D 477 " --> pdb=" O GLN D 473 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 517 Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.938A pdb=" N ILE D 527 " --> pdb=" O LYS D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 541 removed outlier: 4.244A pdb=" N ASP D 535 " --> pdb=" O ASP D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 removed outlier: 3.620A pdb=" N PHE D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 566 Processing helix chain 'D' and resid 616 through 620 removed outlier: 3.955A pdb=" N LYS D 619 " --> pdb=" O ILE D 616 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU D 620 " --> pdb=" O PHE D 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 616 through 620' Processing helix chain 'D' and resid 643 through 653 Processing helix chain 'D' and resid 654 through 664 Processing helix chain 'D' and resid 678 through 692 removed outlier: 3.565A pdb=" N GLU D 687 " --> pdb=" O LYS D 683 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 688 " --> pdb=" O LYS D 684 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 3.798A pdb=" N LEU A 123 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR A 127 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 271 removed outlier: 3.690A pdb=" N PHE A 270 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 401 removed outlier: 3.959A pdb=" N GLU A 410 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 568 through 570 removed outlier: 6.519A pdb=" N ASP A 637 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP A 611 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS A 668 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 614 " --> pdb=" O CYS A 668 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 603 through 607 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.798A pdb=" N LEU B 123 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR B 127 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.690A pdb=" N PHE B 270 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 400 through 401 removed outlier: 3.959A pdb=" N GLU B 410 " --> pdb=" O ARG B 401 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 568 through 570 removed outlier: 6.519A pdb=" N ASP B 637 " --> pdb=" O VAL B 591 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP B 611 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS B 668 " --> pdb=" O VAL B 612 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 614 " --> pdb=" O CYS B 668 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 603 through 607 Processing sheet with id=AB2, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.796A pdb=" N LEU C 123 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR C 127 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 270 through 271 removed outlier: 3.690A pdb=" N PHE C 270 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 400 through 401 removed outlier: 3.959A pdb=" N GLU C 410 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 568 through 570 removed outlier: 6.519A pdb=" N ASP C 637 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP C 611 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS C 668 " --> pdb=" O VAL C 612 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 614 " --> pdb=" O CYS C 668 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 603 through 607 Processing sheet with id=AB7, first strand: chain 'D' and resid 31 through 32 removed outlier: 3.798A pdb=" N LEU D 123 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR D 127 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 270 through 271 removed outlier: 3.690A pdb=" N PHE D 270 " --> pdb=" O ILE D 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 400 through 401 removed outlier: 3.959A pdb=" N GLU D 410 " --> pdb=" O ARG D 401 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 568 through 570 removed outlier: 6.519A pdb=" N ASP D 637 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP D 611 " --> pdb=" O VAL D 590 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS D 668 " --> pdb=" O VAL D 612 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 614 " --> pdb=" O CYS D 668 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 603 through 607 1044 hydrogen bonds defined for protein. 3060 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: 7.16 Time building geometry restraints manager: 9.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6696 1.34 - 1.46: 5176 1.46 - 1.58: 9740 1.58 - 1.70: 0 1.70 - 1.81: 192 Bond restraints: 21804 Sorted by residual: bond pdb=" N GLN C 567 " pdb=" CA GLN C 567 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.55e+00 bond pdb=" N GLN B 567 " pdb=" CA GLN B 567 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.55e+00 bond pdb=" N GLN D 567 " pdb=" CA GLN D 567 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.55e+00 bond pdb=" N GLN A 567 " pdb=" CA GLN A 567 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.55e+00 bond pdb=" C MET B 474 " pdb=" O MET B 474 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.28e-02 6.10e+03 1.26e+00 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.56: 312 105.56 - 112.68: 11815 112.68 - 119.80: 6999 119.80 - 126.92: 10195 126.92 - 134.04: 263 Bond angle restraints: 29584 Sorted by residual: angle pdb=" N ILE B 245 " pdb=" CA ILE B 245 " pdb=" C ILE B 245 " ideal model delta sigma weight residual 113.43 107.72 5.71 1.09e+00 8.42e-01 2.74e+01 angle pdb=" N ILE C 245 " pdb=" CA ILE C 245 " pdb=" C ILE C 245 " ideal model delta sigma weight residual 113.43 107.72 5.71 1.09e+00 8.42e-01 2.74e+01 angle pdb=" N ILE D 245 " pdb=" CA ILE D 245 " pdb=" C ILE D 245 " ideal model delta sigma weight residual 113.43 107.72 5.71 1.09e+00 8.42e-01 2.74e+01 angle pdb=" N ILE A 245 " pdb=" CA ILE A 245 " pdb=" C ILE A 245 " ideal model delta sigma weight residual 113.43 107.72 5.71 1.09e+00 8.42e-01 2.74e+01 angle pdb=" C PHE A 566 " pdb=" N GLN A 567 " pdb=" CA GLN A 567 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 ... (remaining 29579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 11506 17.41 - 34.82: 1198 34.82 - 52.23: 192 52.23 - 69.64: 16 69.64 - 87.05: 20 Dihedral angle restraints: 12932 sinusoidal: 5144 harmonic: 7788 Sorted by residual: dihedral pdb=" CA PRO C 529 " pdb=" C PRO C 529 " pdb=" N LYS C 530 " pdb=" CA LYS C 530 " ideal model delta harmonic sigma weight residual 180.00 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PRO D 529 " pdb=" C PRO D 529 " pdb=" N LYS D 530 " pdb=" CA LYS D 530 " ideal model delta harmonic sigma weight residual -180.00 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PRO B 529 " pdb=" C PRO B 529 " pdb=" N LYS B 530 " pdb=" CA LYS B 530 " ideal model delta harmonic sigma weight residual -180.00 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2043 0.031 - 0.063: 949 0.063 - 0.094: 277 0.094 - 0.125: 111 0.125 - 0.157: 24 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA ILE C 527 " pdb=" N ILE C 527 " pdb=" C ILE C 527 " pdb=" CB ILE C 527 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA ILE D 527 " pdb=" N ILE D 527 " pdb=" C ILE D 527 " pdb=" CB ILE D 527 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA ILE B 527 " pdb=" N ILE B 527 " pdb=" C ILE B 527 " pdb=" CB ILE B 527 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 3401 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 460 " 0.012 2.00e-02 2.50e+03 9.54e-03 1.82e+00 pdb=" CG TYR C 460 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 460 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR C 460 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 460 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 460 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 460 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 460 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 460 " 0.012 2.00e-02 2.50e+03 9.54e-03 1.82e+00 pdb=" CG TYR B 460 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 460 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 460 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 460 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 460 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 460 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 460 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 460 " 0.012 2.00e-02 2.50e+03 9.50e-03 1.80e+00 pdb=" CG TYR A 460 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 460 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 460 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 460 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 460 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 460 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 460 " 0.001 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 6136 2.82 - 3.40: 22699 3.40 - 3.98: 37297 3.98 - 4.56: 52427 4.56 - 5.14: 78962 Nonbonded interactions: 197521 Sorted by model distance: nonbonded pdb=" OD1 ASN D 235 " pdb=" OG1 THR D 240 " model vdw 2.239 2.440 nonbonded pdb=" OD1 ASN A 235 " pdb=" OG1 THR A 240 " model vdw 2.239 2.440 nonbonded pdb=" OD1 ASN C 235 " pdb=" OG1 THR C 240 " model vdw 2.239 2.440 nonbonded pdb=" OD1 ASN B 235 " pdb=" OG1 THR B 240 " model vdw 2.239 2.440 nonbonded pdb=" O LYS D 144 " pdb=" OG1 THR D 147 " model vdw 2.244 2.440 ... (remaining 197516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 692) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.570 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 57.850 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 0.003 0.031 21804 Z= 0.181 Angle : 0.548 8.691 29584 Z= 0.302 Chirality : 0.041 0.157 3404 Planarity : 0.003 0.028 3668 Dihedral : 14.094 87.047 7884 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.84 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.45 (0.17), residues: 2616 helix: 1.34 (0.15), residues: 1344 sheet: -1.49 (0.32), residues: 260 loop : -2.30 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 513 HIS 0.003 0.001 HIS C 118 PHE 0.021 0.001 PHE D 566 TYR 0.023 0.001 TYR C 460 ARG 0.006 0.000 ARG D 677 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 2.347 Fit side-chains REVERT: A 231 MET cc_start: 0.7710 (tpp) cc_final: 0.7396 (tpt) REVERT: A 480 ARG cc_start: 0.7236 (ttm-80) cc_final: 0.7012 (ttm170) REVERT: B 231 MET cc_start: 0.7720 (tpp) cc_final: 0.7412 (tpt) REVERT: B 480 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.7012 (ttm170) REVERT: C 231 MET cc_start: 0.7743 (tpp) cc_final: 0.7417 (tpt) REVERT: C 480 ARG cc_start: 0.7248 (ttm-80) cc_final: 0.7024 (ttm170) REVERT: D 231 MET cc_start: 0.7739 (tpp) cc_final: 0.7406 (tpt) REVERT: D 480 ARG cc_start: 0.7236 (ttm-80) cc_final: 0.7015 (ttm170) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.3001 time to fit residues: 119.2176 Evaluate side-chains 196 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.6980 chunk 200 optimal weight: 0.0770 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 134 optimal weight: 0.0970 chunk 106 optimal weight: 0.1980 chunk 206 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS C 267 HIS D 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21804 Z= 0.137 Angle : 0.469 7.591 29584 Z= 0.254 Chirality : 0.039 0.141 3404 Planarity : 0.003 0.025 3668 Dihedral : 4.067 23.664 2864 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.46 % Favored : 93.23 % Rotamer: Outliers : 1.01 % Allowed : 6.72 % Favored : 92.27 % 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 (0.17), residues: 2616 helix: 1.45 (0.15), residues: 1384 sheet: -1.32 (0.32), residues: 260 loop : -2.26 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 367 HIS 0.004 0.001 HIS D 267 PHE 0.012 0.001 PHE D 566 TYR 0.016 0.001 TYR B 460 ARG 0.003 0.000 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 215 time to evaluate : 2.584 Fit side-chains REVERT: A 169 MET cc_start: 0.4891 (ppp) cc_final: 0.3582 (ptm) REVERT: A 231 MET cc_start: 0.7662 (tpp) cc_final: 0.7378 (tpt) REVERT: A 267 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.7383 (m170) REVERT: A 601 ASP cc_start: 0.7180 (t0) cc_final: 0.6883 (t0) REVERT: B 231 MET cc_start: 0.7671 (tpp) cc_final: 0.7387 (tpt) REVERT: B 267 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7374 (m170) REVERT: B 601 ASP cc_start: 0.7181 (t0) cc_final: 0.6879 (t0) REVERT: C 231 MET cc_start: 0.7699 (tpp) cc_final: 0.7392 (tpt) REVERT: C 601 ASP cc_start: 0.7181 (t0) cc_final: 0.6884 (t0) REVERT: D 231 MET cc_start: 0.7693 (tpp) cc_final: 0.7383 (tpt) REVERT: D 601 ASP cc_start: 0.7180 (t0) cc_final: 0.6890 (t0) outliers start: 24 outliers final: 16 residues processed: 231 average time/residue: 0.2959 time to fit residues: 110.4492 Evaluate side-chains 202 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 526 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 81 optimal weight: 0.0010 chunk 192 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 HIS D 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21804 Z= 0.270 Angle : 0.516 6.921 29584 Z= 0.279 Chirality : 0.042 0.140 3404 Planarity : 0.003 0.025 3668 Dihedral : 4.209 25.047 2864 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.38 % Favored : 92.32 % Rotamer: Outliers : 1.85 % Allowed : 9.75 % Favored : 88.40 % 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: -0.25 (0.17), residues: 2616 helix: 1.38 (0.15), residues: 1384 sheet: -1.21 (0.33), residues: 260 loop : -2.21 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 367 HIS 0.005 0.001 HIS A 267 PHE 0.014 0.002 PHE C 660 TYR 0.020 0.001 TYR B 460 ARG 0.002 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 209 time to evaluate : 2.338 Fit side-chains REVERT: A 601 ASP cc_start: 0.7196 (t0) cc_final: 0.6876 (t0) REVERT: B 169 MET cc_start: 0.4312 (ppp) cc_final: 0.3550 (ptm) REVERT: B 601 ASP cc_start: 0.7199 (t0) cc_final: 0.6877 (t0) REVERT: C 169 MET cc_start: 0.4311 (ppp) cc_final: 0.3548 (ptm) REVERT: C 267 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.7554 (m170) REVERT: C 601 ASP cc_start: 0.7198 (t0) cc_final: 0.6895 (t0) REVERT: D 169 MET cc_start: 0.4306 (ppp) cc_final: 0.3541 (ptm) REVERT: D 267 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7557 (m170) REVERT: D 601 ASP cc_start: 0.7194 (t0) cc_final: 0.6875 (t0) outliers start: 44 outliers final: 30 residues processed: 242 average time/residue: 0.2699 time to fit residues: 108.5626 Evaluate side-chains 239 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 207 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 267 HIS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 526 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.5980 chunk 180 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 482 HIS B 267 HIS B 482 HIS C 267 HIS C 482 HIS D 267 HIS D 482 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21804 Z= 0.193 Angle : 0.481 6.980 29584 Z= 0.259 Chirality : 0.040 0.131 3404 Planarity : 0.002 0.023 3668 Dihedral : 4.123 23.832 2864 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.11 % Favored : 92.58 % Rotamer: Outliers : 1.51 % Allowed : 13.07 % Favored : 85.42 % 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: -0.16 (0.17), residues: 2616 helix: 1.45 (0.15), residues: 1384 sheet: -1.15 (0.33), residues: 260 loop : -2.17 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 513 HIS 0.007 0.001 HIS C 267 PHE 0.010 0.001 PHE D 660 TYR 0.013 0.001 TYR C 460 ARG 0.002 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 198 time to evaluate : 2.314 Fit side-chains REVERT: A 169 MET cc_start: 0.4544 (ppp) cc_final: 0.3827 (ptm) REVERT: A 231 MET cc_start: 0.7794 (tpp) cc_final: 0.7497 (tpt) REVERT: A 295 ILE cc_start: 0.8427 (mm) cc_final: 0.8201 (mm) REVERT: A 601 ASP cc_start: 0.7176 (t0) cc_final: 0.6879 (t0) REVERT: B 169 MET cc_start: 0.4173 (ppp) cc_final: 0.3434 (ptm) REVERT: B 231 MET cc_start: 0.7799 (tpp) cc_final: 0.7506 (tpt) REVERT: B 295 ILE cc_start: 0.8423 (mm) cc_final: 0.8201 (mm) REVERT: B 601 ASP cc_start: 0.7177 (t0) cc_final: 0.6879 (t0) REVERT: C 169 MET cc_start: 0.4175 (ppp) cc_final: 0.3434 (ptm) REVERT: C 231 MET cc_start: 0.7822 (tpp) cc_final: 0.7512 (tpt) REVERT: C 295 ILE cc_start: 0.8426 (mm) cc_final: 0.8207 (mm) REVERT: C 601 ASP cc_start: 0.7182 (t0) cc_final: 0.6898 (t0) REVERT: D 169 MET cc_start: 0.4174 (ppp) cc_final: 0.3427 (ptm) REVERT: D 231 MET cc_start: 0.7819 (tpp) cc_final: 0.7502 (tpt) REVERT: D 295 ILE cc_start: 0.8428 (mm) cc_final: 0.8209 (mm) REVERT: D 601 ASP cc_start: 0.7176 (t0) cc_final: 0.6887 (t0) outliers start: 36 outliers final: 32 residues processed: 222 average time/residue: 0.2803 time to fit residues: 102.6517 Evaluate side-chains 220 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 30.0000 chunk 144 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 190 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.7373 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21804 Z= 0.232 Angle : 0.489 7.088 29584 Z= 0.265 Chirality : 0.041 0.132 3404 Planarity : 0.003 0.023 3668 Dihedral : 4.144 24.287 2864 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.72 % Favored : 91.97 % Rotamer: Outliers : 2.18 % Allowed : 13.91 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2616 helix: 1.41 (0.15), residues: 1388 sheet: -1.13 (0.34), residues: 260 loop : -2.15 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 513 HIS 0.002 0.001 HIS B 570 PHE 0.015 0.001 PHE C 93 TYR 0.014 0.001 TYR C 460 ARG 0.002 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 187 time to evaluate : 2.215 Fit side-chains REVERT: A 169 MET cc_start: 0.4515 (ppp) cc_final: 0.3873 (ptm) REVERT: A 601 ASP cc_start: 0.7170 (t0) cc_final: 0.6893 (t0) REVERT: B 169 MET cc_start: 0.4248 (ppp) cc_final: 0.3539 (ptm) REVERT: B 601 ASP cc_start: 0.7172 (t0) cc_final: 0.6895 (t0) REVERT: C 169 MET cc_start: 0.4246 (ppp) cc_final: 0.3533 (ptm) REVERT: C 601 ASP cc_start: 0.7175 (t0) cc_final: 0.6909 (t0) REVERT: D 169 MET cc_start: 0.4247 (ppp) cc_final: 0.3530 (ptm) REVERT: D 601 ASP cc_start: 0.7172 (t0) cc_final: 0.6897 (t0) outliers start: 52 outliers final: 40 residues processed: 227 average time/residue: 0.2929 time to fit residues: 111.6226 Evaluate side-chains 217 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 177 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 0.0270 chunk 62 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 134 optimal weight: 0.5980 overall best weight: 0.8240 ------------------------------------------------------------------------------- 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: 0.7343 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 21804 Z= 0.176 Angle : 0.463 7.451 29584 Z= 0.251 Chirality : 0.040 0.138 3404 Planarity : 0.002 0.023 3668 Dihedral : 4.040 23.114 2864 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.34 % Favored : 92.35 % Rotamer: Outliers : 2.14 % Allowed : 14.45 % Favored : 83.40 % 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: 0.00 (0.17), residues: 2616 helix: 1.57 (0.15), residues: 1380 sheet: -1.08 (0.34), residues: 260 loop : -2.07 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 513 HIS 0.002 0.001 HIS C 539 PHE 0.012 0.001 PHE B 93 TYR 0.012 0.001 TYR C 460 ARG 0.002 0.000 ARG D 677 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 206 time to evaluate : 2.346 Fit side-chains REVERT: A 169 MET cc_start: 0.4474 (ppp) cc_final: 0.3869 (ptm) REVERT: A 231 MET cc_start: 0.7807 (tpp) cc_final: 0.7520 (tpt) REVERT: A 601 ASP cc_start: 0.7130 (t0) cc_final: 0.6929 (t0) REVERT: B 169 MET cc_start: 0.4308 (ppp) cc_final: 0.3882 (ptp) REVERT: B 231 MET cc_start: 0.7810 (tpp) cc_final: 0.7523 (tpt) REVERT: C 169 MET cc_start: 0.4305 (ppp) cc_final: 0.3876 (ptp) REVERT: C 231 MET cc_start: 0.7837 (tpp) cc_final: 0.7530 (tpt) REVERT: D 169 MET cc_start: 0.4302 (ppp) cc_final: 0.3870 (ptp) REVERT: D 231 MET cc_start: 0.7834 (tpp) cc_final: 0.7525 (tpt) outliers start: 51 outliers final: 34 residues processed: 245 average time/residue: 0.3055 time to fit residues: 119.3835 Evaluate side-chains 232 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 198 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 186 optimal weight: 0.4980 chunk 144 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 155 optimal weight: 0.0970 chunk 117 optimal weight: 2.9990 overall best weight: 0.9138 ------------------------------------------------------------------------------- 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: 0.7354 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21804 Z= 0.195 Angle : 0.488 7.861 29584 Z= 0.260 Chirality : 0.040 0.139 3404 Planarity : 0.002 0.023 3668 Dihedral : 4.043 23.545 2864 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.45 % Favored : 92.24 % Rotamer: Outliers : 2.14 % Allowed : 15.71 % Favored : 82.14 % 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: 0.04 (0.17), residues: 2616 helix: 1.56 (0.15), residues: 1384 sheet: -1.04 (0.34), residues: 260 loop : -2.01 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 513 HIS 0.002 0.001 HIS B 539 PHE 0.010 0.001 PHE D 660 TYR 0.011 0.001 TYR C 368 ARG 0.002 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 197 time to evaluate : 2.362 Fit side-chains REVERT: A 169 MET cc_start: 0.4511 (ppp) cc_final: 0.3902 (ptm) REVERT: A 231 MET cc_start: 0.7794 (tpp) cc_final: 0.7505 (tpt) REVERT: B 169 MET cc_start: 0.4420 (OUTLIER) cc_final: 0.3942 (ptp) REVERT: B 231 MET cc_start: 0.7798 (tpp) cc_final: 0.7513 (tpt) REVERT: C 169 MET cc_start: 0.4423 (OUTLIER) cc_final: 0.3942 (ptp) REVERT: C 231 MET cc_start: 0.7829 (tpp) cc_final: 0.7524 (tpt) REVERT: D 169 MET cc_start: 0.4420 (OUTLIER) cc_final: 0.3932 (ptp) REVERT: D 231 MET cc_start: 0.7817 (tpp) cc_final: 0.7513 (tpt) outliers start: 51 outliers final: 41 residues processed: 226 average time/residue: 0.2697 time to fit residues: 102.2444 Evaluate side-chains 239 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 195 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 151 optimal weight: 7.9990 chunk 76 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 173 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 23 optimal weight: 0.0070 chunk 200 optimal weight: 0.5980 chunk 231 optimal weight: 0.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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: 0.7289 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21804 Z= 0.134 Angle : 0.470 8.097 29584 Z= 0.247 Chirality : 0.039 0.140 3404 Planarity : 0.002 0.023 3668 Dihedral : 3.885 21.868 2864 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.22 % Favored : 92.47 % Rotamer: Outliers : 1.72 % Allowed : 16.60 % Favored : 81.68 % 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: 0.22 (0.17), residues: 2616 helix: 1.74 (0.15), residues: 1384 sheet: -0.88 (0.35), residues: 256 loop : -1.99 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 513 HIS 0.002 0.000 HIS B 539 PHE 0.019 0.001 PHE B 93 TYR 0.008 0.001 TYR A 368 ARG 0.001 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 207 time to evaluate : 2.190 Fit side-chains REVERT: A 169 MET cc_start: 0.4509 (ppp) cc_final: 0.3856 (ptm) REVERT: B 169 MET cc_start: 0.4421 (OUTLIER) cc_final: 0.3906 (ptp) REVERT: C 169 MET cc_start: 0.4420 (OUTLIER) cc_final: 0.3902 (ptp) REVERT: D 169 MET cc_start: 0.4422 (OUTLIER) cc_final: 0.3898 (ptp) outliers start: 41 outliers final: 32 residues processed: 233 average time/residue: 0.3033 time to fit residues: 115.0309 Evaluate side-chains 223 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.7980 chunk 222 optimal weight: 0.9990 chunk 237 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 186 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 214 optimal weight: 6.9990 chunk 224 optimal weight: 0.7980 chunk 236 optimal weight: 0.4980 chunk 155 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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: 0.7300 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21804 Z= 0.147 Angle : 0.482 7.403 29584 Z= 0.252 Chirality : 0.039 0.133 3404 Planarity : 0.002 0.022 3668 Dihedral : 3.855 22.842 2864 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.77 % Favored : 92.93 % Rotamer: Outliers : 1.47 % Allowed : 17.65 % Favored : 80.88 % 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 (0.17), residues: 2616 helix: 1.76 (0.15), residues: 1384 sheet: -0.92 (0.34), residues: 256 loop : -1.99 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 513 HIS 0.003 0.001 HIS B 539 PHE 0.016 0.001 PHE B 93 TYR 0.009 0.001 TYR A 368 ARG 0.001 0.000 ARG C 677 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 199 time to evaluate : 2.348 Fit side-chains REVERT: A 169 MET cc_start: 0.4456 (ppp) cc_final: 0.3804 (ptm) REVERT: B 169 MET cc_start: 0.4381 (OUTLIER) cc_final: 0.3899 (ptp) REVERT: C 169 MET cc_start: 0.4382 (OUTLIER) cc_final: 0.3897 (ptp) REVERT: D 169 MET cc_start: 0.4381 (OUTLIER) cc_final: 0.3890 (ptp) outliers start: 35 outliers final: 28 residues processed: 227 average time/residue: 0.2780 time to fit residues: 105.2155 Evaluate side-chains 220 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 263 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 209 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7325 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21804 Z= 0.183 Angle : 0.506 8.849 29584 Z= 0.266 Chirality : 0.040 0.139 3404 Planarity : 0.002 0.022 3668 Dihedral : 3.907 23.045 2864 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.19 % Favored : 92.51 % Rotamer: Outliers : 1.81 % Allowed : 17.61 % Favored : 80.59 % 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: 0.18 (0.17), residues: 2616 helix: 1.72 (0.15), residues: 1384 sheet: -0.89 (0.34), residues: 256 loop : -2.03 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 513 HIS 0.002 0.001 HIS A 539 PHE 0.018 0.001 PHE D 93 TYR 0.011 0.001 TYR A 368 ARG 0.001 0.000 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 188 time to evaluate : 2.412 Fit side-chains REVERT: A 169 MET cc_start: 0.4466 (ppp) cc_final: 0.3783 (ptm) REVERT: B 169 MET cc_start: 0.4386 (OUTLIER) cc_final: 0.3895 (ptp) REVERT: C 169 MET cc_start: 0.4385 (OUTLIER) cc_final: 0.3893 (ptp) REVERT: D 169 MET cc_start: 0.4387 (OUTLIER) cc_final: 0.3889 (ptp) outliers start: 43 outliers final: 36 residues processed: 220 average time/residue: 0.2727 time to fit residues: 100.6388 Evaluate side-chains 227 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 193 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.185768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.151912 restraints weight = 22847.995| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.81 r_work: 0.3221 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21804 Z= 0.176 Angle : 0.503 8.168 29584 Z= 0.263 Chirality : 0.040 0.137 3404 Planarity : 0.002 0.022 3668 Dihedral : 3.915 23.339 2864 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.53 % Favored : 92.16 % Rotamer: Outliers : 1.55 % Allowed : 17.94 % Favored : 80.50 % 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 (0.17), residues: 2616 helix: 1.75 (0.15), residues: 1376 sheet: -0.87 (0.34), residues: 256 loop : -1.96 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 513 HIS 0.002 0.001 HIS D 539 PHE 0.016 0.001 PHE B 93 TYR 0.011 0.001 TYR C 368 ARG 0.001 0.000 ARG D 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3867.26 seconds wall clock time: 72 minutes 1.72 seconds (4321.72 seconds total)