Starting phenix.real_space_refine on Sun Dec 29 17:40:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ou2_13073/12_2024/7ou2_13073_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ou2_13073/12_2024/7ou2_13073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ou2_13073/12_2024/7ou2_13073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ou2_13073/12_2024/7ou2_13073.map" model { file = "/net/cci-nas-00/data/ceres_data/7ou2_13073/12_2024/7ou2_13073_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ou2_13073/12_2024/7ou2_13073_neut.cif" } resolution = 4.8 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 ------------------------------------------------------------------------------- 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= 0.022 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 54 5.16 5 C 6781 2.51 5 N 1916 2.21 5 O 2043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10798 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5632 Classifications: {'peptide': 721} Link IDs: {'PTRANS': 33, 'TRANS': 687} Chain breaks: 2 Chain: "B" Number of atoms: 5112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5112 Classifications: {'peptide': 650} Link IDs: {'PTRANS': 27, 'TRANS': 622} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.52, per 1000 atoms: 0.60 Number of scatterers: 10798 At special positions: 0 Unit cell: (117.66, 99.64, 127.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 4 15.00 O 2043 8.00 N 1916 7.00 C 6781 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: 2.58 Conformation dependent library (CDL) restraints added in 1.4 seconds 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 10 sheets defined 55.1% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.546A pdb=" N HIS A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 75 through 86 removed outlier: 3.758A pdb=" N TYR A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 186 through 191 removed outlier: 4.063A pdb=" N ILE A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.651A pdb=" N GLU A 203 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 230 through 249 removed outlier: 3.650A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.687A pdb=" N LEU A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 344 Proline residue: A 340 - end of helix removed outlier: 3.744A pdb=" N GLN A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 361 through 385 Proline residue: A 376 - end of helix removed outlier: 3.696A pdb=" N THR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.987A pdb=" N GLY A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 430 through 444 removed outlier: 3.815A pdb=" N ALA A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 536 removed outlier: 3.618A pdb=" N PHE A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 565 Processing helix chain 'A' and resid 585 through 592 Processing helix chain 'A' and resid 619 through 635 removed outlier: 3.504A pdb=" N TYR A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET A 624 " --> pdb=" O LYS A 620 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 684 Processing helix chain 'A' and resid 700 through 718 Processing helix chain 'A' and resid 731 through 733 No H-bonds generated for 'chain 'A' and resid 731 through 733' Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 770 through 778 removed outlier: 4.326A pdb=" N ALA A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.615A pdb=" N HIS B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 75 through 86 removed outlier: 3.685A pdb=" N TYR B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 186 through 191 removed outlier: 4.107A pdb=" N ILE B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.650A pdb=" N GLU B 203 " --> pdb=" O PRO B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.664A pdb=" N ALA B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.521A pdb=" N ARG B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 300 through 313 removed outlier: 3.511A pdb=" N SER B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 333 removed outlier: 3.711A pdb=" N LEU B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 344 Proline residue: B 340 - end of helix removed outlier: 3.716A pdb=" N GLN B 344 " --> pdb=" O PRO B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 361 through 385 Proline residue: B 376 - end of helix removed outlier: 3.619A pdb=" N THR B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 521 through 536 Processing helix chain 'B' and resid 538 through 565 Processing helix chain 'B' and resid 587 through 591 Processing helix chain 'B' and resid 619 through 636 removed outlier: 4.183A pdb=" N MET B 624 " --> pdb=" O LYS B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 684 Processing helix chain 'B' and resid 700 through 718 Processing helix chain 'B' and resid 731 through 733 No H-bonds generated for 'chain 'B' and resid 731 through 733' Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 770 through 778 removed outlier: 3.974A pdb=" N ALA B 774 " --> pdb=" O SER B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 800 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.388A pdb=" N ILE A 66 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 31 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N PHE A 40 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LEU A 29 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 28 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N CYS A 93 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE A 30 " --> pdb=" O CYS A 93 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLN A 95 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N ARG A 32 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU A 94 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL A 110 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.614A pdb=" N LEU A 178 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ARG A 199 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR A 180 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA A 134 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N ALA A 181 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ILE A 136 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 269 removed outlier: 6.926A pdb=" N ILE A 268 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR A 655 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ARG A 652 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LEU A 691 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N PHE A 654 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASP A 693 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG A 656 " --> pdb=" O ASP A 693 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 571 through 572 removed outlier: 6.683A pdb=" N THR A 571 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 644 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU A 582 " --> pdb=" O ASN A 599 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASN A 599 " --> pdb=" O GLU A 582 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 609 through 613 removed outlier: 6.798A pdb=" N MET A 609 " --> pdb=" O ALA A 743 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL A 745 " --> pdb=" O MET A 609 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ILE A 611 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU A 747 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR A 613 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ALA A 749 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP A 748 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N SER A 761 " --> pdb=" O ASP A 748 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU A 750 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET A 759 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N HIS A 752 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ALA A 757 " --> pdb=" O HIS A 752 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.803A pdb=" N TYR B 31 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE B 40 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU B 29 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 32 " --> pdb=" O CYS B 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 199 removed outlier: 6.622A pdb=" N LEU B 178 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ARG B 199 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR B 180 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA B 134 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ALA B 181 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE B 136 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 268 through 269 removed outlier: 6.791A pdb=" N ILE B 268 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N THR B 655 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG B 652 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU B 691 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N PHE B 654 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET B 692 " --> pdb=" O LEU B 724 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 609 " --> pdb=" O ALA B 743 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL B 745 " --> pdb=" O MET B 609 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE B 611 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU B 747 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR B 613 " --> pdb=" O LEU B 747 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 571 through 572 removed outlier: 6.769A pdb=" N THR B 571 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS B 644 " --> pdb=" O THR B 581 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 582 " --> pdb=" O ASN B 599 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN B 599 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 750 through 752 552 hydrogen bonds defined for protein. 1557 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: 4.07 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1839 1.31 - 1.43: 2689 1.43 - 1.56: 6346 1.56 - 1.69: 6 1.69 - 1.82: 96 Bond restraints: 10976 Sorted by residual: bond pdb=" C4 ADP A1801 " pdb=" C5 ADP A1801 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C4 ADP B1801 " pdb=" C5 ADP B1801 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" N ARG A 199 " pdb=" CA ARG A 199 " ideal model delta sigma weight residual 1.453 1.495 -0.042 8.30e-03 1.45e+04 2.51e+01 bond pdb=" N ARG B 199 " pdb=" CA ARG B 199 " ideal model delta sigma weight residual 1.453 1.493 -0.040 8.30e-03 1.45e+04 2.30e+01 bond pdb=" C PRO B 615 " pdb=" O PRO B 615 " ideal model delta sigma weight residual 1.233 1.177 0.056 1.19e-02 7.06e+03 2.21e+01 ... (remaining 10971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 12295 2.51 - 5.03: 2462 5.03 - 7.54: 88 7.54 - 10.05: 23 10.05 - 12.56: 1 Bond angle restraints: 14869 Sorted by residual: angle pdb=" N CYS B 297 " pdb=" CA CYS B 297 " pdb=" C CYS B 297 " ideal model delta sigma weight residual 111.56 101.89 9.67 1.38e+00 5.25e-01 4.91e+01 angle pdb=" N CYS A 297 " pdb=" CA CYS A 297 " pdb=" C CYS A 297 " ideal model delta sigma weight residual 111.71 102.87 8.84 1.34e+00 5.57e-01 4.35e+01 angle pdb=" C THR B 669 " pdb=" CA THR B 669 " pdb=" CB THR B 669 " ideal model delta sigma weight residual 110.88 101.06 9.82 1.57e+00 4.06e-01 3.91e+01 angle pdb=" N ARG A 697 " pdb=" CA ARG A 697 " pdb=" C ARG A 697 " ideal model delta sigma weight residual 112.93 106.08 6.85 1.12e+00 7.97e-01 3.74e+01 angle pdb=" N ILE A 636 " pdb=" CA ILE A 636 " pdb=" C ILE A 636 " ideal model delta sigma weight residual 112.80 105.92 6.88 1.15e+00 7.56e-01 3.58e+01 ... (remaining 14864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.73: 6456 26.73 - 53.45: 244 53.45 - 80.18: 26 80.18 - 106.91: 3 106.91 - 133.63: 3 Dihedral angle restraints: 6732 sinusoidal: 2754 harmonic: 3978 Sorted by residual: dihedral pdb=" O2A ADP A1801 " pdb=" O3A ADP A1801 " pdb=" PA ADP A1801 " pdb=" PB ADP A1801 " ideal model delta sinusoidal sigma weight residual -60.00 73.64 -133.63 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" O2A ADP B1801 " pdb=" O3A ADP B1801 " pdb=" PA ADP B1801 " pdb=" PB ADP B1801 " ideal model delta sinusoidal sigma weight residual -60.00 60.77 -120.77 1 2.00e+01 2.50e-03 3.63e+01 dihedral pdb=" O1B ADP B1801 " pdb=" O3A ADP B1801 " pdb=" PB ADP B1801 " pdb=" PA ADP B1801 " ideal model delta sinusoidal sigma weight residual 300.00 179.79 120.21 1 2.00e+01 2.50e-03 3.61e+01 ... (remaining 6729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 768 0.081 - 0.163: 641 0.163 - 0.244: 252 0.244 - 0.325: 42 0.325 - 0.406: 3 Chirality restraints: 1706 Sorted by residual: chirality pdb=" CA TYR B 528 " pdb=" N TYR B 528 " pdb=" C TYR B 528 " pdb=" CB TYR B 528 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CA TYR B 635 " pdb=" N TYR B 635 " pdb=" C TYR B 635 " pdb=" CB TYR B 635 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA TYR A 635 " pdb=" N TYR A 635 " pdb=" C TYR A 635 " pdb=" CB TYR A 635 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 1703 not shown) Planarity restraints: 1934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 275 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ARG B 275 " 0.060 2.00e-02 2.50e+03 pdb=" O ARG B 275 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN B 276 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 642 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ALA B 642 " 0.057 2.00e-02 2.50e+03 pdb=" O ALA B 642 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN B 643 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 378 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.53e+00 pdb=" C LEU A 378 " 0.053 2.00e-02 2.50e+03 pdb=" O LEU A 378 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG A 379 " -0.018 2.00e-02 2.50e+03 ... (remaining 1931 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 4421 2.95 - 3.44: 11219 3.44 - 3.93: 18368 3.93 - 4.41: 20845 4.41 - 4.90: 33099 Nonbonded interactions: 87952 Sorted by model distance: nonbonded pdb=" N ASP A 139 " pdb=" O ASP A 139 " model vdw 2.465 2.496 nonbonded pdb=" N VAL B 781 " pdb=" O VAL B 781 " model vdw 2.473 2.496 nonbonded pdb=" N VAL A 781 " pdb=" O VAL A 781 " model vdw 2.486 2.496 nonbonded pdb=" N ASP B 139 " pdb=" O ASP B 139 " model vdw 2.489 2.496 nonbonded pdb=" N THR A 56 " pdb=" O THR A 56 " model vdw 2.510 2.496 ... (remaining 87947 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' and (resid 17 through 56 or resid 67 through 94 or resid 109 through \ 412 or resid 520 through 800 or resid 1801)) selection = (chain 'B' and (resid 17 through 662 or resid 667 through 800 or resid 1801)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.870 Find NCS groups from input model: 0.460 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 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 : 0.013 0.112 10976 Z= 0.866 Angle : 1.801 12.564 14869 Z= 1.382 Chirality : 0.120 0.406 1706 Planarity : 0.008 0.034 1934 Dihedral : 14.072 133.634 4156 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.21), residues: 1355 helix: 2.66 (0.18), residues: 649 sheet: -0.52 (0.37), residues: 148 loop : -0.55 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 137 HIS 0.007 0.002 HIS B 312 PHE 0.021 0.004 PHE A 730 TYR 0.037 0.005 TYR B 528 ARG 0.025 0.002 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 THR cc_start: 0.9234 (m) cc_final: 0.8768 (p) REVERT: A 260 MET cc_start: 0.6887 (tpt) cc_final: 0.6471 (tpp) REVERT: A 323 GLU cc_start: 0.8661 (tt0) cc_final: 0.8196 (tm-30) REVERT: A 365 LEU cc_start: 0.8581 (mt) cc_final: 0.7161 (mt) REVERT: A 441 ASP cc_start: 0.8751 (m-30) cc_final: 0.8443 (p0) REVERT: A 528 TYR cc_start: 0.6743 (t80) cc_final: 0.6098 (t80) REVERT: A 552 LEU cc_start: 0.9147 (tp) cc_final: 0.8843 (mp) REVERT: A 615 PRO cc_start: 0.6031 (Cg_endo) cc_final: 0.3607 (Cg_exo) REVERT: A 617 MET cc_start: 0.8204 (mmm) cc_final: 0.7295 (mmt) REVERT: A 740 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8134 (pm20) REVERT: B 73 TYR cc_start: 0.5483 (p90) cc_final: 0.5127 (p90) REVERT: B 157 LEU cc_start: 0.7350 (tp) cc_final: 0.6803 (pp) REVERT: B 158 SER cc_start: 0.5808 (p) cc_final: 0.5407 (t) REVERT: B 173 THR cc_start: 0.7410 (p) cc_final: 0.6974 (t) REVERT: B 333 ASP cc_start: 0.8353 (m-30) cc_final: 0.7833 (t0) REVERT: B 368 MET cc_start: 0.7736 (ttm) cc_final: 0.7527 (ttm) REVERT: B 524 GLU cc_start: 0.7075 (pt0) cc_final: 0.6849 (mm-30) REVERT: B 602 ASN cc_start: 0.7724 (m-40) cc_final: 0.7449 (m-40) REVERT: B 687 TYR cc_start: 0.7565 (m-80) cc_final: 0.7021 (m-80) REVERT: B 718 LYS cc_start: 0.7581 (mttp) cc_final: 0.7194 (tmtt) outliers start: 1 outliers final: 0 residues processed: 366 average time/residue: 0.3489 time to fit residues: 163.3265 Evaluate side-chains 236 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 79 optimal weight: 0.3980 chunk 124 optimal weight: 7.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 326 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN B 171 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10976 Z= 0.277 Angle : 0.758 10.278 14869 Z= 0.390 Chirality : 0.045 0.183 1706 Planarity : 0.006 0.087 1934 Dihedral : 7.395 123.329 1532 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.44 % Allowed : 3.26 % Favored : 96.30 % 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: 0.67 (0.21), residues: 1355 helix: 1.56 (0.19), residues: 665 sheet: -0.58 (0.34), residues: 178 loop : -0.60 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 709 HIS 0.010 0.002 HIS B 370 PHE 0.031 0.002 PHE B 155 TYR 0.034 0.003 TYR B 528 ARG 0.012 0.001 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 264 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.7925 (tp) cc_final: 0.7198 (tp) REVERT: A 155 PHE cc_start: 0.8172 (t80) cc_final: 0.7692 (t80) REVERT: A 206 ILE cc_start: 0.8985 (mp) cc_final: 0.8755 (tp) REVERT: A 222 LEU cc_start: 0.7954 (mt) cc_final: 0.7641 (pt) REVERT: A 229 ASN cc_start: 0.8927 (t0) cc_final: 0.8692 (t0) REVERT: A 258 ILE cc_start: 0.7744 (tt) cc_final: 0.7436 (tt) REVERT: A 323 GLU cc_start: 0.8512 (tt0) cc_final: 0.8270 (tm-30) REVERT: A 365 LEU cc_start: 0.8566 (mt) cc_final: 0.7491 (mt) REVERT: A 382 LEU cc_start: 0.8476 (mt) cc_final: 0.8053 (mt) REVERT: A 397 MET cc_start: 0.8631 (mtm) cc_final: 0.8180 (mtt) REVERT: A 419 VAL cc_start: 0.8309 (t) cc_final: 0.8092 (t) REVERT: A 441 ASP cc_start: 0.8689 (m-30) cc_final: 0.8325 (p0) REVERT: A 528 TYR cc_start: 0.6608 (t80) cc_final: 0.6402 (t80) REVERT: A 552 LEU cc_start: 0.9187 (tp) cc_final: 0.8953 (mt) REVERT: A 617 MET cc_start: 0.7576 (mmm) cc_final: 0.7348 (mmt) REVERT: B 20 LEU cc_start: 0.8951 (tp) cc_final: 0.8646 (tp) REVERT: B 49 GLN cc_start: 0.4648 (OUTLIER) cc_final: 0.4426 (pm20) REVERT: B 155 PHE cc_start: 0.6062 (t80) cc_final: 0.5835 (t80) REVERT: B 333 ASP cc_start: 0.8343 (m-30) cc_final: 0.8002 (t0) REVERT: B 368 MET cc_start: 0.7624 (ttm) cc_final: 0.7405 (ttm) REVERT: B 524 GLU cc_start: 0.7392 (pt0) cc_final: 0.5623 (mm-30) REVERT: B 529 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8165 (tm-30) REVERT: B 533 ASP cc_start: 0.7563 (m-30) cc_final: 0.7361 (m-30) REVERT: B 552 LEU cc_start: 0.8446 (mm) cc_final: 0.8166 (mm) REVERT: B 617 MET cc_start: 0.7162 (mmt) cc_final: 0.6386 (mmp) REVERT: B 644 LYS cc_start: 0.7997 (tmtt) cc_final: 0.7196 (tptt) REVERT: B 692 MET cc_start: 0.5024 (ttm) cc_final: 0.4245 (ttm) outliers start: 5 outliers final: 2 residues processed: 269 average time/residue: 0.3165 time to fit residues: 110.8324 Evaluate side-chains 201 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 198 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 134 optimal weight: 0.0040 chunk 110 optimal weight: 7.9990 chunk 123 optimal weight: 0.2980 chunk 42 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 overall best weight: 3.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 326 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN B 683 ASN ** B 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10976 Z= 0.234 Angle : 0.709 7.679 14869 Z= 0.361 Chirality : 0.044 0.188 1706 Planarity : 0.006 0.081 1934 Dihedral : 7.163 121.063 1532 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.26 % Allowed : 3.61 % Favored : 96.13 % 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: 0.41 (0.21), residues: 1355 helix: 1.31 (0.19), residues: 663 sheet: -0.35 (0.34), residues: 188 loop : -0.82 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 709 HIS 0.008 0.001 HIS B 370 PHE 0.017 0.002 PHE B 155 TYR 0.029 0.002 TYR B 31 ARG 0.009 0.001 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 248 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.6208 (m-10) cc_final: 0.5949 (m-80) REVERT: A 83 LEU cc_start: 0.8020 (mt) cc_final: 0.7723 (mt) REVERT: A 143 PHE cc_start: 0.6011 (m-80) cc_final: 0.5757 (m-80) REVERT: A 155 PHE cc_start: 0.7892 (t80) cc_final: 0.7653 (t80) REVERT: A 206 ILE cc_start: 0.9033 (mp) cc_final: 0.8782 (tp) REVERT: A 222 LEU cc_start: 0.8118 (mt) cc_final: 0.7689 (pt) REVERT: A 229 ASN cc_start: 0.9027 (t0) cc_final: 0.8669 (t0) REVERT: A 308 LYS cc_start: 0.6984 (ttmt) cc_final: 0.6736 (ttpt) REVERT: A 323 GLU cc_start: 0.8444 (tt0) cc_final: 0.8064 (tm-30) REVERT: A 397 MET cc_start: 0.8730 (mtm) cc_final: 0.8242 (mtt) REVERT: A 441 ASP cc_start: 0.8728 (m-30) cc_final: 0.8388 (p0) REVERT: A 552 LEU cc_start: 0.9213 (tp) cc_final: 0.8974 (mt) REVERT: A 615 PRO cc_start: 0.6463 (Cg_endo) cc_final: 0.4960 (Cg_exo) REVERT: A 617 MET cc_start: 0.7740 (mmm) cc_final: 0.7498 (mmm) REVERT: B 174 ASN cc_start: 0.8454 (t0) cc_final: 0.8051 (t0) REVERT: B 289 ASN cc_start: 0.8437 (t0) cc_final: 0.8148 (t0) REVERT: B 529 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8049 (tm-30) REVERT: B 533 ASP cc_start: 0.7479 (m-30) cc_final: 0.7197 (m-30) REVERT: B 552 LEU cc_start: 0.8600 (mm) cc_final: 0.8345 (mm) REVERT: B 644 LYS cc_start: 0.7757 (tmtt) cc_final: 0.7420 (tptt) REVERT: B 654 PHE cc_start: 0.4510 (m-80) cc_final: 0.4215 (m-80) REVERT: B 692 MET cc_start: 0.4787 (ttm) cc_final: 0.3899 (ttm) REVERT: B 705 LEU cc_start: 0.7714 (tp) cc_final: 0.7466 (tp) outliers start: 3 outliers final: 0 residues processed: 250 average time/residue: 0.3019 time to fit residues: 100.1793 Evaluate side-chains 183 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN B 126 GLN B 131 ASN B 242 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10976 Z= 0.323 Angle : 0.772 10.097 14869 Z= 0.395 Chirality : 0.045 0.186 1706 Planarity : 0.006 0.050 1934 Dihedral : 7.165 120.814 1532 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.18 % Allowed : 4.23 % Favored : 95.60 % 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 (0.21), residues: 1355 helix: 0.99 (0.19), residues: 657 sheet: -0.64 (0.37), residues: 157 loop : -0.97 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 709 HIS 0.008 0.001 HIS B 24 PHE 0.020 0.002 PHE B 725 TYR 0.023 0.003 TYR A 635 ARG 0.009 0.001 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.6558 (m-10) cc_final: 0.6324 (m-80) REVERT: A 143 PHE cc_start: 0.6457 (m-80) cc_final: 0.6029 (m-80) REVERT: A 166 MET cc_start: 0.6264 (tpt) cc_final: 0.5940 (tpt) REVERT: A 207 ASP cc_start: 0.9093 (m-30) cc_final: 0.8880 (m-30) REVERT: A 222 LEU cc_start: 0.8035 (mt) cc_final: 0.7641 (pt) REVERT: A 229 ASN cc_start: 0.9084 (t0) cc_final: 0.8661 (t0) REVERT: A 308 LYS cc_start: 0.6910 (ttmt) cc_final: 0.6689 (ttpt) REVERT: A 323 GLU cc_start: 0.8324 (tt0) cc_final: 0.8123 (tm-30) REVERT: A 397 MET cc_start: 0.8706 (mtm) cc_final: 0.8189 (mtt) REVERT: A 441 ASP cc_start: 0.8753 (m-30) cc_final: 0.8482 (p0) REVERT: A 552 LEU cc_start: 0.9241 (tp) cc_final: 0.9027 (mt) REVERT: A 615 PRO cc_start: 0.7017 (Cg_endo) cc_final: 0.5890 (Cg_exo) REVERT: A 617 MET cc_start: 0.7906 (mmm) cc_final: 0.7652 (mmm) REVERT: B 155 PHE cc_start: 0.6833 (t80) cc_final: 0.6588 (t80) REVERT: B 269 MET cc_start: 0.8595 (ttm) cc_final: 0.8332 (ttm) REVERT: B 529 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8101 (tm-30) REVERT: B 533 ASP cc_start: 0.7380 (m-30) cc_final: 0.7007 (m-30) REVERT: B 565 LEU cc_start: 0.8162 (mt) cc_final: 0.7925 (tt) REVERT: B 692 MET cc_start: 0.4646 (ttm) cc_final: 0.3840 (ttm) outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 0.2872 time to fit residues: 86.9739 Evaluate side-chains 176 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 chunk 54 optimal weight: 0.0470 chunk 113 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN B 746 HIS ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10976 Z= 0.234 Angle : 0.693 7.563 14869 Z= 0.349 Chirality : 0.043 0.157 1706 Planarity : 0.005 0.049 1934 Dihedral : 6.800 121.168 1532 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.18 % Allowed : 2.20 % Favored : 97.62 % 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: 0.30 (0.22), residues: 1355 helix: 1.26 (0.19), residues: 663 sheet: -0.49 (0.37), residues: 165 loop : -0.90 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 709 HIS 0.004 0.001 HIS A 312 PHE 0.017 0.002 PHE B 725 TYR 0.020 0.002 TYR A 635 ARG 0.006 0.001 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6315 (m-80) cc_final: 0.5901 (m-80) REVERT: A 170 LEU cc_start: 0.7813 (mt) cc_final: 0.7532 (mt) REVERT: A 201 LEU cc_start: 0.7630 (tp) cc_final: 0.7166 (tp) REVERT: A 222 LEU cc_start: 0.8060 (mt) cc_final: 0.7661 (pt) REVERT: A 229 ASN cc_start: 0.9110 (t0) cc_final: 0.8673 (t0) REVERT: A 397 MET cc_start: 0.8653 (mtm) cc_final: 0.8069 (mtt) REVERT: A 432 GLU cc_start: 0.8478 (tt0) cc_final: 0.7906 (tp30) REVERT: A 441 ASP cc_start: 0.8810 (m-30) cc_final: 0.8350 (p0) REVERT: A 552 LEU cc_start: 0.9188 (tp) cc_final: 0.8973 (mt) REVERT: A 615 PRO cc_start: 0.6797 (Cg_endo) cc_final: 0.5612 (Cg_exo) REVERT: A 617 MET cc_start: 0.7867 (mmm) cc_final: 0.7630 (mmm) REVERT: B 155 PHE cc_start: 0.6900 (t80) cc_final: 0.6638 (t80) REVERT: B 223 VAL cc_start: 0.7360 (t) cc_final: 0.7095 (t) REVERT: B 269 MET cc_start: 0.8633 (ttm) cc_final: 0.8351 (ttm) REVERT: B 386 ASP cc_start: 0.7643 (p0) cc_final: 0.7434 (p0) REVERT: B 529 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8088 (tm-30) REVERT: B 533 ASP cc_start: 0.7393 (m-30) cc_final: 0.7001 (m-30) REVERT: B 552 LEU cc_start: 0.8639 (mm) cc_final: 0.8382 (mm) REVERT: B 565 LEU cc_start: 0.8050 (mt) cc_final: 0.7745 (tt) REVERT: B 717 ASN cc_start: 0.8091 (t0) cc_final: 0.7372 (t0) REVERT: B 759 MET cc_start: 0.8286 (mmp) cc_final: 0.8071 (mmp) REVERT: B 795 GLU cc_start: 0.8125 (pp20) cc_final: 0.7860 (pp20) outliers start: 2 outliers final: 1 residues processed: 214 average time/residue: 0.2725 time to fit residues: 79.1633 Evaluate side-chains 175 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 40.0000 chunk 11 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN B 276 ASN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.6483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10976 Z= 0.223 Angle : 0.698 10.721 14869 Z= 0.351 Chirality : 0.042 0.174 1706 Planarity : 0.005 0.041 1934 Dihedral : 6.664 119.373 1532 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.09 % Allowed : 2.55 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1355 helix: 1.29 (0.19), residues: 662 sheet: -0.39 (0.38), residues: 169 loop : -0.97 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 709 HIS 0.003 0.001 HIS A 312 PHE 0.019 0.002 PHE B 670 TYR 0.042 0.002 TYR B 31 ARG 0.007 0.001 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.6496 (m-10) cc_final: 0.6269 (m-10) REVERT: A 143 PHE cc_start: 0.6279 (m-80) cc_final: 0.5892 (m-80) REVERT: A 170 LEU cc_start: 0.7809 (mt) cc_final: 0.7569 (mt) REVERT: A 222 LEU cc_start: 0.8070 (mt) cc_final: 0.7682 (pt) REVERT: A 229 ASN cc_start: 0.9117 (t0) cc_final: 0.8672 (t0) REVERT: A 397 MET cc_start: 0.8623 (mtm) cc_final: 0.8032 (mtt) REVERT: A 432 GLU cc_start: 0.8450 (tt0) cc_final: 0.7760 (tp30) REVERT: A 441 ASP cc_start: 0.8801 (m-30) cc_final: 0.8369 (p0) REVERT: A 552 LEU cc_start: 0.9201 (tp) cc_final: 0.8975 (mt) REVERT: A 615 PRO cc_start: 0.6804 (Cg_endo) cc_final: 0.5748 (Cg_exo) REVERT: B 269 MET cc_start: 0.8617 (ttm) cc_final: 0.8347 (ttm) REVERT: B 529 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8002 (tm-30) REVERT: B 533 ASP cc_start: 0.7408 (m-30) cc_final: 0.7023 (m-30) REVERT: B 565 LEU cc_start: 0.8049 (mt) cc_final: 0.7774 (tt) REVERT: B 759 MET cc_start: 0.8275 (mmp) cc_final: 0.8000 (mmp) REVERT: B 795 GLU cc_start: 0.8205 (pp20) cc_final: 0.7964 (pp20) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.2871 time to fit residues: 82.4496 Evaluate side-chains 173 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 GLN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN B 734 GLN ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.7071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10976 Z= 0.314 Angle : 0.784 8.025 14869 Z= 0.403 Chirality : 0.046 0.192 1706 Planarity : 0.005 0.043 1934 Dihedral : 6.862 120.269 1532 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.09 % Allowed : 1.58 % Favored : 98.33 % 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: -0.19 (0.21), residues: 1355 helix: 0.89 (0.19), residues: 651 sheet: -0.57 (0.41), residues: 155 loop : -1.18 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 709 HIS 0.008 0.001 HIS A 312 PHE 0.022 0.002 PHE B 155 TYR 0.027 0.002 TYR B 31 ARG 0.009 0.001 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.7036 (m-10) cc_final: 0.6789 (m-10) REVERT: A 73 TYR cc_start: 0.6127 (p90) cc_final: 0.5886 (p90) REVERT: A 88 GLU cc_start: 0.7494 (tp30) cc_final: 0.7255 (tp30) REVERT: A 133 LEU cc_start: 0.7734 (tp) cc_final: 0.7487 (tp) REVERT: A 143 PHE cc_start: 0.6597 (m-80) cc_final: 0.6194 (m-80) REVERT: A 149 ASP cc_start: 0.7584 (t0) cc_final: 0.7381 (t0) REVERT: A 184 PHE cc_start: 0.4762 (t80) cc_final: 0.4503 (t80) REVERT: A 222 LEU cc_start: 0.8231 (mt) cc_final: 0.7803 (pt) REVERT: A 229 ASN cc_start: 0.9065 (t0) cc_final: 0.8766 (t0) REVERT: A 397 MET cc_start: 0.8667 (mtm) cc_final: 0.8031 (mtt) REVERT: A 409 ARG cc_start: 0.7068 (ptt-90) cc_final: 0.6823 (mtm110) REVERT: A 432 GLU cc_start: 0.8467 (tt0) cc_final: 0.7794 (tp30) REVERT: A 441 ASP cc_start: 0.8798 (m-30) cc_final: 0.8415 (p0) REVERT: A 552 LEU cc_start: 0.9222 (tp) cc_final: 0.8994 (mt) REVERT: A 615 PRO cc_start: 0.7078 (Cg_endo) cc_final: 0.6084 (Cg_exo) REVERT: B 73 TYR cc_start: 0.6296 (p90) cc_final: 0.6053 (p90) REVERT: B 269 MET cc_start: 0.8679 (ttm) cc_final: 0.8416 (ttm) REVERT: B 386 ASP cc_start: 0.7545 (p0) cc_final: 0.7301 (p0) REVERT: B 529 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8063 (tm-30) REVERT: B 533 ASP cc_start: 0.7507 (m-30) cc_final: 0.7115 (m-30) REVERT: B 552 LEU cc_start: 0.8705 (mm) cc_final: 0.8431 (mm) REVERT: B 752 HIS cc_start: 0.8262 (p-80) cc_final: 0.8061 (p-80) REVERT: B 759 MET cc_start: 0.8341 (mmp) cc_final: 0.8056 (mmp) REVERT: B 795 GLU cc_start: 0.8322 (pp20) cc_final: 0.8056 (pp20) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.2800 time to fit residues: 72.6390 Evaluate side-chains 159 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 83 optimal weight: 0.0470 chunk 89 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.7298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10976 Z= 0.250 Angle : 0.747 11.883 14869 Z= 0.377 Chirality : 0.045 0.187 1706 Planarity : 0.005 0.041 1934 Dihedral : 6.702 120.683 1532 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.09 % Allowed : 0.97 % Favored : 98.94 % 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: 0.11 (0.22), residues: 1355 helix: 1.25 (0.20), residues: 651 sheet: -0.45 (0.40), residues: 166 loop : -1.20 (0.24), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 709 HIS 0.006 0.001 HIS A 312 PHE 0.037 0.002 PHE B 730 TYR 0.024 0.002 TYR B 31 ARG 0.009 0.001 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.6639 (m-10) cc_final: 0.6327 (m-10) REVERT: A 73 TYR cc_start: 0.5953 (p90) cc_final: 0.5685 (p90) REVERT: A 133 LEU cc_start: 0.7985 (tp) cc_final: 0.7476 (tp) REVERT: A 143 PHE cc_start: 0.6232 (m-80) cc_final: 0.5910 (m-10) REVERT: A 149 ASP cc_start: 0.7602 (t0) cc_final: 0.7400 (t0) REVERT: A 166 MET cc_start: 0.6090 (tpt) cc_final: 0.5817 (tpt) REVERT: A 170 LEU cc_start: 0.7748 (mt) cc_final: 0.7478 (mt) REVERT: A 222 LEU cc_start: 0.8357 (mt) cc_final: 0.8000 (pt) REVERT: A 229 ASN cc_start: 0.9040 (t0) cc_final: 0.8713 (t0) REVERT: A 397 MET cc_start: 0.8526 (mtm) cc_final: 0.7962 (mtt) REVERT: A 432 GLU cc_start: 0.8433 (tt0) cc_final: 0.7805 (tp30) REVERT: A 441 ASP cc_start: 0.8791 (m-30) cc_final: 0.8384 (p0) REVERT: A 552 LEU cc_start: 0.9175 (tp) cc_final: 0.8923 (mt) REVERT: A 615 PRO cc_start: 0.7028 (Cg_endo) cc_final: 0.6084 (Cg_exo) REVERT: B 269 MET cc_start: 0.8719 (ttm) cc_final: 0.8422 (ttt) REVERT: B 386 ASP cc_start: 0.7366 (p0) cc_final: 0.7050 (p0) REVERT: B 795 GLU cc_start: 0.8337 (pp20) cc_final: 0.8065 (pp20) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.2760 time to fit residues: 72.4974 Evaluate side-chains 157 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 80 optimal weight: 0.0060 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN B 752 HIS ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.7490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10976 Z= 0.252 Angle : 0.748 9.293 14869 Z= 0.378 Chirality : 0.044 0.169 1706 Planarity : 0.005 0.042 1934 Dihedral : 6.625 119.961 1532 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.09 % Allowed : 0.70 % Favored : 99.21 % 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: 0.11 (0.22), residues: 1355 helix: 1.22 (0.20), residues: 653 sheet: -0.58 (0.37), residues: 181 loop : -1.12 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 709 HIS 0.004 0.001 HIS A 312 PHE 0.048 0.002 PHE B 730 TYR 0.026 0.002 TYR B 31 ARG 0.010 0.001 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6423 (m-80) cc_final: 0.6037 (m-10) REVERT: A 170 LEU cc_start: 0.7756 (mt) cc_final: 0.7452 (mt) REVERT: A 229 ASN cc_start: 0.9079 (t0) cc_final: 0.8800 (t0) REVERT: A 397 MET cc_start: 0.8499 (mtm) cc_final: 0.7944 (mtt) REVERT: A 432 GLU cc_start: 0.8434 (tt0) cc_final: 0.7806 (tp30) REVERT: A 441 ASP cc_start: 0.8803 (m-30) cc_final: 0.8377 (p0) REVERT: A 552 LEU cc_start: 0.9177 (tp) cc_final: 0.8932 (mt) REVERT: A 615 PRO cc_start: 0.7039 (Cg_endo) cc_final: 0.6098 (Cg_exo) REVERT: A 674 MET cc_start: 0.6302 (ptt) cc_final: 0.5776 (ptt) REVERT: B 269 MET cc_start: 0.8754 (ttm) cc_final: 0.8443 (ttt) REVERT: B 386 ASP cc_start: 0.7306 (p0) cc_final: 0.6992 (p0) REVERT: B 529 GLU cc_start: 0.9000 (mm-30) cc_final: 0.7748 (tm-30) REVERT: B 718 LYS cc_start: 0.6927 (tmmt) cc_final: 0.6563 (mmmm) REVERT: B 752 HIS cc_start: 0.8219 (p90) cc_final: 0.7978 (p-80) REVERT: B 795 GLU cc_start: 0.8362 (pp20) cc_final: 0.8129 (pp20) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.2720 time to fit residues: 68.6414 Evaluate side-chains 156 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 90 optimal weight: 0.0870 chunk 136 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 83 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 overall best weight: 3.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.7632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10976 Z= 0.240 Angle : 0.753 10.616 14869 Z= 0.379 Chirality : 0.044 0.178 1706 Planarity : 0.005 0.043 1934 Dihedral : 6.527 118.582 1532 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.12 (0.22), residues: 1355 helix: 1.24 (0.20), residues: 652 sheet: -0.37 (0.39), residues: 166 loop : -1.21 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 709 HIS 0.005 0.001 HIS A 312 PHE 0.041 0.002 PHE B 730 TYR 0.025 0.002 TYR A 528 ARG 0.011 0.001 ARG B 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.6312 (m-80) cc_final: 0.5892 (m-10) REVERT: A 170 LEU cc_start: 0.7697 (mt) cc_final: 0.7405 (mt) REVERT: A 222 LEU cc_start: 0.8320 (mt) cc_final: 0.7949 (pt) REVERT: A 229 ASN cc_start: 0.9059 (t0) cc_final: 0.8724 (t0) REVERT: A 397 MET cc_start: 0.8507 (mtm) cc_final: 0.7971 (mtt) REVERT: A 432 GLU cc_start: 0.8417 (tt0) cc_final: 0.7786 (tp30) REVERT: A 441 ASP cc_start: 0.8766 (m-30) cc_final: 0.8314 (p0) REVERT: A 552 LEU cc_start: 0.9163 (tp) cc_final: 0.8912 (mt) REVERT: A 615 PRO cc_start: 0.7110 (Cg_endo) cc_final: 0.6190 (Cg_exo) REVERT: B 269 MET cc_start: 0.8817 (ttm) cc_final: 0.8498 (ttt) REVERT: B 386 ASP cc_start: 0.7317 (p0) cc_final: 0.7007 (p0) REVERT: B 529 GLU cc_start: 0.8976 (mm-30) cc_final: 0.7682 (tm-30) REVERT: B 609 MET cc_start: 0.8088 (tpt) cc_final: 0.7774 (tpp) REVERT: B 705 LEU cc_start: 0.7876 (tp) cc_final: 0.7639 (mt) REVERT: B 718 LYS cc_start: 0.7031 (tmmt) cc_final: 0.6615 (mmmm) REVERT: B 778 LEU cc_start: 0.8628 (tt) cc_final: 0.8348 (tt) REVERT: B 795 GLU cc_start: 0.8358 (pp20) cc_final: 0.8111 (pp20) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.3282 time to fit residues: 82.0980 Evaluate side-chains 150 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 HIS ** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.070073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.061711 restraints weight = 72069.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.063091 restraints weight = 52432.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.064115 restraints weight = 39924.235| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.7836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10976 Z= 0.256 Angle : 0.751 9.619 14869 Z= 0.380 Chirality : 0.044 0.188 1706 Planarity : 0.005 0.043 1934 Dihedral : 6.478 117.360 1532 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: 0.08 (0.22), residues: 1355 helix: 1.20 (0.20), residues: 650 sheet: -0.35 (0.39), residues: 166 loop : -1.21 (0.24), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 137 HIS 0.004 0.001 HIS A 312 PHE 0.048 0.002 PHE B 730 TYR 0.024 0.002 TYR B 31 ARG 0.013 0.001 ARG B 608 =============================================================================== Job complete usr+sys time: 2334.57 seconds wall clock time: 43 minutes 58.88 seconds (2638.88 seconds total)