Starting phenix.real_space_refine on Sun Jul 21 07:50:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrn_36599/07_2024/8jrn_36599_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrn_36599/07_2024/8jrn_36599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrn_36599/07_2024/8jrn_36599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrn_36599/07_2024/8jrn_36599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrn_36599/07_2024/8jrn_36599_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrn_36599/07_2024/8jrn_36599_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic. 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 Zn 4 6.06 5 S 78 5.16 5 C 8720 2.51 5 N 2294 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 36": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C GLU 431": "OE1" <-> "OE2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 580": "OE1" <-> "OE2" Residue "C GLU 581": "OE1" <-> "OE2" Residue "C GLU 594": "OE1" <-> "OE2" Residue "C GLU 727": "OE1" <-> "OE2" Residue "C GLU 743": "OE1" <-> "OE2" Residue "C GLU 772": "OE1" <-> "OE2" Residue "C GLU 835": "OE1" <-> "OE2" Residue "C GLU 851": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A GLU 772": "OE1" <-> "OE2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A GLU 851": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13672 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1191 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "C" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5643 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 28, 'TRANS': 660} Chain breaks: 1 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1191 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "A" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5643 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 28, 'TRANS': 660} Chain breaks: 1 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 241 SG CYS D 37 80.325 76.845 88.839 1.00 26.36 S ATOM 266 SG CYS D 40 81.531 74.319 91.219 1.00 38.33 S ATOM 522 SG CYS D 70 82.722 74.229 87.529 1.00 39.32 S ATOM 545 SG CYS D 73 79.254 73.116 88.390 1.00 44.29 S ATOM 864 SG CYS D 110 81.003 74.553 71.069 1.00 32.36 S ATOM 886 SG CYS D 113 83.147 75.923 73.849 1.00 28.84 S ATOM 1148 SG CYS D 143 84.650 74.990 70.447 1.00 41.28 S ATOM 1168 SG CYS D 146 83.506 72.219 72.728 1.00 41.86 S ATOM 7075 SG CYS B 37 63.189 34.539 88.839 1.00 26.36 S ATOM 7100 SG CYS B 40 61.983 37.065 91.219 1.00 38.33 S ATOM 7356 SG CYS B 70 60.792 37.155 87.529 1.00 39.32 S ATOM 7379 SG CYS B 73 64.260 38.268 88.390 1.00 44.29 S ATOM 7698 SG CYS B 110 62.511 36.831 71.069 1.00 32.36 S ATOM 7720 SG CYS B 113 60.367 35.461 73.849 1.00 28.84 S ATOM 7982 SG CYS B 143 58.864 36.394 70.447 1.00 41.28 S ATOM 8002 SG CYS B 146 60.008 39.165 72.728 1.00 41.86 S Time building chain proxies: 7.63, per 1000 atoms: 0.56 Number of scatterers: 13672 At special positions: 0 Unit cell: (144.585, 112.455, 109.242, 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) Zn 4 29.99 S 78 16.00 O 2576 8.00 N 2294 7.00 C 8720 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: 5.29 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 70 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 73 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 110 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 143 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 113 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 146 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 70 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 40 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 37 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 73 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 110 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 143 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 146 " Number of angles added : 24 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 14 sheets defined 61.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'D' and resid 18 through 26 Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 70 through 85 Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 118 through 128 Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 159 through 165 removed outlier: 3.502A pdb=" N GLN C 165 " --> pdb=" O GLU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 247 removed outlier: 3.615A pdb=" N ILE C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 273 removed outlier: 3.582A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Proline residue: C 265 - end of helix removed outlier: 3.635A pdb=" N CYS C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 removed outlier: 4.086A pdb=" N ARG C 279 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 275 through 280' Processing helix chain 'C' and resid 281 through 283 No H-bonds generated for 'chain 'C' and resid 281 through 283' Processing helix chain 'C' and resid 284 through 292 removed outlier: 3.588A pdb=" N ILE C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 298 Processing helix chain 'C' and resid 304 through 314 removed outlier: 3.544A pdb=" N LEU C 308 " --> pdb=" O MET C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 330 removed outlier: 3.872A pdb=" N LYS C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 354 removed outlier: 3.599A pdb=" N PHE C 343 " --> pdb=" O MET C 339 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.612A pdb=" N MET C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 413 Processing helix chain 'C' and resid 426 through 433 removed outlier: 3.601A pdb=" N THR C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.583A pdb=" N ILE C 450 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 456 Processing helix chain 'C' and resid 459 through 469 removed outlier: 3.606A pdb=" N THR C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 Proline residue: C 481 - end of helix Processing helix chain 'C' and resid 485 through 515 Processing helix chain 'C' and resid 528 through 530 No H-bonds generated for 'chain 'C' and resid 528 through 530' Processing helix chain 'C' and resid 531 through 547 Processing helix chain 'C' and resid 548 through 553 Processing helix chain 'C' and resid 568 through 583 Processing helix chain 'C' and resid 584 through 588 Processing helix chain 'C' and resid 608 through 625 Processing helix chain 'C' and resid 634 through 642 removed outlier: 3.914A pdb=" N TYR C 638 " --> pdb=" O PRO C 634 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 650 through 655 removed outlier: 3.543A pdb=" N SER C 654 " --> pdb=" O ASP C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 667 removed outlier: 3.961A pdb=" N LEU C 665 " --> pdb=" O SER C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 676 Processing helix chain 'C' and resid 709 through 723 Processing helix chain 'C' and resid 726 through 742 removed outlier: 3.977A pdb=" N VAL C 740 " --> pdb=" O GLY C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 751 through 760 removed outlier: 3.874A pdb=" N GLU C 756 " --> pdb=" O PRO C 752 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU C 757 " --> pdb=" O GLU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 774 Processing helix chain 'C' and resid 784 through 796 Processing helix chain 'C' and resid 798 through 811 Processing helix chain 'C' and resid 842 through 844 No H-bonds generated for 'chain 'C' and resid 842 through 844' Processing helix chain 'C' and resid 854 through 867 Processing helix chain 'B' and resid 18 through 26 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 70 through 85 Processing helix chain 'B' and resid 91 through 100 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.502A pdb=" N GLN A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 removed outlier: 3.615A pdb=" N ILE A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 273 removed outlier: 3.582A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Proline residue: A 265 - end of helix removed outlier: 3.635A pdb=" N CYS A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 4.086A pdb=" N ARG A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 280' Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.588A pdb=" N ILE A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 304 through 314 removed outlier: 3.544A pdb=" N LEU A 308 " --> pdb=" O MET A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 330 removed outlier: 3.872A pdb=" N LYS A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 354 removed outlier: 3.599A pdb=" N PHE A 343 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.612A pdb=" N MET A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'A' and resid 426 through 433 removed outlier: 3.601A pdb=" N THR A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.583A pdb=" N ILE A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 Processing helix chain 'A' and resid 459 through 469 removed outlier: 3.606A pdb=" N THR A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 485 through 515 Processing helix chain 'A' and resid 528 through 530 No H-bonds generated for 'chain 'A' and resid 528 through 530' Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 568 through 583 Processing helix chain 'A' and resid 584 through 588 Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 634 through 642 removed outlier: 3.914A pdb=" N TYR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 650 through 655 removed outlier: 3.543A pdb=" N SER A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 667 removed outlier: 3.961A pdb=" N LEU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 726 through 742 removed outlier: 3.977A pdb=" N VAL A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 751 through 760 removed outlier: 3.874A pdb=" N GLU A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 774 Processing helix chain 'A' and resid 784 through 796 Processing helix chain 'A' and resid 798 through 811 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 854 through 867 Processing sheet with id=AA1, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'D' and resid 86 through 90 removed outlier: 6.738A pdb=" N ASN D 134 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER D 89 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE D 132 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARG D 109 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 387 through 388 removed outlier: 6.595A pdb=" N GLU C 387 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 522 through 527 Processing sheet with id=AA5, first strand: chain 'C' and resid 590 through 593 Processing sheet with id=AA6, first strand: chain 'C' and resid 681 through 685 Processing sheet with id=AA7, first strand: chain 'C' and resid 775 through 777 removed outlier: 6.490A pdb=" N GLU C 775 " --> pdb=" O ILE C 827 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS C 829 " --> pdb=" O GLU C 775 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP C 777 " --> pdb=" O LYS C 829 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE C 826 " --> pdb=" O LEU C 847 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU C 849 " --> pdb=" O ILE C 826 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA C 828 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA9, first strand: chain 'B' and resid 86 through 90 removed outlier: 6.738A pdb=" N ASN B 134 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER B 89 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE B 132 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARG B 109 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.595A pdb=" N GLU A 387 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 527 Processing sheet with id=AB3, first strand: chain 'A' and resid 590 through 593 Processing sheet with id=AB4, first strand: chain 'A' and resid 681 through 685 Processing sheet with id=AB5, first strand: chain 'A' and resid 775 through 777 removed outlier: 6.490A pdb=" N GLU A 775 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS A 829 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP A 777 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE A 826 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU A 849 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA A 828 " --> pdb=" O LEU A 849 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1848 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: 4.29 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4488 1.34 - 1.46: 3003 1.46 - 1.58: 6337 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 13948 Sorted by residual: bond pdb=" N LEU A 806 " pdb=" CA LEU A 806 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.34e+00 bond pdb=" N ASP A 397 " pdb=" CA ASP A 397 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.29e+00 bond pdb=" N ASP C 397 " pdb=" CA ASP C 397 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 5.78e+00 bond pdb=" N LEU C 806 " pdb=" CA LEU C 806 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.76e+00 bond pdb=" N THR C 809 " pdb=" CA THR C 809 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.28e-02 6.10e+03 5.55e+00 ... (remaining 13943 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.81: 274 105.81 - 112.84: 7248 112.84 - 119.88: 4803 119.88 - 126.92: 6393 126.92 - 133.96: 114 Bond angle restraints: 18832 Sorted by residual: angle pdb=" CA ASP A 396 " pdb=" C ASP A 396 " pdb=" O ASP A 396 " ideal model delta sigma weight residual 120.96 118.02 2.94 1.09e+00 8.42e-01 7.27e+00 angle pdb=" CA ASP C 396 " pdb=" C ASP C 396 " pdb=" O ASP C 396 " ideal model delta sigma weight residual 120.96 118.07 2.89 1.09e+00 8.42e-01 7.01e+00 angle pdb=" CA ASP C 397 " pdb=" C ASP C 397 " pdb=" O ASP C 397 " ideal model delta sigma weight residual 121.19 118.34 2.85 1.10e+00 8.26e-01 6.70e+00 angle pdb=" CA ASP A 397 " pdb=" C ASP A 397 " pdb=" O ASP A 397 " ideal model delta sigma weight residual 121.19 118.36 2.83 1.10e+00 8.26e-01 6.60e+00 angle pdb=" N ARG A 498 " pdb=" CA ARG A 498 " pdb=" C ARG A 498 " ideal model delta sigma weight residual 111.07 108.33 2.74 1.07e+00 8.73e-01 6.54e+00 ... (remaining 18827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 7299 17.67 - 35.35: 883 35.35 - 53.02: 270 53.02 - 70.70: 56 70.70 - 88.37: 20 Dihedral angle restraints: 8528 sinusoidal: 3612 harmonic: 4916 Sorted by residual: dihedral pdb=" CA ASP C 686 " pdb=" CB ASP C 686 " pdb=" CG ASP C 686 " pdb=" OD1 ASP C 686 " ideal model delta sinusoidal sigma weight residual -30.00 -89.60 59.60 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP A 686 " pdb=" CB ASP A 686 " pdb=" CG ASP A 686 " pdb=" OD1 ASP A 686 " ideal model delta sinusoidal sigma weight residual -30.00 -89.60 59.60 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CB GLU A 161 " pdb=" CG GLU A 161 " pdb=" CD GLU A 161 " pdb=" OE1 GLU A 161 " ideal model delta sinusoidal sigma weight residual 0.00 -88.34 88.34 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 8525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1334 0.032 - 0.064: 522 0.064 - 0.096: 143 0.096 - 0.128: 59 0.128 - 0.160: 2 Chirality restraints: 2060 Sorted by residual: chirality pdb=" CA GLN C 807 " pdb=" N GLN C 807 " pdb=" C GLN C 807 " pdb=" CB GLN C 807 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CA GLN A 807 " pdb=" N GLN A 807 " pdb=" C GLN A 807 " pdb=" CB GLN A 807 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE C 826 " pdb=" N ILE C 826 " pdb=" C ILE C 826 " pdb=" CB ILE C 826 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 2057 not shown) Planarity restraints: 2442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 444 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO A 445 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 444 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO C 445 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 445 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 445 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 764 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C ASN A 764 " -0.024 2.00e-02 2.50e+03 pdb=" O ASN A 764 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU A 765 " 0.008 2.00e-02 2.50e+03 ... (remaining 2439 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 38 2.45 - 3.06: 8875 3.06 - 3.68: 21456 3.68 - 4.29: 32921 4.29 - 4.90: 53217 Nonbonded interactions: 116507 Sorted by model distance: nonbonded pdb=" O GLU C 161 " pdb=" OE1 GLN C 165 " model vdw 1.840 3.040 nonbonded pdb=" O GLU A 161 " pdb=" OE1 GLN A 165 " model vdw 1.840 3.040 nonbonded pdb=" O ARG A 836 " pdb=" OH TYR A 852 " model vdw 2.158 2.440 nonbonded pdb=" O ARG C 836 " pdb=" OH TYR C 852 " model vdw 2.158 2.440 nonbonded pdb=" O LEU C 863 " pdb=" OG1 THR C 867 " model vdw 2.294 2.440 ... (remaining 116502 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' selection = chain 'C' } ncs_group { reference = chain 'B' 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 41.160 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 : 0.004 0.047 13948 Z= 0.245 Angle : 0.509 6.311 18832 Z= 0.283 Chirality : 0.040 0.160 2060 Planarity : 0.003 0.041 2442 Dihedral : 17.312 88.369 5352 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.26 % Allowed : 25.33 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1648 helix: 0.20 (0.17), residues: 874 sheet: -1.41 (0.55), residues: 72 loop : 0.80 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 139 HIS 0.003 0.001 HIS B 85 PHE 0.012 0.001 PHE A 287 TYR 0.017 0.001 TYR D 77 ARG 0.006 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 395 time to evaluate : 1.683 Fit side-chains revert: symmetry clash REVERT: D 130 GLN cc_start: 0.8244 (mt0) cc_final: 0.7960 (mt0) REVERT: D 131 ARG cc_start: 0.8543 (mtm-85) cc_final: 0.8310 (mtt180) REVERT: C 132 LYS cc_start: 0.7390 (tppt) cc_final: 0.7176 (tppp) REVERT: C 264 SER cc_start: 0.7862 (m) cc_final: 0.7655 (m) REVERT: C 451 ASN cc_start: 0.8371 (t0) cc_final: 0.8148 (t0) REVERT: C 462 LYS cc_start: 0.8134 (ptpt) cc_final: 0.7894 (mtmm) REVERT: C 542 MET cc_start: 0.7160 (tpp) cc_final: 0.6955 (tpp) REVERT: C 586 ASP cc_start: 0.7550 (m-30) cc_final: 0.7234 (m-30) REVERT: C 593 ASP cc_start: 0.7032 (t0) cc_final: 0.6759 (t0) REVERT: C 692 MET cc_start: 0.6197 (mmm) cc_final: 0.5792 (mmm) REVERT: C 693 MET cc_start: 0.7108 (mtt) cc_final: 0.6471 (mtt) REVERT: C 768 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8186 (mm-40) REVERT: C 783 ASP cc_start: 0.7094 (m-30) cc_final: 0.6840 (m-30) REVERT: B 17 ARG cc_start: 0.6750 (ptm-80) cc_final: 0.6392 (ptm-80) REVERT: B 18 LYS cc_start: 0.8640 (mptp) cc_final: 0.8428 (mmtm) REVERT: B 130 GLN cc_start: 0.8115 (mt0) cc_final: 0.7770 (mt0) REVERT: B 131 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.8316 (mtt180) REVERT: A 132 LYS cc_start: 0.7372 (tppt) cc_final: 0.7141 (tptp) REVERT: A 338 ARG cc_start: 0.7379 (mtp85) cc_final: 0.7167 (mtp85) REVERT: A 355 GLU cc_start: 0.6572 (tm-30) cc_final: 0.6298 (tm-30) REVERT: A 447 GLU cc_start: 0.7086 (mp0) cc_final: 0.6876 (mp0) REVERT: A 460 MET cc_start: 0.8799 (mmm) cc_final: 0.8528 (mmt) REVERT: A 526 LYS cc_start: 0.7940 (tppp) cc_final: 0.7103 (ttmm) REVERT: A 542 MET cc_start: 0.7082 (tpp) cc_final: 0.6832 (tpp) REVERT: A 593 ASP cc_start: 0.7060 (t0) cc_final: 0.6753 (t0) REVERT: A 663 LYS cc_start: 0.7613 (ptmm) cc_final: 0.7350 (ttpp) REVERT: A 681 GLN cc_start: 0.7340 (tt0) cc_final: 0.6705 (tt0) REVERT: A 692 MET cc_start: 0.6081 (mmm) cc_final: 0.5663 (mmm) REVERT: A 693 MET cc_start: 0.6702 (mtt) cc_final: 0.6084 (mtt) REVERT: A 783 ASP cc_start: 0.7103 (m-30) cc_final: 0.6850 (m-30) outliers start: 4 outliers final: 2 residues processed: 397 average time/residue: 1.4255 time to fit residues: 610.5793 Evaluate side-chains 359 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 357 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain A residue 233 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 GLN D 43 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN C 321 GLN C 497 ASN C 517 GLN C 520 ASN C 531 HIS C 584 ASN C 626 ASN C 715 ASN C 795 HIS B 43 GLN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 497 ASN A 531 HIS A 576 GLN A 602 ASN A 611 GLN A 626 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN A 764 ASN A 795 HIS A 807 GLN A 841 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13948 Z= 0.253 Angle : 0.509 8.646 18832 Z= 0.263 Chirality : 0.040 0.152 2060 Planarity : 0.004 0.037 2442 Dihedral : 3.877 15.524 1848 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.11 % Allowed : 23.69 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1648 helix: 1.03 (0.18), residues: 866 sheet: -1.16 (0.58), residues: 72 loop : 0.66 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 139 HIS 0.003 0.001 HIS C 297 PHE 0.012 0.002 PHE A 730 TYR 0.016 0.001 TYR B 77 ARG 0.004 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 369 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 130 GLN cc_start: 0.8180 (mt0) cc_final: 0.7878 (mt0) REVERT: D 131 ARG cc_start: 0.8654 (mtm-85) cc_final: 0.8316 (mtt180) REVERT: C 128 LEU cc_start: 0.8063 (mp) cc_final: 0.7852 (mm) REVERT: C 132 LYS cc_start: 0.7460 (tppt) cc_final: 0.7220 (tppp) REVERT: C 264 SER cc_start: 0.7873 (m) cc_final: 0.7659 (m) REVERT: C 327 LEU cc_start: 0.8228 (tt) cc_final: 0.7958 (tp) REVERT: C 447 GLU cc_start: 0.6908 (pp20) cc_final: 0.6668 (pm20) REVERT: C 462 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7880 (mtmt) REVERT: C 576 GLN cc_start: 0.8148 (tt0) cc_final: 0.7839 (tt0) REVERT: C 595 SER cc_start: 0.8241 (p) cc_final: 0.8009 (m) REVERT: C 692 MET cc_start: 0.6341 (mmm) cc_final: 0.6045 (mmm) REVERT: C 693 MET cc_start: 0.6770 (mtt) cc_final: 0.6364 (mtt) REVERT: C 703 ILE cc_start: 0.8114 (mp) cc_final: 0.7909 (tt) REVERT: C 825 MET cc_start: 0.8630 (ttm) cc_final: 0.8375 (ttt) REVERT: B 18 LYS cc_start: 0.8604 (mptp) cc_final: 0.8385 (mmtm) REVERT: B 130 GLN cc_start: 0.8122 (mt0) cc_final: 0.7819 (mt0) REVERT: B 136 ARG cc_start: 0.7769 (mmm-85) cc_final: 0.7474 (mmm-85) REVERT: A 128 LEU cc_start: 0.8078 (mp) cc_final: 0.7851 (mm) REVERT: A 132 LYS cc_start: 0.7450 (tppt) cc_final: 0.7147 (tptp) REVERT: A 161 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5796 (pm20) REVERT: A 165 GLN cc_start: 0.7785 (mp10) cc_final: 0.7224 (mp10) REVERT: A 338 ARG cc_start: 0.7329 (mtp85) cc_final: 0.7057 (mtp85) REVERT: A 447 GLU cc_start: 0.7166 (mp0) cc_final: 0.6936 (mp0) REVERT: A 460 MET cc_start: 0.8787 (mmm) cc_final: 0.8469 (mmt) REVERT: A 526 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7727 (tppp) REVERT: A 542 MET cc_start: 0.7158 (tpp) cc_final: 0.6778 (tpp) REVERT: A 593 ASP cc_start: 0.6809 (t0) cc_final: 0.6492 (t0) REVERT: A 605 SER cc_start: 0.7950 (t) cc_final: 0.7697 (p) REVERT: A 663 LYS cc_start: 0.7531 (ptmm) cc_final: 0.7160 (ttpp) REVERT: A 667 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: A 692 MET cc_start: 0.6235 (mmm) cc_final: 0.5947 (mmm) REVERT: A 693 MET cc_start: 0.6732 (mtt) cc_final: 0.6454 (mtt) REVERT: A 714 VAL cc_start: 0.8315 (t) cc_final: 0.8112 (t) REVERT: A 743 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7229 (mm-30) REVERT: A 783 ASP cc_start: 0.7154 (m-30) cc_final: 0.6908 (m-30) outliers start: 63 outliers final: 29 residues processed: 395 average time/residue: 1.5151 time to fit residues: 644.8449 Evaluate side-chains 384 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 351 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 764 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 123 optimal weight: 0.0670 chunk 101 optimal weight: 0.0980 chunk 41 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN C 517 GLN C 626 ASN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 112 ASN A 382 ASN A 626 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13948 Z= 0.188 Angle : 0.471 7.035 18832 Z= 0.244 Chirality : 0.038 0.120 2060 Planarity : 0.003 0.033 2442 Dihedral : 3.746 15.519 1846 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.98 % Allowed : 25.13 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.21), residues: 1648 helix: 1.20 (0.18), residues: 892 sheet: -1.38 (0.56), residues: 72 loop : 0.68 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 139 HIS 0.003 0.001 HIS A 841 PHE 0.009 0.001 PHE A 730 TYR 0.013 0.001 TYR B 77 ARG 0.004 0.000 ARG C 649 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 357 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 ARG cc_start: 0.8379 (tpp-160) cc_final: 0.8092 (tpm170) REVERT: D 131 ARG cc_start: 0.8671 (mtm-85) cc_final: 0.8312 (mtt180) REVERT: C 132 LYS cc_start: 0.7478 (tppt) cc_final: 0.7259 (tppp) REVERT: C 137 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7663 (tp) REVERT: C 264 SER cc_start: 0.7865 (m) cc_final: 0.7645 (m) REVERT: C 323 LYS cc_start: 0.8105 (mtpm) cc_final: 0.7823 (mtpp) REVERT: C 327 LEU cc_start: 0.8193 (tt) cc_final: 0.7948 (tp) REVERT: C 447 GLU cc_start: 0.6794 (pp20) cc_final: 0.6525 (pm20) REVERT: C 692 MET cc_start: 0.6370 (mmm) cc_final: 0.6060 (mmm) REVERT: C 693 MET cc_start: 0.6719 (mtt) cc_final: 0.6225 (mtt) REVERT: C 703 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7946 (tt) REVERT: C 825 MET cc_start: 0.8618 (ttm) cc_final: 0.8374 (ttt) REVERT: B 130 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7790 (mt0) REVERT: B 136 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.7409 (mmm-85) REVERT: A 132 LYS cc_start: 0.7486 (tppt) cc_final: 0.7141 (tptp) REVERT: A 165 GLN cc_start: 0.7780 (mp10) cc_final: 0.7320 (mp10) REVERT: A 327 LEU cc_start: 0.8030 (tp) cc_final: 0.7826 (tt) REVERT: A 447 GLU cc_start: 0.7079 (mp0) cc_final: 0.6831 (mp0) REVERT: A 605 SER cc_start: 0.7869 (t) cc_final: 0.7658 (p) REVERT: A 663 LYS cc_start: 0.7546 (ptmm) cc_final: 0.7241 (ttpp) REVERT: A 667 GLU cc_start: 0.7583 (pm20) cc_final: 0.7049 (pm20) REVERT: A 692 MET cc_start: 0.6254 (mmm) cc_final: 0.6005 (mmm) REVERT: A 693 MET cc_start: 0.6758 (mtt) cc_final: 0.6479 (mtt) REVERT: A 743 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7216 (mm-30) outliers start: 61 outliers final: 27 residues processed: 380 average time/residue: 1.5027 time to fit residues: 615.3553 Evaluate side-chains 378 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 348 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 812 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN C 517 GLN C 626 ASN B 43 GLN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13948 Z= 0.377 Angle : 0.544 7.815 18832 Z= 0.279 Chirality : 0.043 0.131 2060 Planarity : 0.004 0.033 2442 Dihedral : 4.051 17.463 1846 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.77 % Allowed : 23.04 % Favored : 72.19 % 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: 0.96 (0.21), residues: 1648 helix: 1.04 (0.17), residues: 888 sheet: -1.51 (0.55), residues: 72 loop : 0.56 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 139 HIS 0.003 0.001 HIS B 85 PHE 0.019 0.002 PHE A 730 TYR 0.021 0.002 TYR B 77 ARG 0.004 0.000 ARG C 735 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 381 time to evaluate : 1.723 Fit side-chains revert: symmetry clash REVERT: D 46 ARG cc_start: 0.8412 (tpp-160) cc_final: 0.8210 (tpm170) REVERT: D 131 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8265 (mtt180) REVERT: C 132 LYS cc_start: 0.7489 (tppt) cc_final: 0.7237 (tppp) REVERT: C 264 SER cc_start: 0.7899 (m) cc_final: 0.7694 (m) REVERT: C 268 GLU cc_start: 0.6886 (tt0) cc_final: 0.6552 (tt0) REVERT: C 327 LEU cc_start: 0.8206 (tt) cc_final: 0.7963 (tp) REVERT: C 355 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6345 (tm-30) REVERT: C 447 GLU cc_start: 0.7042 (pp20) cc_final: 0.6763 (pm20) REVERT: C 692 MET cc_start: 0.6410 (mmm) cc_final: 0.6095 (mmm) REVERT: C 693 MET cc_start: 0.6698 (mtt) cc_final: 0.6172 (mtt) REVERT: C 703 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7920 (tt) REVERT: C 739 MET cc_start: 0.8312 (ptm) cc_final: 0.8108 (ptm) REVERT: C 825 MET cc_start: 0.8627 (ttm) cc_final: 0.8406 (ttt) REVERT: B 130 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: A 132 LYS cc_start: 0.7482 (tppt) cc_final: 0.7160 (tptp) REVERT: A 165 GLN cc_start: 0.7817 (mp10) cc_final: 0.7065 (mp-120) REVERT: A 323 LYS cc_start: 0.7958 (mtpm) cc_final: 0.7648 (mtpp) REVERT: A 435 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7369 (mtpt) REVERT: A 447 GLU cc_start: 0.7169 (mp0) cc_final: 0.6881 (mp0) REVERT: A 605 SER cc_start: 0.7941 (t) cc_final: 0.7730 (p) REVERT: A 663 LYS cc_start: 0.7540 (ptmm) cc_final: 0.7259 (ttpp) REVERT: A 667 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7044 (pm20) REVERT: A 692 MET cc_start: 0.6437 (mmm) cc_final: 0.6108 (mmm) REVERT: A 693 MET cc_start: 0.6898 (mtt) cc_final: 0.6605 (mtt) REVERT: A 743 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7229 (mm-30) outliers start: 73 outliers final: 41 residues processed: 404 average time/residue: 1.5477 time to fit residues: 673.3177 Evaluate side-chains 417 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 371 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 747 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 796 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 626 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13948 Z= 0.196 Angle : 0.482 8.840 18832 Z= 0.246 Chirality : 0.039 0.188 2060 Planarity : 0.003 0.032 2442 Dihedral : 3.798 16.648 1846 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.52 % Allowed : 25.00 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), residues: 1648 helix: 1.30 (0.18), residues: 888 sheet: -1.46 (0.56), residues: 72 loop : 0.56 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 139 HIS 0.002 0.001 HIS A 531 PHE 0.011 0.001 PHE B 76 TYR 0.014 0.001 TYR D 77 ARG 0.007 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 363 time to evaluate : 1.583 Fit side-chains REVERT: D 46 ARG cc_start: 0.8333 (tpp-160) cc_final: 0.8119 (tpm170) REVERT: D 131 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.8240 (mtt180) REVERT: C 132 LYS cc_start: 0.7506 (tppt) cc_final: 0.7235 (tppp) REVERT: C 137 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7651 (tp) REVERT: C 264 SER cc_start: 0.7901 (m) cc_final: 0.7668 (m) REVERT: C 268 GLU cc_start: 0.6870 (tt0) cc_final: 0.6526 (tt0) REVERT: C 311 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8207 (mttp) REVERT: C 327 LEU cc_start: 0.8210 (tt) cc_final: 0.8001 (tp) REVERT: C 692 MET cc_start: 0.6407 (mmm) cc_final: 0.6095 (mmm) REVERT: C 693 MET cc_start: 0.6660 (mtt) cc_final: 0.6348 (mtt) REVERT: C 703 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7928 (tt) REVERT: C 825 MET cc_start: 0.8603 (ttm) cc_final: 0.8389 (ttt) REVERT: C 856 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: B 131 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.8330 (mtt180) REVERT: A 132 LYS cc_start: 0.7522 (tppt) cc_final: 0.7157 (tptp) REVERT: A 165 GLN cc_start: 0.7820 (mp10) cc_final: 0.7365 (mp-120) REVERT: A 323 LYS cc_start: 0.7874 (mtpm) cc_final: 0.7630 (ttpp) REVERT: A 435 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7363 (mtpt) REVERT: A 447 GLU cc_start: 0.7074 (mp0) cc_final: 0.6767 (mp0) REVERT: A 526 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7471 (tppp) REVERT: A 663 LYS cc_start: 0.7544 (ptmm) cc_final: 0.7215 (ttpp) REVERT: A 667 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7040 (pm20) REVERT: A 692 MET cc_start: 0.6466 (mmm) cc_final: 0.6131 (mmm) REVERT: A 693 MET cc_start: 0.6895 (mtt) cc_final: 0.6588 (mtt) REVERT: A 743 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7191 (mm-30) outliers start: 54 outliers final: 28 residues processed: 386 average time/residue: 1.4943 time to fit residues: 620.4316 Evaluate side-chains 393 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 358 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 681 GLN Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 856 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 716 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 0.0980 chunk 142 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN C 517 GLN C 626 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN A 382 ASN A 626 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13948 Z= 0.280 Angle : 0.521 9.014 18832 Z= 0.265 Chirality : 0.041 0.181 2060 Planarity : 0.003 0.053 2442 Dihedral : 3.901 16.766 1846 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.59 % Allowed : 25.13 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.21), residues: 1648 helix: 1.22 (0.18), residues: 890 sheet: -1.48 (0.57), residues: 72 loop : 0.58 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 139 HIS 0.003 0.001 HIS D 133 PHE 0.014 0.002 PHE A 730 TYR 0.018 0.001 TYR B 77 ARG 0.008 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 371 time to evaluate : 1.590 Fit side-chains REVERT: D 46 ARG cc_start: 0.8339 (tpp-160) cc_final: 0.8094 (tpm170) REVERT: D 131 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8235 (mtt180) REVERT: C 132 LYS cc_start: 0.7521 (tppt) cc_final: 0.7313 (tppp) REVERT: C 264 SER cc_start: 0.7897 (m) cc_final: 0.7685 (m) REVERT: C 268 GLU cc_start: 0.6876 (tt0) cc_final: 0.6533 (tt0) REVERT: C 311 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8225 (mttp) REVERT: C 447 GLU cc_start: 0.6945 (pp20) cc_final: 0.6707 (pm20) REVERT: C 676 MET cc_start: 0.7343 (mtm) cc_final: 0.6960 (mpt) REVERT: C 692 MET cc_start: 0.6426 (mmm) cc_final: 0.6121 (mmm) REVERT: C 693 MET cc_start: 0.6679 (mtt) cc_final: 0.6380 (mtt) REVERT: C 703 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7935 (tt) REVERT: C 856 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: A 132 LYS cc_start: 0.7551 (tppt) cc_final: 0.7206 (tptp) REVERT: A 165 GLN cc_start: 0.7821 (mp10) cc_final: 0.7192 (mp-120) REVERT: A 323 LYS cc_start: 0.7910 (mtpm) cc_final: 0.7613 (mtpp) REVERT: A 435 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7392 (mtpt) REVERT: A 447 GLU cc_start: 0.7192 (mp0) cc_final: 0.6869 (mp0) REVERT: A 663 LYS cc_start: 0.7540 (ptmm) cc_final: 0.7212 (ttpp) REVERT: A 667 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7050 (pm20) REVERT: A 692 MET cc_start: 0.6475 (mmm) cc_final: 0.6125 (mmm) REVERT: A 693 MET cc_start: 0.6942 (mtt) cc_final: 0.6639 (mtt) REVERT: A 743 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7208 (mm-30) outliers start: 55 outliers final: 35 residues processed: 393 average time/residue: 1.4755 time to fit residues: 624.7398 Evaluate side-chains 406 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 366 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 681 GLN Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 747 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 856 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 739 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.9990 chunk 17 optimal weight: 0.0570 chunk 90 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 133 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 98 optimal weight: 0.0170 chunk 96 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN C 517 GLN C 626 ASN A 345 GLN A 626 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13948 Z= 0.168 Angle : 0.485 10.652 18832 Z= 0.246 Chirality : 0.038 0.143 2060 Planarity : 0.003 0.030 2442 Dihedral : 3.727 17.020 1846 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.39 % Allowed : 25.72 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.21), residues: 1648 helix: 1.51 (0.18), residues: 876 sheet: -1.47 (0.57), residues: 72 loop : 0.56 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 139 HIS 0.002 0.000 HIS C 841 PHE 0.010 0.001 PHE C 733 TYR 0.013 0.001 TYR D 77 ARG 0.008 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 364 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: D 46 ARG cc_start: 0.8320 (tpp-160) cc_final: 0.8081 (tpm170) REVERT: D 131 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.8182 (mtt180) REVERT: C 129 THR cc_start: 0.7716 (OUTLIER) cc_final: 0.7325 (p) REVERT: C 132 LYS cc_start: 0.7491 (tppt) cc_final: 0.7229 (tppp) REVERT: C 264 SER cc_start: 0.7872 (m) cc_final: 0.7622 (m) REVERT: C 268 GLU cc_start: 0.6854 (tt0) cc_final: 0.6482 (tm-30) REVERT: C 311 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8282 (mttp) REVERT: C 327 LEU cc_start: 0.8247 (tt) cc_final: 0.7994 (tp) REVERT: C 447 GLU cc_start: 0.6791 (pp20) cc_final: 0.6563 (pm20) REVERT: C 676 MET cc_start: 0.7281 (mtm) cc_final: 0.6884 (mpt) REVERT: C 692 MET cc_start: 0.6465 (mmm) cc_final: 0.6115 (mmm) REVERT: C 703 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7951 (tt) REVERT: B 130 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7782 (mt0) REVERT: A 132 LYS cc_start: 0.7550 (tppt) cc_final: 0.7167 (tptp) REVERT: A 165 GLN cc_start: 0.7855 (mp10) cc_final: 0.7305 (mp-120) REVERT: A 447 GLU cc_start: 0.7043 (mp0) cc_final: 0.6737 (mp0) REVERT: A 663 LYS cc_start: 0.7562 (ptmm) cc_final: 0.7215 (ttpp) REVERT: A 667 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7033 (pm20) REVERT: A 692 MET cc_start: 0.6456 (mmm) cc_final: 0.6095 (mmm) REVERT: A 693 MET cc_start: 0.6900 (mtt) cc_final: 0.6579 (mtt) REVERT: A 743 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7236 (mm-30) outliers start: 52 outliers final: 29 residues processed: 385 average time/residue: 1.4836 time to fit residues: 614.9959 Evaluate side-chains 385 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 351 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 681 GLN Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 0.4980 chunk 63 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN C 275 ASN C 344 GLN C 360 ASN C 517 GLN C 626 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN A 473 ASN A 626 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13948 Z= 0.230 Angle : 0.522 9.677 18832 Z= 0.265 Chirality : 0.040 0.146 2060 Planarity : 0.003 0.030 2442 Dihedral : 3.805 19.150 1846 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.20 % Allowed : 25.98 % Favored : 70.82 % 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: 1.32 (0.21), residues: 1648 helix: 1.45 (0.18), residues: 878 sheet: -1.40 (0.57), residues: 72 loop : 0.57 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 139 HIS 0.002 0.001 HIS C 297 PHE 0.011 0.001 PHE A 730 TYR 0.017 0.001 TYR C 502 ARG 0.008 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 368 time to evaluate : 1.543 Fit side-chains revert: symmetry clash REVERT: D 46 ARG cc_start: 0.8328 (tpp-160) cc_final: 0.8100 (tpm170) REVERT: D 131 ARG cc_start: 0.8670 (mtm-85) cc_final: 0.8170 (mtt180) REVERT: C 129 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7305 (p) REVERT: C 132 LYS cc_start: 0.7479 (tppt) cc_final: 0.7222 (tppp) REVERT: C 264 SER cc_start: 0.7868 (m) cc_final: 0.7641 (m) REVERT: C 268 GLU cc_start: 0.6867 (tt0) cc_final: 0.6511 (tm-30) REVERT: C 311 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8304 (mttp) REVERT: C 327 LEU cc_start: 0.8254 (tt) cc_final: 0.7996 (tp) REVERT: C 447 GLU cc_start: 0.6797 (pp20) cc_final: 0.6581 (pm20) REVERT: C 459 GLU cc_start: 0.7190 (pt0) cc_final: 0.6988 (pt0) REVERT: C 676 MET cc_start: 0.7329 (mtm) cc_final: 0.6890 (mpt) REVERT: C 692 MET cc_start: 0.6332 (mmm) cc_final: 0.6040 (mmm) REVERT: C 703 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7958 (tt) REVERT: B 131 ARG cc_start: 0.8609 (mtm-85) cc_final: 0.8340 (mtt180) REVERT: A 132 LYS cc_start: 0.7554 (tppt) cc_final: 0.7188 (tptp) REVERT: A 165 GLN cc_start: 0.7846 (mp10) cc_final: 0.7190 (mp-120) REVERT: A 323 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7661 (mtpp) REVERT: A 341 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7483 (mt-10) REVERT: A 447 GLU cc_start: 0.7057 (mp0) cc_final: 0.6756 (mp0) REVERT: A 594 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6904 (mm-30) REVERT: A 663 LYS cc_start: 0.7557 (ptmm) cc_final: 0.7182 (ttpp) REVERT: A 667 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7026 (pm20) REVERT: A 692 MET cc_start: 0.6489 (mmm) cc_final: 0.6148 (mmm) REVERT: A 693 MET cc_start: 0.6925 (mtt) cc_final: 0.6721 (mtt) REVERT: A 743 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7195 (mm-30) outliers start: 49 outliers final: 33 residues processed: 391 average time/residue: 1.4642 time to fit residues: 616.8212 Evaluate side-chains 400 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 363 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 796 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 147 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 146 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 626 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN A 473 ASN A 626 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13948 Z= 0.235 Angle : 0.531 10.806 18832 Z= 0.268 Chirality : 0.040 0.159 2060 Planarity : 0.003 0.039 2442 Dihedral : 3.834 17.794 1846 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.26 % Allowed : 25.78 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1648 helix: 1.44 (0.18), residues: 878 sheet: -1.38 (0.57), residues: 72 loop : 0.58 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 139 HIS 0.002 0.001 HIS C 297 PHE 0.011 0.001 PHE A 730 TYR 0.019 0.001 TYR C 502 ARG 0.006 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 364 time to evaluate : 1.596 Fit side-chains revert: symmetry clash REVERT: D 46 ARG cc_start: 0.8323 (tpp-160) cc_final: 0.8095 (tpm170) REVERT: D 131 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8126 (mtt180) REVERT: C 129 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7259 (p) REVERT: C 132 LYS cc_start: 0.7448 (tppt) cc_final: 0.7201 (tppp) REVERT: C 264 SER cc_start: 0.7875 (m) cc_final: 0.7634 (m) REVERT: C 268 GLU cc_start: 0.6885 (tt0) cc_final: 0.6499 (tm-30) REVERT: C 311 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8300 (mttp) REVERT: C 327 LEU cc_start: 0.8238 (tt) cc_final: 0.7977 (tp) REVERT: C 447 GLU cc_start: 0.6774 (pp20) cc_final: 0.6564 (pm20) REVERT: C 676 MET cc_start: 0.7325 (mtm) cc_final: 0.6889 (mpt) REVERT: C 692 MET cc_start: 0.6280 (mmm) cc_final: 0.6019 (mmm) REVERT: C 703 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7943 (tt) REVERT: C 824 LYS cc_start: 0.8010 (mmtm) cc_final: 0.7747 (mmtm) REVERT: C 856 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: A 132 LYS cc_start: 0.7579 (tppt) cc_final: 0.7196 (tptp) REVERT: A 165 GLN cc_start: 0.7845 (mp10) cc_final: 0.7249 (mp-120) REVERT: A 323 LYS cc_start: 0.7886 (ttmt) cc_final: 0.7672 (mtpp) REVERT: A 435 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7376 (mtpt) REVERT: A 447 GLU cc_start: 0.7123 (mp0) cc_final: 0.6799 (mp0) REVERT: A 526 LYS cc_start: 0.7995 (tppp) cc_final: 0.7634 (tppp) REVERT: A 663 LYS cc_start: 0.7552 (ptmm) cc_final: 0.7210 (ttpp) REVERT: A 667 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7017 (pm20) REVERT: A 692 MET cc_start: 0.6474 (mmm) cc_final: 0.6135 (mmm) REVERT: A 693 MET cc_start: 0.6941 (mtt) cc_final: 0.6731 (mtt) REVERT: A 743 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7211 (mm-30) outliers start: 50 outliers final: 36 residues processed: 387 average time/residue: 1.5423 time to fit residues: 643.1347 Evaluate side-chains 397 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 355 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 856 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 796 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 150 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 100 optimal weight: 0.0060 chunk 79 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN C 344 GLN C 517 GLN C 626 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN A 473 ASN A 626 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13948 Z= 0.192 Angle : 0.517 10.981 18832 Z= 0.261 Chirality : 0.039 0.158 2060 Planarity : 0.003 0.041 2442 Dihedral : 3.770 16.771 1846 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.07 % Allowed : 26.04 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.21), residues: 1648 helix: 1.51 (0.18), residues: 878 sheet: -1.40 (0.56), residues: 72 loop : 0.55 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 139 HIS 0.002 0.001 HIS C 841 PHE 0.010 0.001 PHE A 730 TYR 0.019 0.001 TYR C 502 ARG 0.006 0.000 ARG C 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 363 time to evaluate : 1.562 Fit side-chains revert: symmetry clash REVERT: D 46 ARG cc_start: 0.8307 (tpp-160) cc_final: 0.8065 (tpm170) REVERT: D 131 ARG cc_start: 0.8668 (mtm-85) cc_final: 0.8157 (mtt180) REVERT: C 129 THR cc_start: 0.7576 (OUTLIER) cc_final: 0.7172 (p) REVERT: C 132 LYS cc_start: 0.7444 (tppt) cc_final: 0.7202 (tptp) REVERT: C 137 LEU cc_start: 0.7585 (tp) cc_final: 0.7358 (tt) REVERT: C 264 SER cc_start: 0.7870 (m) cc_final: 0.7623 (m) REVERT: C 268 GLU cc_start: 0.6861 (tt0) cc_final: 0.6508 (tm-30) REVERT: C 311 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8290 (mttp) REVERT: C 447 GLU cc_start: 0.6782 (pp20) cc_final: 0.6549 (pm20) REVERT: C 676 MET cc_start: 0.7315 (mtm) cc_final: 0.6885 (mpt) REVERT: C 703 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7947 (tt) REVERT: C 856 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: B 131 ARG cc_start: 0.8598 (mtm-85) cc_final: 0.8232 (mtm-85) REVERT: A 132 LYS cc_start: 0.7583 (tppt) cc_final: 0.7190 (tptp) REVERT: A 165 GLN cc_start: 0.7843 (mp10) cc_final: 0.7222 (mp-120) REVERT: A 323 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7664 (mtpp) REVERT: A 341 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 435 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7376 (mtpt) REVERT: A 447 GLU cc_start: 0.7045 (mp0) cc_final: 0.6742 (mp0) REVERT: A 663 LYS cc_start: 0.7531 (ptmm) cc_final: 0.7201 (ttpp) REVERT: A 667 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7025 (pm20) REVERT: A 692 MET cc_start: 0.6477 (mmm) cc_final: 0.6155 (mmm) REVERT: A 693 MET cc_start: 0.6927 (mtt) cc_final: 0.6709 (mtt) REVERT: A 743 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7209 (mm-30) outliers start: 47 outliers final: 35 residues processed: 383 average time/residue: 1.5215 time to fit residues: 626.5272 Evaluate side-chains 392 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 351 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 856 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 796 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 39 optimal weight: 0.0170 chunk 119 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 133 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 626 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN A 626 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.147709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126329 restraints weight = 17938.018| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.76 r_work: 0.3470 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 13948 Z= 0.233 Angle : 0.756 59.200 18832 Z= 0.429 Chirality : 0.040 0.227 2060 Planarity : 0.003 0.038 2442 Dihedral : 3.799 18.886 1846 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.26 % Allowed : 25.85 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.21), residues: 1648 helix: 1.49 (0.18), residues: 878 sheet: -1.40 (0.57), residues: 72 loop : 0.54 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 139 HIS 0.003 0.001 HIS C 841 PHE 0.010 0.001 PHE A 730 TYR 0.019 0.001 TYR C 502 ARG 0.013 0.000 ARG C 539 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8537.25 seconds wall clock time: 148 minutes 24.86 seconds (8904.86 seconds total)