Starting phenix.real_space_refine on Fri Feb 16 14:47:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/02_2024/8f56_28861.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/02_2024/8f56_28861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/02_2024/8f56_28861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/02_2024/8f56_28861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/02_2024/8f56_28861.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/02_2024/8f56_28861.pdb" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 9992 2.51 5 N 2634 2.21 5 O 2917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 311": "OD1" <-> "OD2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15631 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7730 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 966} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7901 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 41, 'TRANS': 990} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 8.50, per 1000 atoms: 0.54 Number of scatterers: 15631 At special positions: 0 Unit cell: (79.18, 123.05, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 2917 8.00 N 2634 7.00 C 9992 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: 6.21 Conformation dependent library (CDL) restraints added in 2.9 seconds 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 15 sheets defined 61.2% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 3.593A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 29 removed outlier: 3.828A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 70 Processing helix chain 'A' and resid 99 through 118 removed outlier: 3.766A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.765A pdb=" N ASN A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.668A pdb=" N PHE A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 329 through 359 Processing helix chain 'A' and resid 361 through 387 Proline residue: A 368 - end of helix removed outlier: 3.724A pdb=" N ALA A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 423 removed outlier: 3.785A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 452 removed outlier: 5.589A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 458 removed outlier: 4.419A pdb=" N MET A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 458' Processing helix chain 'A' and resid 460 through 486 Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.820A pdb=" N ALA A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.974A pdb=" N LYS A 501 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 502' Processing helix chain 'A' and resid 510 through 536 Processing helix chain 'A' and resid 536 through 558 removed outlier: 4.019A pdb=" N TRP A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 600 Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 690 through 708 Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 740 through 752 Processing helix chain 'A' and resid 775 through 778 Processing helix chain 'A' and resid 780 through 786 Processing helix chain 'A' and resid 834 through 848 removed outlier: 3.720A pdb=" N GLN A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 891 removed outlier: 3.521A pdb=" N GLN A 863 " --> pdb=" O ALA A 859 " (cutoff:3.500A) Proline residue: A 872 - end of helix Processing helix chain 'A' and resid 893 through 901 removed outlier: 3.517A pdb=" N LEU A 901 " --> pdb=" O PHE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 918 removed outlier: 3.550A pdb=" N GLY A 906 " --> pdb=" O VAL A 902 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 954 removed outlier: 4.417A pdb=" N PHE A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 988 removed outlier: 4.975A pdb=" N ARG A 970 " --> pdb=" O ARG A 966 " (cutoff:3.500A) Proline residue: A 971 - end of helix Proline residue: A 985 - end of helix Processing helix chain 'A' and resid 993 through 1030 removed outlier: 4.332A pdb=" N GLY A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A1004 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Proline residue: A1020 - end of helix Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.586A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.584A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 Processing helix chain 'B' and resid 99 through 116 removed outlier: 4.620A pdb=" N ARG B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 removed outlier: 3.513A pdb=" N ARG B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.624A pdb=" N PHE B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 298 through 315 Processing helix chain 'B' and resid 329 through 359 Processing helix chain 'B' and resid 361 through 386 Proline residue: B 368 - end of helix removed outlier: 3.874A pdb=" N ALA B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 423 removed outlier: 4.380A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 452 removed outlier: 5.716A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 removed outlier: 4.572A pdb=" N MET B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 457' Processing helix chain 'B' and resid 460 through 486 Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.941A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 536 Processing helix chain 'B' and resid 536 through 558 removed outlier: 3.976A pdb=" N TRP B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 600 Processing helix chain 'B' and resid 642 through 657 removed outlier: 3.527A pdb=" N ALA B 653 " --> pdb=" O ARG B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 708 Processing helix chain 'B' and resid 730 through 738 Processing helix chain 'B' and resid 740 through 753 Processing helix chain 'B' and resid 782 through 786 removed outlier: 4.058A pdb=" N ASN B 785 " --> pdb=" O ASP B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 802 No H-bonds generated for 'chain 'B' and resid 799 through 802' Processing helix chain 'B' and resid 834 through 849 Processing helix chain 'B' and resid 858 through 891 Proline residue: B 872 - end of helix Processing helix chain 'B' and resid 893 through 901 removed outlier: 3.514A pdb=" N LEU B 901 " --> pdb=" O PHE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 918 removed outlier: 3.685A pdb=" N GLY B 906 " --> pdb=" O VAL B 902 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 954 removed outlier: 4.435A pdb=" N PHE B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 988 removed outlier: 5.111A pdb=" N ARG B 970 " --> pdb=" O ARG B 966 " (cutoff:3.500A) Proline residue: B 971 - end of helix Proline residue: B 985 - end of helix Processing helix chain 'B' and resid 993 through 1030 removed outlier: 4.285A pdb=" N GLY B1003 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B1004 " --> pdb=" O VAL B1000 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Proline residue: B1020 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.035A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 12.362A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU A 828 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARG A 713 " --> pdb=" O GLU A 828 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.035A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 12.362A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER A 821 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.821A pdb=" N LEU A 138 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 293 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN A 136 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE A 137 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU A 328 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR A 139 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.993A pdb=" N TYR A 182 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS A 768 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 758 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL A 771 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR A 756 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 253 removed outlier: 3.744A pdb=" N ARG A 252 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA7, first strand: chain 'A' and resid 803 through 810 removed outlier: 3.829A pdb=" N THR B 233 " --> pdb=" O PRO A 723 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 217 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.044A pdb=" N GLN B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.579A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 138 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 293 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN B 136 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N ILE B 137 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU B 328 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 139 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.579A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 612 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.970A pdb=" N ASN B 758 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL B 771 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR B 756 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA B 773 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N SER B 754 " --> pdb=" O ALA B 773 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 716 removed outlier: 4.872A pdb=" N ARG B 713 " --> pdb=" O GLU B 828 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU B 828 " --> pdb=" O ARG B 713 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 722 through 729 removed outlier: 3.639A pdb=" N ARG B 806 " --> pdb=" O GLN B 726 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 788 through 790 1088 hydrogen bonds defined for protein. 3186 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: 6.35 Time building geometry restraints manager: 6.71 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: 5118 1.34 - 1.46: 2193 1.46 - 1.57: 8455 1.57 - 1.69: 0 1.69 - 1.80: 168 Bond restraints: 15934 Sorted by residual: bond pdb=" CA VAL B 306 " pdb=" C VAL B 306 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.22e-02 6.72e+03 2.60e+00 bond pdb=" CA GLU B 66 " pdb=" C GLU B 66 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.27e-02 6.20e+03 2.16e+00 bond pdb=" CA LEU A 737 " pdb=" C LEU A 737 " ideal model delta sigma weight residual 1.523 1.502 0.020 1.41e-02 5.03e+03 2.08e+00 bond pdb=" CA ASP B 922 " pdb=" C ASP B 922 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.45e-02 4.76e+03 2.06e+00 bond pdb=" N LEU B 307 " pdb=" CA LEU B 307 " ideal model delta sigma weight residual 1.459 1.442 0.017 1.21e-02 6.83e+03 1.99e+00 ... (remaining 15929 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.48: 447 106.48 - 113.35: 8782 113.35 - 120.23: 5442 120.23 - 127.10: 6823 127.10 - 133.97: 145 Bond angle restraints: 21639 Sorted by residual: angle pdb=" C ALA B 859 " pdb=" CA ALA B 859 " pdb=" CB ALA B 859 " ideal model delta sigma weight residual 116.63 110.03 6.60 1.16e+00 7.43e-01 3.23e+01 angle pdb=" C VAL B 61 " pdb=" CA VAL B 61 " pdb=" CB VAL B 61 " ideal model delta sigma weight residual 111.71 107.76 3.95 8.50e-01 1.38e+00 2.16e+01 angle pdb=" CA ALA B 859 " pdb=" C ALA B 859 " pdb=" N MET B 860 " ideal model delta sigma weight residual 119.63 116.20 3.43 8.10e-01 1.52e+00 1.80e+01 angle pdb=" N VAL B 61 " pdb=" CA VAL B 61 " pdb=" C VAL B 61 " ideal model delta sigma weight residual 111.48 115.35 -3.87 9.40e-01 1.13e+00 1.70e+01 angle pdb=" N THR B 462 " pdb=" CA THR B 462 " pdb=" C THR B 462 " ideal model delta sigma weight residual 111.28 107.16 4.12 1.09e+00 8.42e-01 1.43e+01 ... (remaining 21634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.59: 8842 13.59 - 27.17: 498 27.17 - 40.76: 132 40.76 - 54.34: 36 54.34 - 67.93: 9 Dihedral angle restraints: 9517 sinusoidal: 3661 harmonic: 5856 Sorted by residual: dihedral pdb=" CA ILE B 249 " pdb=" C ILE B 249 " pdb=" N THR B 250 " pdb=" CA THR B 250 " ideal model delta harmonic sigma weight residual -180.00 -163.45 -16.55 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP A 311 " pdb=" CB ASP A 311 " pdb=" CG ASP A 311 " pdb=" OD1 ASP A 311 " ideal model delta sinusoidal sigma weight residual -30.00 -87.08 57.08 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CB ARG B 661 " pdb=" CG ARG B 661 " pdb=" CD ARG B 661 " pdb=" NE ARG B 661 " ideal model delta sinusoidal sigma weight residual 180.00 120.27 59.73 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 9514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1671 0.029 - 0.058: 556 0.058 - 0.087: 167 0.087 - 0.115: 110 0.115 - 0.144: 8 Chirality restraints: 2512 Sorted by residual: chirality pdb=" CA THR B 489 " pdb=" N THR B 489 " pdb=" C THR B 489 " pdb=" CB THR B 489 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA THR A 489 " pdb=" N THR A 489 " pdb=" C THR A 489 " pdb=" CB THR A 489 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CB VAL A 482 " pdb=" CA VAL A 482 " pdb=" CG1 VAL A 482 " pdb=" CG2 VAL A 482 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 2509 not shown) Planarity restraints: 2786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 921 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C ASN A 921 " 0.028 2.00e-02 2.50e+03 pdb=" O ASN A 921 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP A 922 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 250 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C THR B 250 " -0.026 2.00e-02 2.50e+03 pdb=" O THR B 250 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU B 251 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 454 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C VAL B 454 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL B 454 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO B 455 " -0.009 2.00e-02 2.50e+03 ... (remaining 2783 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1621 2.74 - 3.28: 16429 3.28 - 3.82: 27105 3.82 - 4.36: 31663 4.36 - 4.90: 55207 Nonbonded interactions: 132025 Sorted by model distance: nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 759 " model vdw 2.200 2.440 nonbonded pdb=" OE2 GLU A 601 " pdb=" ND2 ASN A 604 " model vdw 2.202 2.520 nonbonded pdb=" OG SER B 279 " pdb=" O ALA B 286 " model vdw 2.213 2.440 nonbonded pdb=" OG SER A 279 " pdb=" O ALA A 286 " model vdw 2.276 2.440 nonbonded pdb=" OD1 ASN A 415 " pdb=" NH1 ARG A 418 " model vdw 2.281 2.520 ... (remaining 132020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 508 or (resid 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 through 1032)) selection = (chain 'B' and (resid 1 through 211 or resid 237 through 505 or (resid 506 and ( \ name N or name CA or name C or name O or name CB )) or resid 507 through 1032)) } 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 9.960 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 44.410 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.070 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:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 0.036 15934 Z= 0.266 Angle : 0.557 9.097 21639 Z= 0.327 Chirality : 0.036 0.144 2512 Planarity : 0.003 0.029 2786 Dihedral : 9.889 67.925 5757 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.64 % Allowed : 4.61 % Favored : 92.75 % 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: 1.81 (0.19), residues: 2033 helix: 2.22 (0.15), residues: 1165 sheet: -0.18 (0.32), residues: 282 loop : -0.11 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 540 HIS 0.002 0.001 HIS A 686 PHE 0.011 0.001 PHE B 958 TYR 0.009 0.001 TYR A 77 ARG 0.003 0.000 ARG B 636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 495 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.7049 (mt0) cc_final: 0.6792 (mt0) REVERT: B 184 MET cc_start: 0.7433 (tpp) cc_final: 0.7154 (tpp) REVERT: B 395 MET cc_start: 0.8094 (mmm) cc_final: 0.7760 (mmm) REVERT: B 900 MET cc_start: 0.6754 (mmm) cc_final: 0.6390 (mmp) outliers start: 44 outliers final: 8 residues processed: 525 average time/residue: 1.1262 time to fit residues: 657.9955 Evaluate side-chains 269 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 261 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 103 optimal weight: 0.0000 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 108 GLN A 152 GLN A 197 GLN A 308 ASN A 319 HIS A 517 GLN ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN A 686 HIS A 691 HIS A 716 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 GLN A 926 GLN A 955 HIS A 967 GLN B 55 GLN B 59 ASN B 63 GLN B 81 GLN B 108 GLN B 112 GLN B 213 GLN B 228 GLN B 237 GLN B 254 ASN B 255 GLN B 361 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN B 604 ASN B 699 ASN B 708 ASN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15934 Z= 0.189 Angle : 0.541 8.397 21639 Z= 0.281 Chirality : 0.039 0.153 2512 Planarity : 0.004 0.045 2786 Dihedral : 4.365 58.378 2201 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.61 % Allowed : 16.00 % Favored : 79.39 % 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: 1.89 (0.19), residues: 2033 helix: 2.29 (0.15), residues: 1173 sheet: -0.14 (0.30), residues: 296 loop : -0.15 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 540 HIS 0.005 0.001 HIS A 319 PHE 0.021 0.001 PHE A 4 TYR 0.015 0.002 TYR A 384 ARG 0.011 0.001 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 288 time to evaluate : 1.970 Fit side-chains revert: symmetry clash REVERT: A 28 PHE cc_start: 0.7339 (m-80) cc_final: 0.7089 (m-80) REVERT: A 151 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8185 (ptmm) REVERT: B 151 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7682 (ptpp) REVERT: B 456 MET cc_start: 0.7649 (mtm) cc_final: 0.7394 (mtm) REVERT: B 522 ASN cc_start: 0.6651 (m-40) cc_final: 0.6446 (m110) REVERT: B 701 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7786 (tt) outliers start: 77 outliers final: 27 residues processed: 336 average time/residue: 1.1571 time to fit residues: 433.4633 Evaluate side-chains 253 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 223 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 199 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 437 GLN A 584 GLN ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 951 ASN B 3 ASN B 59 ASN B 67 GLN B 213 GLN B 241 GLN B 361 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15934 Z= 0.208 Angle : 0.524 7.746 21639 Z= 0.271 Chirality : 0.039 0.160 2512 Planarity : 0.004 0.046 2786 Dihedral : 4.276 54.825 2196 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.97 % Allowed : 18.39 % Favored : 76.63 % 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: 1.87 (0.19), residues: 2033 helix: 2.31 (0.15), residues: 1176 sheet: -0.19 (0.30), residues: 300 loop : -0.21 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 540 HIS 0.006 0.001 HIS B 319 PHE 0.012 0.001 PHE A 571 TYR 0.010 0.001 TYR B 924 ARG 0.017 0.001 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 261 time to evaluate : 2.008 Fit side-chains revert: symmetry clash REVERT: A 486 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7213 (mtp) REVERT: B 68 ASN cc_start: 0.7173 (t0) cc_final: 0.6952 (t0) REVERT: B 447 MET cc_start: 0.6514 (ttm) cc_final: 0.6088 (mtt) REVERT: B 779 MET cc_start: 0.5284 (tpp) cc_final: 0.5048 (tpp) outliers start: 83 outliers final: 40 residues processed: 317 average time/residue: 1.2585 time to fit residues: 444.1341 Evaluate side-chains 252 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 211 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.0970 chunk 138 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN B 213 GLN B 361 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15934 Z= 0.172 Angle : 0.500 8.447 21639 Z= 0.256 Chirality : 0.039 0.164 2512 Planarity : 0.004 0.038 2786 Dihedral : 4.218 56.739 2196 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.01 % Allowed : 20.73 % Favored : 75.25 % 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: 1.94 (0.19), residues: 2033 helix: 2.39 (0.15), residues: 1169 sheet: -0.22 (0.29), residues: 306 loop : -0.17 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 540 HIS 0.006 0.001 HIS B 319 PHE 0.013 0.001 PHE B 946 TYR 0.013 0.001 TYR B 77 ARG 0.010 0.001 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 241 time to evaluate : 1.737 Fit side-chains revert: symmetry clash REVERT: A 184 MET cc_start: 0.7377 (mmt) cc_final: 0.7133 (tpt) REVERT: A 656 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7203 (mt0) REVERT: A 860 MET cc_start: 0.7005 (tmm) cc_final: 0.6617 (tmt) REVERT: B 447 MET cc_start: 0.6524 (ttm) cc_final: 0.6130 (mtt) REVERT: B 659 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.6173 (mt-10) REVERT: B 1002 THR cc_start: 0.8075 (m) cc_final: 0.7808 (m) outliers start: 67 outliers final: 32 residues processed: 288 average time/residue: 1.1756 time to fit residues: 378.9874 Evaluate side-chains 250 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 216 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15934 Z= 0.262 Angle : 0.544 9.338 21639 Z= 0.279 Chirality : 0.040 0.201 2512 Planarity : 0.004 0.040 2786 Dihedral : 4.370 57.677 2196 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.27 % Allowed : 20.55 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2033 helix: 2.26 (0.15), residues: 1167 sheet: -0.12 (0.29), residues: 307 loop : -0.26 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 540 HIS 0.005 0.001 HIS B 319 PHE 0.013 0.001 PHE A 981 TYR 0.011 0.001 TYR A 597 ARG 0.009 0.001 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 235 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7431 (mmt) cc_final: 0.7094 (tpt) REVERT: A 656 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7486 (mt0) REVERT: A 732 ARG cc_start: 0.7217 (ttm110) cc_final: 0.6971 (ttm110) REVERT: A 860 MET cc_start: 0.6964 (tmm) cc_final: 0.6579 (tmt) REVERT: A 970 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7499 (tmm-80) REVERT: B 447 MET cc_start: 0.6697 (ttm) cc_final: 0.6290 (mtt) REVERT: B 659 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6198 (mt-10) outliers start: 88 outliers final: 42 residues processed: 299 average time/residue: 1.2312 time to fit residues: 411.3865 Evaluate side-chains 261 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 216 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 986 MET Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.9980 chunk 176 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 196 optimal weight: 0.0070 chunk 163 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 0.0870 chunk 103 optimal weight: 0.9980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 68 ASN ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15934 Z= 0.152 Angle : 0.489 6.498 21639 Z= 0.250 Chirality : 0.038 0.171 2512 Planarity : 0.003 0.040 2786 Dihedral : 4.223 59.501 2196 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.13 % Allowed : 22.29 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.19), residues: 2033 helix: 2.38 (0.15), residues: 1169 sheet: -0.11 (0.29), residues: 302 loop : -0.27 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 540 HIS 0.005 0.001 HIS B 319 PHE 0.020 0.001 PHE B 946 TYR 0.009 0.001 TYR A 384 ARG 0.007 0.000 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 231 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7396 (mmt) cc_final: 0.7121 (tpt) REVERT: A 860 MET cc_start: 0.6944 (tmm) cc_final: 0.6578 (tmt) REVERT: A 970 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7510 (tmm-80) REVERT: B 659 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.6077 (mt-10) REVERT: B 779 MET cc_start: 0.5267 (tpp) cc_final: 0.4939 (tpp) outliers start: 69 outliers final: 39 residues processed: 281 average time/residue: 1.1627 time to fit residues: 365.1771 Evaluate side-chains 250 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 209 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 chunk 122 optimal weight: 0.1980 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN A 745 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15934 Z= 0.204 Angle : 0.520 9.593 21639 Z= 0.266 Chirality : 0.039 0.201 2512 Planarity : 0.004 0.049 2786 Dihedral : 4.245 59.867 2196 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.95 % Allowed : 23.25 % Favored : 72.80 % 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: 1.83 (0.19), residues: 2033 helix: 2.31 (0.15), residues: 1175 sheet: -0.13 (0.30), residues: 302 loop : -0.36 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 540 HIS 0.004 0.001 HIS B 319 PHE 0.027 0.001 PHE B 883 TYR 0.009 0.001 TYR B 277 ARG 0.012 0.000 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 221 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 570 MET cc_start: 0.8689 (ptp) cc_final: 0.8215 (pmm) REVERT: A 656 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7465 (mt0) REVERT: A 860 MET cc_start: 0.6949 (tmm) cc_final: 0.6606 (tmt) REVERT: A 970 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7507 (tmm-80) REVERT: B 398 MET cc_start: 0.7689 (mmt) cc_final: 0.7151 (mmt) REVERT: B 659 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.6118 (mt-10) outliers start: 66 outliers final: 43 residues processed: 271 average time/residue: 1.2290 time to fit residues: 373.0803 Evaluate side-chains 259 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 213 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 177 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15934 Z= 0.174 Angle : 0.513 9.414 21639 Z= 0.259 Chirality : 0.039 0.202 2512 Planarity : 0.004 0.055 2786 Dihedral : 4.210 58.957 2196 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.36 % Allowed : 24.09 % Favored : 72.56 % 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: 1.82 (0.19), residues: 2033 helix: 2.34 (0.15), residues: 1175 sheet: -0.24 (0.29), residues: 310 loop : -0.38 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 540 HIS 0.004 0.001 HIS B 319 PHE 0.022 0.001 PHE B 883 TYR 0.008 0.001 TYR A 35 ARG 0.013 0.000 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 226 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 MET cc_start: 0.8698 (ptp) cc_final: 0.8465 (ptp) REVERT: A 860 MET cc_start: 0.6941 (tmm) cc_final: 0.6602 (tmt) REVERT: A 970 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7507 (tmm-80) REVERT: B 447 MET cc_start: 0.6757 (ttm) cc_final: 0.6504 (mtt) REVERT: B 659 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.6097 (mt-10) outliers start: 56 outliers final: 38 residues processed: 274 average time/residue: 1.2320 time to fit residues: 375.7191 Evaluate side-chains 248 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 208 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 715 ARG Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 55 optimal weight: 0.0870 chunk 164 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN B 437 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15934 Z= 0.182 Angle : 0.528 9.539 21639 Z= 0.265 Chirality : 0.039 0.214 2512 Planarity : 0.004 0.056 2786 Dihedral : 4.216 58.316 2196 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.06 % Allowed : 24.75 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 2033 helix: 2.34 (0.15), residues: 1175 sheet: -0.24 (0.29), residues: 308 loop : -0.36 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 540 HIS 0.004 0.001 HIS B 319 PHE 0.021 0.001 PHE B 883 TYR 0.009 0.001 TYR B 277 ARG 0.013 0.000 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 212 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7341 (mmt) cc_final: 0.7001 (tpt) REVERT: A 570 MET cc_start: 0.8694 (ptp) cc_final: 0.8443 (ptp) REVERT: A 656 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7442 (mt0) REVERT: A 685 ASP cc_start: 0.7126 (p0) cc_final: 0.6899 (p0) REVERT: A 799 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8427 (t80) REVERT: A 860 MET cc_start: 0.6933 (tmm) cc_final: 0.6611 (tmt) REVERT: A 970 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7533 (tmm-80) REVERT: B 398 MET cc_start: 0.7665 (mmt) cc_final: 0.7169 (mmt) REVERT: B 447 MET cc_start: 0.6715 (ttm) cc_final: 0.6450 (mtt) REVERT: B 659 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.6091 (mt-10) outliers start: 51 outliers final: 40 residues processed: 255 average time/residue: 1.2363 time to fit residues: 350.2235 Evaluate side-chains 247 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 203 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 715 ARG Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 59 ASN A 63 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15934 Z= 0.317 Angle : 0.589 9.877 21639 Z= 0.298 Chirality : 0.042 0.215 2512 Planarity : 0.004 0.047 2786 Dihedral : 4.431 59.414 2196 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.94 % Allowed : 24.39 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.19), residues: 2033 helix: 2.09 (0.15), residues: 1174 sheet: -0.29 (0.29), residues: 309 loop : -0.41 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 540 HIS 0.005 0.001 HIS B 955 PHE 0.020 0.002 PHE B 883 TYR 0.015 0.002 TYR A 35 ARG 0.012 0.001 ARG A 732 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 208 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7371 (mmt) cc_final: 0.7033 (tpt) REVERT: A 322 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6447 (tt0) REVERT: A 570 MET cc_start: 0.8715 (ptp) cc_final: 0.8447 (ptp) REVERT: A 656 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7451 (mt0) REVERT: A 799 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8472 (t80) REVERT: A 970 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7633 (tmm-80) REVERT: B 7 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: B 398 MET cc_start: 0.7707 (mmt) cc_final: 0.7262 (mmt) REVERT: B 447 MET cc_start: 0.6795 (ttm) cc_final: 0.6542 (mtt) REVERT: B 659 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.6087 (mt-10) REVERT: B 779 MET cc_start: 0.5292 (tpp) cc_final: 0.5089 (tpp) outliers start: 49 outliers final: 32 residues processed: 249 average time/residue: 1.3128 time to fit residues: 363.2141 Evaluate side-chains 240 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 202 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 63 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN B 735 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.109016 restraints weight = 20908.204| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.58 r_work: 0.3113 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15934 Z= 0.239 Angle : 0.562 10.281 21639 Z= 0.283 Chirality : 0.040 0.206 2512 Planarity : 0.004 0.046 2786 Dihedral : 4.404 58.854 2196 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.88 % Allowed : 24.51 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.19), residues: 2033 helix: 2.14 (0.15), residues: 1173 sheet: -0.12 (0.30), residues: 295 loop : -0.47 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 540 HIS 0.005 0.001 HIS B 955 PHE 0.020 0.001 PHE B 883 TYR 0.013 0.001 TYR A 35 ARG 0.012 0.000 ARG A 732 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6432.97 seconds wall clock time: 115 minutes 24.46 seconds (6924.46 seconds total)