Starting phenix.real_space_refine on Thu Nov 16 14:20:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/11_2023/8f56_28861.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/11_2023/8f56_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_28861/11_2023/8f56_28861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/11_2023/8f56_28861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/11_2023/8f56_28861.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/11_2023/8f56_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 8.20, per 1000 atoms: 0.52 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: 6.83 Conformation dependent library (CDL) restraints added in 3.0 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: 1.96 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: 5.97 Time building geometry restraints manager: 7.26 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.870 Check model and map are aligned: 0.250 Set scattering table: 0.130 Process input model: 45.250 Find NCS groups from input model: 0.960 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: 0.000 Load rotamer database and sin/cos tables:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.580 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 8 residues processed: 525 average time/residue: 1.1598 time to fit residues: 678.4634 Evaluate side-chains 268 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 260 time to evaluate : 1.765 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.3570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15934 Z= 0.190 Angle : 0.537 8.376 21639 Z= 0.280 Chirality : 0.039 0.151 2512 Planarity : 0.004 0.046 2786 Dihedral : 3.831 14.720 2188 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.49 % Allowed : 16.42 % Favored : 79.09 % 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: 2.30 (0.15), residues: 1173 sheet: -0.15 (0.30), residues: 296 loop : -0.14 (0.27), residues: 564 *********************** 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 367 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 292 time to evaluate : 1.879 Fit side-chains revert: symmetry clash outliers start: 75 outliers final: 27 residues processed: 341 average time/residue: 1.1226 time to fit residues: 428.3070 Evaluate side-chains 254 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 227 time to evaluate : 1.714 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 4 average time/residue: 0.1618 time to fit residues: 3.4675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 0.4980 chunk 153 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 183 optimal weight: 0.0020 chunk 62 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 361 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15934 Z= 0.188 Angle : 0.515 7.339 21639 Z= 0.266 Chirality : 0.039 0.159 2512 Planarity : 0.004 0.044 2786 Dihedral : 3.778 15.297 2188 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.73 % Allowed : 18.33 % Favored : 76.93 % 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: 1.88 (0.19), residues: 2033 helix: 2.32 (0.15), residues: 1176 sheet: -0.23 (0.29), residues: 308 loop : -0.16 (0.27), residues: 549 *********************** 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 352 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 273 time to evaluate : 1.835 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 42 residues processed: 328 average time/residue: 1.1969 time to fit residues: 440.7149 Evaluate side-chains 257 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 215 time to evaluate : 1.929 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 35 residues processed: 7 average time/residue: 0.5998 time to fit residues: 7.7294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN B 68 ASN B 213 GLN B 361 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15934 Z= 0.242 Angle : 0.537 8.854 21639 Z= 0.276 Chirality : 0.040 0.170 2512 Planarity : 0.004 0.036 2786 Dihedral : 3.862 15.722 2188 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.75 % Allowed : 19.41 % Favored : 74.84 % 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: 2.27 (0.15), residues: 1167 sheet: -0.17 (0.29), residues: 307 loop : -0.21 (0.27), residues: 559 *********************** 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 339 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 243 time to evaluate : 1.604 Fit side-chains revert: symmetry clash outliers start: 96 outliers final: 43 residues processed: 310 average time/residue: 1.1827 time to fit residues: 409.4526 Evaluate side-chains 263 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 220 time to evaluate : 1.832 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 38 residues processed: 5 average time/residue: 0.3650 time to fit residues: 5.1208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 0.1980 chunk 111 optimal weight: 5.9990 chunk 2 optimal weight: 0.0980 chunk 146 optimal weight: 2.9990 chunk 80 optimal weight: 0.0020 chunk 167 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15934 Z= 0.150 Angle : 0.490 9.421 21639 Z= 0.250 Chirality : 0.038 0.236 2512 Planarity : 0.003 0.045 2786 Dihedral : 3.731 15.279 2188 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.73 % Allowed : 21.15 % Favored : 74.12 % 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: 1.95 (0.19), residues: 2033 helix: 2.40 (0.15), residues: 1165 sheet: -0.21 (0.28), residues: 317 loop : -0.14 (0.27), residues: 551 *********************** 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 315 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 236 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 41 residues processed: 297 average time/residue: 1.1159 time to fit residues: 375.0568 Evaluate side-chains 255 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 214 time to evaluate : 1.736 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 38 residues processed: 3 average time/residue: 0.2055 time to fit residues: 3.4350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 38 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 64 optimal weight: 0.0020 chunk 103 optimal weight: 2.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15934 Z= 0.148 Angle : 0.481 8.309 21639 Z= 0.245 Chirality : 0.038 0.212 2512 Planarity : 0.003 0.034 2786 Dihedral : 3.652 14.908 2188 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.19 % Allowed : 22.17 % Favored : 73.64 % 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: 1.95 (0.19), residues: 2033 helix: 2.41 (0.15), residues: 1176 sheet: -0.17 (0.29), residues: 312 loop : -0.25 (0.27), residues: 545 *********************** 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 298 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 228 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 42 residues processed: 282 average time/residue: 1.1512 time to fit residues: 364.2383 Evaluate side-chains 250 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 208 time to evaluate : 1.781 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 39 residues processed: 3 average time/residue: 0.5139 time to fit residues: 4.3543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 111 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** 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: 0.7677 moved from start: 0.4797 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 : 0.514 8.886 21639 Z= 0.261 Chirality : 0.039 0.212 2512 Planarity : 0.003 0.035 2786 Dihedral : 3.729 16.985 2188 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.19 % Allowed : 22.05 % Favored : 73.76 % 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: 1.91 (0.19), residues: 2033 helix: 2.40 (0.15), residues: 1169 sheet: -0.27 (0.29), residues: 317 loop : -0.25 (0.27), residues: 547 *********************** 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 285 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 215 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 43 residues processed: 269 average time/residue: 1.1783 time to fit residues: 355.1989 Evaluate side-chains 252 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 209 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 39 residues processed: 4 average time/residue: 0.5218 time to fit residues: 5.2035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 177 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 ASN B 213 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4953 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= 0.193 Angle : 0.510 8.097 21639 Z= 0.260 Chirality : 0.039 0.205 2512 Planarity : 0.003 0.037 2786 Dihedral : 3.737 16.284 2188 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.18 % Allowed : 23.55 % Favored : 73.28 % 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: 1.88 (0.19), residues: 2033 helix: 2.38 (0.15), residues: 1170 sheet: -0.22 (0.30), residues: 301 loop : -0.33 (0.26), residues: 562 *********************** 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 267 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 214 time to evaluate : 1.814 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 39 residues processed: 264 average time/residue: 1.2336 time to fit residues: 365.0623 Evaluate side-chains 241 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 202 time to evaluate : 1.707 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 39 residues processed: 0 time to fit residues: 2.4349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 143 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** 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: 0.7687 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15934 Z= 0.198 Angle : 0.524 8.067 21639 Z= 0.268 Chirality : 0.039 0.199 2512 Planarity : 0.003 0.037 2786 Dihedral : 3.766 18.044 2188 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.77 % Allowed : 23.67 % 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: 1.85 (0.19), residues: 2033 helix: 2.37 (0.15), residues: 1170 sheet: -0.25 (0.30), residues: 301 loop : -0.33 (0.26), residues: 562 *********************** 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 269 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 206 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 49 residues processed: 257 average time/residue: 1.1989 time to fit residues: 345.3707 Evaluate side-chains 249 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 200 time to evaluate : 1.790 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 40 residues processed: 9 average time/residue: 0.8267 time to fit residues: 11.9273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 415 ASN B 437 GLN ** 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: 0.7693 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15934 Z= 0.200 Angle : 0.527 10.471 21639 Z= 0.267 Chirality : 0.040 0.184 2512 Planarity : 0.004 0.037 2786 Dihedral : 3.777 16.002 2188 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.00 % Allowed : 24.15 % Favored : 72.86 % 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: 2.35 (0.15), residues: 1169 sheet: -0.25 (0.30), residues: 301 loop : -0.37 (0.26), residues: 563 ********************** 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 260 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 210 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 43 residues processed: 258 average time/residue: 1.2100 time to fit residues: 349.5105 Evaluate side-chains 246 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 203 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 41 residues processed: 3 average time/residue: 0.6231 time to fit residues: 4.9618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 23 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN 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 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 254 ASN ** 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 = 0.3502 r_free = 0.3502 target = 0.131958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.110924 restraints weight = 20863.527| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.58 r_work: 0.3119 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15934 Z= 0.214 Angle : 0.535 9.021 21639 Z= 0.272 Chirality : 0.040 0.194 2512 Planarity : 0.004 0.038 2786 Dihedral : 3.796 16.012 2188 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.12 % Allowed : 24.09 % 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: 1.79 (0.19), residues: 2033 helix: 2.32 (0.15), residues: 1169 sheet: -0.37 (0.29), residues: 309 loop : -0.32 (0.26), residues: 555 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6427.35 seconds wall clock time: 114 minutes 35.96 seconds (6875.96 seconds total)