Starting phenix.real_space_refine on Sat Mar 16 18:47:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzg_24759/03_2024/7rzg_24759.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzg_24759/03_2024/7rzg_24759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzg_24759/03_2024/7rzg_24759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzg_24759/03_2024/7rzg_24759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzg_24759/03_2024/7rzg_24759.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzg_24759/03_2024/7rzg_24759.pdb" } resolution = 4.1 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= 0.004 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 43 5.16 5 C 9912 2.51 5 N 2588 2.21 5 O 2842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 65": "NH1" <-> "NH2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A ASP 490": "OD1" <-> "OD2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A GLU 860": "OE1" <-> "OE2" Residue "A ARG 862": "NH1" <-> "NH2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A ARG 892": "NH1" <-> "NH2" Residue "A GLU 910": "OE1" <-> "OE2" Residue "A GLU 962": "OE1" <-> "OE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B ASP 469": "OD1" <-> "OD2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 792": "OE1" <-> "OE2" Residue "B TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 853": "OE1" <-> "OE2" Residue "B GLU 860": "OE1" <-> "OE2" Residue "B ARG 862": "NH1" <-> "NH2" Residue "B GLU 864": "OE1" <-> "OE2" Residue "B ARG 892": "NH1" <-> "NH2" Residue "B GLU 903": "OE1" <-> "OE2" Residue "B ASP 947": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15385 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7718 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 50, 'TRANS': 897} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 7667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7667 Classifications: {'peptide': 940} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 49, 'TRANS': 890} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 7.83, per 1000 atoms: 0.51 Number of scatterers: 15385 At special positions: 0 Unit cell: (109.504, 130.104, 159.377, 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 43 16.00 O 2842 8.00 N 2588 7.00 C 9912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.78 Conformation dependent library (CDL) restraints added in 2.9 seconds 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 14 sheets defined 48.1% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.599A pdb=" N SER A 98 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 157 through 167 removed outlier: 3.585A pdb=" N ARG A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 removed outlier: 4.429A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 236 through 248 removed outlier: 3.651A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.998A pdb=" N LYS A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.514A pdb=" N TYR A 326 " --> pdb=" O GLN A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.794A pdb=" N TYR A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 386 Processing helix chain 'A' and resid 386 through 405 removed outlier: 3.818A pdb=" N ILE A 390 " --> pdb=" O HIS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 424 Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.777A pdb=" N ILE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 516 Processing helix chain 'A' and resid 581 through 584 removed outlier: 4.006A pdb=" N TYR A 584 " --> pdb=" O PRO A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 586 through 604 Processing helix chain 'A' and resid 604 through 615 removed outlier: 5.029A pdb=" N ALA A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 removed outlier: 3.764A pdb=" N THR A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 4.156A pdb=" N ASN A 671 " --> pdb=" O MET A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 Processing helix chain 'A' and resid 677 through 690 Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 708 through 722 Proline residue: A 717 - end of helix removed outlier: 4.549A pdb=" N ARG A 722 " --> pdb=" O GLN A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 754 Processing helix chain 'A' and resid 801 through 815 removed outlier: 3.902A pdb=" N MET A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 855 through 877 removed outlier: 4.042A pdb=" N GLU A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP A 876 " --> pdb=" O LYS A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 894 removed outlier: 4.794A pdb=" N ALA A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 912 removed outlier: 3.701A pdb=" N GLU A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 removed outlier: 3.624A pdb=" N LYS A 929 " --> pdb=" O VAL A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 944 removed outlier: 4.117A pdb=" N GLU A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1001 removed outlier: 4.472A pdb=" N GLY A1001 " --> pdb=" O GLU A 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.793A pdb=" N LEU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 removed outlier: 4.073A pdb=" N ASN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 removed outlier: 3.818A pdb=" N THR B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 222 through 228 removed outlier: 3.668A pdb=" N LEU B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.672A pdb=" N GLN B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 249 removed outlier: 3.862A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.590A pdb=" N LYS B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 429 through 442 removed outlier: 3.921A pdb=" N TYR B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N SER B 435 " --> pdb=" O ARG B 431 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N HIS B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 471 Processing helix chain 'B' and resid 506 through 515 removed outlier: 3.747A pdb=" N TRP B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 removed outlier: 4.190A pdb=" N TYR B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 584' Processing helix chain 'B' and resid 586 through 613 removed outlier: 4.872A pdb=" N GLU B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TYR B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 651 removed outlier: 3.627A pdb=" N THR B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 673 through 676 removed outlier: 4.230A pdb=" N GLU B 676 " --> pdb=" O PHE B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 676' Processing helix chain 'B' and resid 677 through 690 Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 704 through 707 removed outlier: 3.822A pdb=" N VAL B 707 " --> pdb=" O LEU B 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 707' Processing helix chain 'B' and resid 708 through 722 Proline residue: B 717 - end of helix removed outlier: 4.438A pdb=" N ARG B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 754 Processing helix chain 'B' and resid 801 through 815 removed outlier: 4.155A pdb=" N MET B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 855 through 876 removed outlier: 3.682A pdb=" N GLU B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 894 removed outlier: 3.622A pdb=" N PHE B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 912 Processing helix chain 'B' and resid 919 through 929 removed outlier: 3.888A pdb=" N LYS B 929 " --> pdb=" O VAL B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 945 removed outlier: 3.811A pdb=" N ILE B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU B 942 " --> pdb=" O LYS B 938 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET B 943 " --> pdb=" O PHE B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1001 removed outlier: 4.503A pdb=" N GLY B1001 " --> pdb=" O GLU B 997 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 69 removed outlier: 6.038A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA A 88 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 141 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 69 removed outlier: 6.038A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 91 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 141 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.561A pdb=" N MET A 371 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 491 through 492 removed outlier: 3.523A pdb=" N ARG A 491 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 549 through 553 removed outlier: 6.680A pdb=" N LEU A 559 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP A 560 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY A 731 " --> pdb=" O TRP A 560 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS A 562 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 633 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 549 through 553 removed outlier: 6.680A pdb=" N LEU A 559 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP A 560 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY A 731 " --> pdb=" O TRP A 560 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS A 562 " --> pdb=" O GLY A 731 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 776 through 777 removed outlier: 5.936A pdb=" N PHE A 777 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N HIS A 957 " --> pdb=" O PHE A 777 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN A 781 " --> pdb=" O LEU A 959 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 776 through 777 removed outlier: 5.936A pdb=" N PHE A 777 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N HIS A 957 " --> pdb=" O PHE A 777 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLY A 790 " --> pdb=" O SER A 852 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N SER A 852 " --> pdb=" O GLY A 790 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU A 792 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE A 850 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR A 794 " --> pdb=" O PHE A 848 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N PHE A 848 " --> pdb=" O TYR A 794 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLN A 796 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU A 846 " --> pdb=" O GLN A 796 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP A 798 " --> pdb=" O GLN A 844 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 836 " --> pdb=" O ARG A 847 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE A 832 " --> pdb=" O GLN A 851 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 69 removed outlier: 3.653A pdb=" N GLU B 63 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL B 258 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B 78 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B 260 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 87 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 141 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 303 through 304 Processing sheet with id=AB2, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AB3, first strand: chain 'B' and resid 549 through 553 removed outlier: 5.878A pdb=" N LEU B 550 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE B 561 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 552 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS B 558 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU B 729 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP B 560 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLY B 731 " --> pdb=" O TRP B 560 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS B 562 " --> pdb=" O GLY B 731 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 776 through 777 removed outlier: 6.054A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 776 through 777 removed outlier: 6.054A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 792 " --> pdb=" O VAL B 956 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 836 " --> pdb=" O ARG B 847 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 832 " --> pdb=" O GLN B 851 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 2031 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: 5.76 Time building geometry restraints manager: 6.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4460 1.33 - 1.46: 3022 1.46 - 1.58: 8201 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 15769 Sorted by residual: bond pdb=" N ILE B 94 " pdb=" CA ILE B 94 " ideal model delta sigma weight residual 1.456 1.497 -0.042 1.11e-02 8.12e+03 1.41e+01 bond pdb=" N ILE A 843 " pdb=" CA ILE A 843 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.19e-02 7.06e+03 1.08e+01 bond pdb=" N GLY B 95 " pdb=" CA GLY B 95 " ideal model delta sigma weight residual 1.444 1.476 -0.032 1.02e-02 9.61e+03 1.00e+01 bond pdb=" CA PRO B 100 " pdb=" C PRO B 100 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.94e+00 bond pdb=" N ILE A 874 " pdb=" CA ILE A 874 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.14e+00 ... (remaining 15764 not shown) Histogram of bond angle deviations from ideal: 96.73 - 104.20: 281 104.20 - 111.68: 6639 111.68 - 119.15: 6262 119.15 - 126.62: 7943 126.62 - 134.10: 203 Bond angle restraints: 21328 Sorted by residual: angle pdb=" N PRO B 100 " pdb=" CA PRO B 100 " pdb=" C PRO B 100 " ideal model delta sigma weight residual 110.70 118.98 -8.28 1.22e+00 6.72e-01 4.60e+01 angle pdb=" CB ARG A 658 " pdb=" CG ARG A 658 " pdb=" CD ARG A 658 " ideal model delta sigma weight residual 111.30 100.23 11.07 2.30e+00 1.89e-01 2.32e+01 angle pdb=" N GLY B1001 " pdb=" CA GLY B1001 " pdb=" C GLY B1001 " ideal model delta sigma weight residual 113.18 123.56 -10.38 2.37e+00 1.78e-01 1.92e+01 angle pdb=" CA GLY A 830 " pdb=" C GLY A 830 " pdb=" N TYR A 831 " ideal model delta sigma weight residual 114.58 118.19 -3.61 8.60e-01 1.35e+00 1.76e+01 angle pdb=" CA GLY A 830 " pdb=" C GLY A 830 " pdb=" O GLY A 830 " ideal model delta sigma weight residual 121.49 117.55 3.94 9.60e-01 1.09e+00 1.68e+01 ... (remaining 21323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 8734 17.07 - 34.14: 644 34.14 - 51.21: 129 51.21 - 68.28: 13 68.28 - 85.35: 17 Dihedral angle restraints: 9537 sinusoidal: 3968 harmonic: 5569 Sorted by residual: dihedral pdb=" CA SER B 57 " pdb=" C SER B 57 " pdb=" N PRO B 58 " pdb=" CA PRO B 58 " ideal model delta harmonic sigma weight residual -180.00 -153.62 -26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA TYR B 940 " pdb=" C TYR B 940 " pdb=" N LYS B 941 " pdb=" CA LYS B 941 " ideal model delta harmonic sigma weight residual -180.00 -154.62 -25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLN B 800 " pdb=" C GLN B 800 " pdb=" N SER B 801 " pdb=" CA SER B 801 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 9534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1541 0.057 - 0.114: 562 0.114 - 0.172: 159 0.172 - 0.229: 24 0.229 - 0.286: 7 Chirality restraints: 2293 Sorted by residual: chirality pdb=" CB ILE B 505 " pdb=" CA ILE B 505 " pdb=" CG1 ILE B 505 " pdb=" CG2 ILE B 505 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA LYS B 884 " pdb=" N LYS B 884 " pdb=" C LYS B 884 " pdb=" CB LYS B 884 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB THR B 380 " pdb=" CA THR B 380 " pdb=" OG1 THR B 380 " pdb=" CG2 THR B 380 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2290 not shown) Planarity restraints: 2760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 224 " 0.024 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C TYR B 224 " -0.084 2.00e-02 2.50e+03 pdb=" O TYR B 224 " 0.031 2.00e-02 2.50e+03 pdb=" N THR B 225 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 472 " 0.078 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO A 473 " -0.208 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 245 " -0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C HIS B 245 " 0.077 2.00e-02 2.50e+03 pdb=" O HIS B 245 " -0.029 2.00e-02 2.50e+03 pdb=" N SER B 246 " -0.026 2.00e-02 2.50e+03 ... (remaining 2757 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 248 2.64 - 3.21: 14576 3.21 - 3.77: 23347 3.77 - 4.34: 31984 4.34 - 4.90: 51089 Nonbonded interactions: 121244 Sorted by model distance: nonbonded pdb=" O HIS A 297 " pdb=" NH1 ARG A 477 " model vdw 2.077 2.520 nonbonded pdb=" OG SER B 348 " pdb=" OE2 GLU B 606 " model vdw 2.156 2.440 nonbonded pdb=" OE1 GLN A 887 " pdb=" NZ LYS A 929 " model vdw 2.168 2.520 nonbonded pdb=" O ARG A 668 " pdb=" ND2 ASN A 672 " model vdw 2.184 2.520 nonbonded pdb=" O VAL B 785 " pdb=" NH1 ARG B 961 " model vdw 2.187 2.520 ... (remaining 121239 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 46 through 585 or (resid 586 and (name N or name CA or nam \ e C or name O or name CB )) or resid 587 through 656 or (resid 657 and (name N o \ r name CA or name C or name O or name CB )) or resid 658 through 704 or (resid 7 \ 05 and (name N or name CA or name C or name O or name CB )) or resid 706 through \ 763 or (resid 764 through 765 and (name N or name CA or name C or name O or nam \ e CB )) or resid 766 through 769 or (resid 770 and (name N or name CA or name C \ or name O or name CB )) or resid 771 through 962 or resid 989 through 1011)) selection = (chain 'B' and (resid 46 through 57 or resid 59 through 257 or (resid 258 and (n \ ame N or name CA or name C or name O or name CB )) or resid 259 through 349 or ( \ resid 350 and (name N or name CA or name C or name O or name CB )) or resid 351 \ through 439 or (resid 440 and (name N or name CA or name C or name O or name CB \ )) or resid 441 through 541 or (resid 542 through 544 and (name N or name CA or \ name C or name O or name CB )) or resid 545 through 573 or (resid 574 and (name \ N or name CA or name C or name O or name CB )) or resid 575 through 587 or (resi \ d 588 and (name N or name CA or name C or name O or name CB )) or resid 589 thro \ ugh 603 or (resid 604 and (name N or name CA or name C or name O or name CB )) o \ r resid 605 through 757 or (resid 758 and (name N or name CA or name C or name O \ or name CB )) or resid 759 through 1011)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 4.490 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 42.020 Find NCS groups from input model: 0.930 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 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 : 0.007 0.069 15769 Z= 0.437 Angle : 1.165 11.074 21328 Z= 0.670 Chirality : 0.064 0.286 2293 Planarity : 0.009 0.120 2760 Dihedral : 12.777 85.351 5937 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.18 % Allowed : 2.11 % Favored : 97.71 % 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: -3.80 (0.16), residues: 1878 helix: -2.57 (0.14), residues: 785 sheet: -1.76 (0.26), residues: 344 loop : -2.62 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP B 695 HIS 0.014 0.003 HIS B 146 PHE 0.056 0.003 PHE A 168 TYR 0.047 0.003 TYR A 584 ARG 0.006 0.001 ARG A 951 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 258 time to evaluate : 1.721 Fit side-chains revert: symmetry clash REVERT: A 153 VAL cc_start: 0.7624 (OUTLIER) cc_final: 0.7249 (t) REVERT: A 158 LEU cc_start: 0.8012 (tp) cc_final: 0.7774 (tp) REVERT: A 470 LYS cc_start: 0.7850 (mppt) cc_final: 0.7558 (mptt) REVERT: A 1002 LEU cc_start: 0.8351 (mt) cc_final: 0.8150 (mt) REVERT: B 97 LEU cc_start: 0.1718 (OUTLIER) cc_final: 0.1358 (pt) REVERT: B 248 TYR cc_start: 0.5690 (m-80) cc_final: 0.5418 (m-80) REVERT: B 338 ILE cc_start: 0.8239 (mm) cc_final: 0.7891 (mm) REVERT: B 391 ILE cc_start: 0.7995 (mt) cc_final: 0.7774 (mt) REVERT: B 466 MET cc_start: 0.6473 (mtp) cc_final: 0.6010 (ttm) REVERT: B 799 MET cc_start: 0.4954 (ttt) cc_final: 0.4735 (ttt) REVERT: B 806 MET cc_start: 0.7108 (mmm) cc_final: 0.6714 (mmm) outliers start: 3 outliers final: 0 residues processed: 259 average time/residue: 0.2556 time to fit residues: 99.4163 Evaluate side-chains 171 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 76 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 736 GLN A 828 GLN B 146 HIS B 329 ASN B 332 HIS ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN B 762 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15769 Z= 0.222 Angle : 0.683 7.367 21328 Z= 0.357 Chirality : 0.045 0.202 2293 Planarity : 0.006 0.081 2760 Dihedral : 5.585 23.678 2050 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.18 % Allowed : 3.50 % Favored : 96.32 % 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: -1.99 (0.18), residues: 1878 helix: -0.51 (0.17), residues: 820 sheet: -1.30 (0.26), residues: 344 loop : -2.17 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 776 HIS 0.009 0.001 HIS B 681 PHE 0.020 0.002 PHE A 168 TYR 0.015 0.002 TYR A 433 ARG 0.005 0.001 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 266 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 LYS cc_start: 0.7094 (mmtm) cc_final: 0.6253 (ptpp) REVERT: A 357 ASN cc_start: 0.7825 (m110) cc_final: 0.7569 (m110) REVERT: A 505 ILE cc_start: 0.8102 (mm) cc_final: 0.7704 (mt) REVERT: A 742 MET cc_start: 0.6582 (tpt) cc_final: 0.6279 (mmm) REVERT: A 799 MET cc_start: 0.7447 (mtm) cc_final: 0.7191 (mtm) REVERT: A 846 LEU cc_start: 0.7729 (tp) cc_final: 0.7434 (tt) REVERT: B 338 ILE cc_start: 0.7983 (mm) cc_final: 0.7637 (mm) REVERT: B 357 ASN cc_start: 0.7026 (m-40) cc_final: 0.6714 (m-40) REVERT: B 466 MET cc_start: 0.6258 (mtp) cc_final: 0.5976 (ttm) REVERT: B 691 THR cc_start: 0.5903 (t) cc_final: 0.5668 (t) REVERT: B 806 MET cc_start: 0.7612 (mmm) cc_final: 0.7171 (mmm) REVERT: B 860 GLU cc_start: 0.6400 (pp20) cc_final: 0.6119 (pp20) REVERT: B 864 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 891 ILE cc_start: 0.7205 (mm) cc_final: 0.6945 (tp) outliers start: 3 outliers final: 0 residues processed: 268 average time/residue: 0.2623 time to fit residues: 105.7373 Evaluate side-chains 177 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 332 HIS ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 GLN B 442 HIS B 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15769 Z= 0.233 Angle : 0.656 9.017 21328 Z= 0.340 Chirality : 0.044 0.183 2293 Planarity : 0.005 0.066 2760 Dihedral : 5.286 21.980 2050 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % 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: -1.30 (0.19), residues: 1878 helix: 0.09 (0.17), residues: 832 sheet: -1.00 (0.26), residues: 358 loop : -1.85 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 776 HIS 0.008 0.001 HIS B 681 PHE 0.016 0.002 PHE A 169 TYR 0.020 0.002 TYR B 594 ARG 0.008 0.001 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 2.465 Fit side-chains revert: symmetry clash REVERT: A 217 LYS cc_start: 0.7324 (mmtm) cc_final: 0.6513 (pttp) REVERT: A 505 ILE cc_start: 0.8411 (mm) cc_final: 0.7970 (mt) REVERT: A 742 MET cc_start: 0.6535 (tpt) cc_final: 0.6300 (mmm) REVERT: A 963 MET cc_start: 0.6811 (pmm) cc_final: 0.6244 (pmm) REVERT: B 113 MET cc_start: -0.2142 (ttt) cc_final: -0.2495 (tmm) REVERT: B 357 ASN cc_start: 0.7029 (m-40) cc_final: 0.6704 (m-40) REVERT: B 466 MET cc_start: 0.6278 (mtp) cc_final: 0.6049 (ttm) REVERT: B 806 MET cc_start: 0.7590 (mmm) cc_final: 0.7157 (mmm) REVERT: B 998 PHE cc_start: 0.8575 (t80) cc_final: 0.8178 (t80) outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.2669 time to fit residues: 94.3871 Evaluate side-chains 174 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 18 optimal weight: 0.0570 chunk 81 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 48 optimal weight: 0.0000 overall best weight: 3.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS A 805 ASN ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 HIS B 762 GLN ** B 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15769 Z= 0.253 Angle : 0.662 7.544 21328 Z= 0.342 Chirality : 0.044 0.170 2293 Planarity : 0.005 0.059 2760 Dihedral : 5.239 22.260 2050 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.19), residues: 1878 helix: 0.37 (0.17), residues: 816 sheet: -0.81 (0.26), residues: 353 loop : -1.69 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 776 HIS 0.008 0.001 HIS B 681 PHE 0.018 0.002 PHE A 169 TYR 0.021 0.002 TYR A 584 ARG 0.005 0.001 ARG A 839 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LYS cc_start: 0.7224 (mmtm) cc_final: 0.6511 (pttp) REVERT: A 505 ILE cc_start: 0.8466 (mm) cc_final: 0.8230 (mm) REVERT: A 823 LEU cc_start: 0.8303 (mp) cc_final: 0.7865 (mt) REVERT: B 113 MET cc_start: -0.1555 (ttt) cc_final: -0.2234 (tmm) REVERT: B 357 ASN cc_start: 0.7227 (m-40) cc_final: 0.6929 (m-40) REVERT: B 466 MET cc_start: 0.6334 (mtp) cc_final: 0.6082 (ttm) REVERT: B 806 MET cc_start: 0.7631 (mmm) cc_final: 0.6991 (mmm) REVERT: B 860 GLU cc_start: 0.6777 (pp20) cc_final: 0.6375 (pp20) REVERT: B 998 PHE cc_start: 0.8580 (t80) cc_final: 0.8286 (t80) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.2832 time to fit residues: 97.0941 Evaluate side-chains 171 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 2 optimal weight: 0.5980 chunk 135 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN B 762 GLN B 786 HIS ** B 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15769 Z= 0.250 Angle : 0.664 8.219 21328 Z= 0.343 Chirality : 0.045 0.165 2293 Planarity : 0.005 0.054 2760 Dihedral : 5.243 25.649 2050 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.12 % Allowed : 3.68 % Favored : 96.20 % 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: -0.95 (0.19), residues: 1878 helix: 0.40 (0.17), residues: 816 sheet: -0.76 (0.27), residues: 351 loop : -1.71 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 355 HIS 0.006 0.001 HIS A 93 PHE 0.015 0.002 PHE A 659 TYR 0.020 0.002 TYR A 584 ARG 0.005 0.001 ARG B 767 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 227 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6389 (m-10) cc_final: 0.5900 (m-80) REVERT: A 217 LYS cc_start: 0.7309 (mmtm) cc_final: 0.6578 (pttm) REVERT: A 505 ILE cc_start: 0.8585 (mm) cc_final: 0.8372 (mm) REVERT: A 776 TRP cc_start: 0.4270 (t60) cc_final: 0.3967 (t60) REVERT: A 823 LEU cc_start: 0.8321 (mp) cc_final: 0.7845 (mt) REVERT: B 113 MET cc_start: -0.1780 (ttt) cc_final: -0.2495 (tmm) REVERT: B 357 ASN cc_start: 0.7111 (m-40) cc_final: 0.6896 (m-40) REVERT: B 466 MET cc_start: 0.6276 (mtp) cc_final: 0.6074 (ttm) REVERT: B 649 MET cc_start: 0.8225 (pmm) cc_final: 0.7897 (pmm) REVERT: B 806 MET cc_start: 0.7525 (mmm) cc_final: 0.7082 (mmm) REVERT: B 860 GLU cc_start: 0.6682 (pp20) cc_final: 0.6354 (pp20) REVERT: B 998 PHE cc_start: 0.8628 (t80) cc_final: 0.8327 (t80) outliers start: 2 outliers final: 0 residues processed: 228 average time/residue: 0.2764 time to fit residues: 93.8311 Evaluate side-chains 159 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.6980 chunk 163 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 0.3980 chunk 95 optimal weight: 9.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN B 762 GLN ** B 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15769 Z= 0.163 Angle : 0.604 7.378 21328 Z= 0.308 Chirality : 0.043 0.162 2293 Planarity : 0.004 0.050 2760 Dihedral : 4.933 23.636 2050 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1878 helix: 0.71 (0.18), residues: 816 sheet: -0.60 (0.27), residues: 353 loop : -1.57 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 513 HIS 0.007 0.001 HIS A 93 PHE 0.012 0.001 PHE B 174 TYR 0.022 0.001 TYR B 609 ARG 0.005 0.000 ARG B 668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6340 (m-10) cc_final: 0.5822 (m-80) REVERT: A 217 LYS cc_start: 0.7370 (mmtm) cc_final: 0.6628 (pttm) REVERT: A 505 ILE cc_start: 0.8563 (mm) cc_final: 0.8343 (mm) REVERT: A 776 TRP cc_start: 0.4413 (t60) cc_final: 0.4148 (t60) REVERT: A 823 LEU cc_start: 0.8145 (mp) cc_final: 0.7772 (mt) REVERT: A 963 MET cc_start: 0.6906 (pmm) cc_final: 0.6364 (pmm) REVERT: B 649 MET cc_start: 0.8300 (pmm) cc_final: 0.8058 (pmm) REVERT: B 806 MET cc_start: 0.7422 (mmm) cc_final: 0.6947 (mmm) REVERT: B 860 GLU cc_start: 0.6639 (pp20) cc_final: 0.6407 (pp20) REVERT: B 998 PHE cc_start: 0.8557 (t80) cc_final: 0.8262 (t80) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2678 time to fit residues: 97.4785 Evaluate side-chains 168 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 0.0010 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN A 821 ASN B 112 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15769 Z= 0.151 Angle : 0.595 9.519 21328 Z= 0.301 Chirality : 0.042 0.190 2293 Planarity : 0.004 0.048 2760 Dihedral : 4.735 23.189 2050 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.06 % Allowed : 1.81 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.19), residues: 1878 helix: 0.87 (0.18), residues: 819 sheet: -0.47 (0.27), residues: 348 loop : -1.49 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 776 HIS 0.007 0.001 HIS A 108 PHE 0.013 0.001 PHE B 174 TYR 0.017 0.001 TYR A 333 ARG 0.008 0.000 ARG B 767 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6377 (m-10) cc_final: 0.5867 (m-80) REVERT: A 217 LYS cc_start: 0.7377 (mmtm) cc_final: 0.6670 (pttm) REVERT: A 226 LEU cc_start: 0.7540 (mm) cc_final: 0.7141 (mm) REVERT: A 505 ILE cc_start: 0.8505 (mm) cc_final: 0.8259 (mm) REVERT: A 776 TRP cc_start: 0.4387 (t60) cc_final: 0.4124 (t60) REVERT: A 963 MET cc_start: 0.7094 (pmm) cc_final: 0.6577 (pmm) REVERT: B 113 MET cc_start: -0.2030 (ttt) cc_final: -0.2289 (tmm) REVERT: B 359 LEU cc_start: 0.3427 (pp) cc_final: 0.3219 (pp) REVERT: B 505 ILE cc_start: 0.7153 (tp) cc_final: 0.6952 (tp) REVERT: B 806 MET cc_start: 0.7363 (mmm) cc_final: 0.6771 (mmm) REVERT: B 860 GLU cc_start: 0.6624 (pp20) cc_final: 0.6407 (pp20) REVERT: B 998 PHE cc_start: 0.8449 (t80) cc_final: 0.8197 (t80) outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.2572 time to fit residues: 98.8100 Evaluate side-chains 186 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 677 GLN ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN A 851 GLN B 112 HIS B 184 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 HIS B 762 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15769 Z= 0.312 Angle : 0.742 9.064 21328 Z= 0.381 Chirality : 0.047 0.257 2293 Planarity : 0.005 0.048 2760 Dihedral : 5.326 24.432 2050 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.19), residues: 1878 helix: 0.54 (0.17), residues: 813 sheet: -0.66 (0.27), residues: 351 loop : -1.73 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 776 HIS 0.014 0.002 HIS A 213 PHE 0.048 0.003 PHE A 215 TYR 0.019 0.002 TYR A 314 ARG 0.008 0.001 ARG B 767 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7424 (mm) cc_final: 0.6984 (mm) REVERT: A 470 LYS cc_start: 0.7978 (mppt) cc_final: 0.7350 (mptt) REVERT: A 963 MET cc_start: 0.6321 (pmm) cc_final: 0.5801 (pmm) REVERT: B 113 MET cc_start: -0.2214 (ttt) cc_final: -0.2755 (tmm) REVERT: B 606 GLU cc_start: 0.7222 (tp30) cc_final: 0.6971 (tp30) REVERT: B 860 GLU cc_start: 0.6760 (pp20) cc_final: 0.6507 (pp20) REVERT: B 998 PHE cc_start: 0.8543 (t80) cc_final: 0.8300 (t80) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2780 time to fit residues: 95.7154 Evaluate side-chains 165 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 ASN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15769 Z= 0.282 Angle : 0.720 9.054 21328 Z= 0.369 Chirality : 0.047 0.367 2293 Planarity : 0.005 0.049 2760 Dihedral : 5.359 24.131 2050 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.19), residues: 1878 helix: 0.47 (0.18), residues: 814 sheet: -0.67 (0.27), residues: 342 loop : -1.80 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 513 HIS 0.011 0.002 HIS A 155 PHE 0.027 0.002 PHE A 866 TYR 0.018 0.002 TYR A 584 ARG 0.007 0.001 ARG B 767 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.5622 (m-80) cc_final: 0.4784 (m-80) REVERT: A 226 LEU cc_start: 0.7442 (mm) cc_final: 0.6961 (mm) REVERT: A 592 MET cc_start: 0.6455 (mmp) cc_final: 0.6158 (mmt) REVERT: B 113 MET cc_start: -0.2184 (ttt) cc_final: -0.2737 (tmm) REVERT: B 649 MET cc_start: 0.8564 (pmm) cc_final: 0.8195 (pmm) REVERT: B 860 GLU cc_start: 0.6827 (pp20) cc_final: 0.6548 (pp20) REVERT: B 998 PHE cc_start: 0.8600 (t80) cc_final: 0.8324 (t80) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2651 time to fit residues: 86.3714 Evaluate side-chains 164 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN B 146 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS B 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15769 Z= 0.308 Angle : 0.759 8.798 21328 Z= 0.388 Chirality : 0.047 0.270 2293 Planarity : 0.005 0.049 2760 Dihedral : 5.520 25.063 2050 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -1.07 (0.19), residues: 1878 helix: 0.30 (0.17), residues: 815 sheet: -0.69 (0.27), residues: 346 loop : -1.85 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 776 HIS 0.007 0.002 HIS A 93 PHE 0.030 0.002 PHE A 866 TYR 0.020 0.002 TYR A 584 ARG 0.007 0.001 ARG B 782 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8728 (mmm) cc_final: 0.8500 (tpp) REVERT: A 168 PHE cc_start: 0.5512 (m-80) cc_final: 0.4782 (m-80) REVERT: A 226 LEU cc_start: 0.7334 (mm) cc_final: 0.6864 (mm) REVERT: A 673 PHE cc_start: 0.7253 (t80) cc_final: 0.6736 (t80) REVERT: A 823 LEU cc_start: 0.8350 (mp) cc_final: 0.7875 (mt) REVERT: B 113 MET cc_start: -0.2067 (ttt) cc_final: -0.2688 (tmm) REVERT: B 606 GLU cc_start: 0.7079 (tp30) cc_final: 0.6863 (tp30) REVERT: B 649 MET cc_start: 0.8620 (pmm) cc_final: 0.8239 (pmm) REVERT: B 860 GLU cc_start: 0.6930 (pp20) cc_final: 0.6640 (pp20) REVERT: B 998 PHE cc_start: 0.8578 (t80) cc_final: 0.8302 (t80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2622 time to fit residues: 83.5677 Evaluate side-chains 164 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.144754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.121759 restraints weight = 43937.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.123623 restraints weight = 28416.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.124191 restraints weight = 18911.818| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15769 Z= 0.243 Angle : 0.700 10.891 21328 Z= 0.358 Chirality : 0.045 0.188 2293 Planarity : 0.005 0.049 2760 Dihedral : 5.308 24.558 2050 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.19), residues: 1878 helix: 0.43 (0.18), residues: 817 sheet: -0.66 (0.28), residues: 350 loop : -1.80 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 513 HIS 0.012 0.001 HIS A 108 PHE 0.032 0.002 PHE A 866 TYR 0.020 0.002 TYR A 584 ARG 0.008 0.001 ARG B 668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2821.40 seconds wall clock time: 52 minutes 15.25 seconds (3135.25 seconds total)