Starting phenix.real_space_refine on Sat Feb 17 15:34:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeh_33773/02_2024/7yeh_33773_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeh_33773/02_2024/7yeh_33773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeh_33773/02_2024/7yeh_33773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeh_33773/02_2024/7yeh_33773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeh_33773/02_2024/7yeh_33773_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeh_33773/02_2024/7yeh_33773_updated.pdb" } resolution = 3.92 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= 0.005 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 113 5.16 5 C 12137 2.51 5 N 3318 2.21 5 O 3552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 675": "OD1" <-> "OD2" Residue "B TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 792": "NH1" <-> "NH2" Residue "B GLU 839": "OE1" <-> "OE2" Residue "B GLU 883": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 675": "OD1" <-> "OD2" Residue "A TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 435": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19122 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 8032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 8032 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 967} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 8032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 8032 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 967} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2773 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 323} Chain breaks: 1 Chain: "D" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 245 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.37, per 1000 atoms: 0.54 Number of scatterers: 19122 At special positions: 0 Unit cell: (114.929, 162.747, 175.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 113 16.00 P 2 15.00 O 3552 8.00 N 3318 7.00 C 12137 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: 8.10 Conformation dependent library (CDL) restraints added in 3.8 seconds 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 118 helices and 10 sheets defined 54.3% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 38 through 48 Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'B' and resid 71 through 84 Processing helix chain 'B' and resid 89 through 102 Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 124 through 136 Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 157 through 169 Processing helix chain 'B' and resid 173 through 186 Processing helix chain 'B' and resid 192 through 204 Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 225 through 238 Processing helix chain 'B' and resid 241 through 254 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 293 through 306 Processing helix chain 'B' and resid 309 through 322 removed outlier: 4.902A pdb=" N GLU B 313 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 339 Processing helix chain 'B' and resid 343 through 356 Processing helix chain 'B' and resid 361 through 373 Processing helix chain 'B' and resid 378 through 390 Processing helix chain 'B' and resid 395 through 407 Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 445 through 458 Processing helix chain 'B' and resid 463 through 475 Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 507 through 512 removed outlier: 4.028A pdb=" N MET B 511 " --> pdb=" O PRO B 507 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU B 512 " --> pdb=" O HIS B 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 507 through 512' Processing helix chain 'B' and resid 517 through 538 removed outlier: 3.887A pdb=" N VAL B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU B 538 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 574 Processing helix chain 'B' and resid 600 through 608 Processing helix chain 'B' and resid 621 through 631 Processing helix chain 'B' and resid 648 through 653 Processing helix chain 'B' and resid 689 through 691 No H-bonds generated for 'chain 'B' and resid 689 through 691' Processing helix chain 'B' and resid 708 through 711 No H-bonds generated for 'chain 'B' and resid 708 through 711' Processing helix chain 'B' and resid 713 through 716 Processing helix chain 'B' and resid 739 through 741 No H-bonds generated for 'chain 'B' and resid 739 through 741' Processing helix chain 'B' and resid 743 through 747 removed outlier: 4.324A pdb=" N SER B 747 " --> pdb=" O ALA B 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 743 through 747' Processing helix chain 'B' and resid 770 through 772 No H-bonds generated for 'chain 'B' and resid 770 through 772' Processing helix chain 'B' and resid 781 through 792 Processing helix chain 'B' and resid 807 through 813 removed outlier: 5.528A pdb=" N THR B 811 " --> pdb=" O LEU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 818 No H-bonds generated for 'chain 'B' and resid 815 through 818' Processing helix chain 'B' and resid 833 through 835 No H-bonds generated for 'chain 'B' and resid 833 through 835' Processing helix chain 'B' and resid 855 through 867 Processing helix chain 'B' and resid 881 through 892 Proline residue: B 884 - end of helix removed outlier: 3.644A pdb=" N GLN B 888 " --> pdb=" O ASN B 885 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 891 " --> pdb=" O GLN B 888 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 892 " --> pdb=" O TYR B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 917 removed outlier: 4.406A pdb=" N GLY B 915 " --> pdb=" O HIS B 911 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN B 916 " --> pdb=" O VAL B 912 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B 917 " --> pdb=" O ARG B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 939 removed outlier: 3.768A pdb=" N MET B 934 " --> pdb=" O HIS B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 963 removed outlier: 3.993A pdb=" N ALA B 956 " --> pdb=" O ALA B 952 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA B 957 " --> pdb=" O SER B 953 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 958 " --> pdb=" O ARG B 954 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 959 " --> pdb=" O VAL B 955 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 973 through 986 Processing helix chain 'B' and resid 989 through 1003 removed outlier: 4.728A pdb=" N ILE B1002 " --> pdb=" O TRP B 998 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER B1003 " --> pdb=" O LYS B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1029 removed outlier: 4.462A pdb=" N ALA B1029 " --> pdb=" O GLU B1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 38 through 48 Processing helix chain 'A' and resid 56 through 67 Processing helix chain 'A' and resid 71 through 84 Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 124 through 136 Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 157 through 169 Processing helix chain 'A' and resid 173 through 186 Processing helix chain 'A' and resid 192 through 204 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 293 through 306 Processing helix chain 'A' and resid 309 through 322 removed outlier: 4.902A pdb=" N GLU A 313 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 339 Processing helix chain 'A' and resid 343 through 356 Processing helix chain 'A' and resid 361 through 373 Processing helix chain 'A' and resid 378 through 390 Processing helix chain 'A' and resid 395 through 407 Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 445 through 458 Processing helix chain 'A' and resid 463 through 475 Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 507 through 512 removed outlier: 4.028A pdb=" N MET A 511 " --> pdb=" O PRO A 507 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU A 512 " --> pdb=" O HIS A 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 507 through 512' Processing helix chain 'A' and resid 517 through 538 removed outlier: 3.887A pdb=" N VAL A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 574 Processing helix chain 'A' and resid 600 through 608 Processing helix chain 'A' and resid 621 through 631 Processing helix chain 'A' and resid 648 through 653 Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 708 through 711 No H-bonds generated for 'chain 'A' and resid 708 through 711' Processing helix chain 'A' and resid 713 through 716 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 743 through 747 removed outlier: 4.324A pdb=" N SER A 747 " --> pdb=" O ALA A 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 743 through 747' Processing helix chain 'A' and resid 770 through 772 No H-bonds generated for 'chain 'A' and resid 770 through 772' Processing helix chain 'A' and resid 781 through 792 Processing helix chain 'A' and resid 807 through 813 removed outlier: 5.528A pdb=" N THR A 811 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 818 No H-bonds generated for 'chain 'A' and resid 815 through 818' Processing helix chain 'A' and resid 833 through 835 No H-bonds generated for 'chain 'A' and resid 833 through 835' Processing helix chain 'A' and resid 855 through 867 Processing helix chain 'A' and resid 881 through 892 Proline residue: A 884 - end of helix removed outlier: 3.644A pdb=" N GLN A 888 " --> pdb=" O ASN A 885 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 891 " --> pdb=" O GLN A 888 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 892 " --> pdb=" O TYR A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 917 removed outlier: 4.405A pdb=" N GLY A 915 " --> pdb=" O HIS A 911 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A 916 " --> pdb=" O VAL A 912 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 917 " --> pdb=" O ARG A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.769A pdb=" N MET A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 963 removed outlier: 3.993A pdb=" N ALA A 956 " --> pdb=" O ALA A 952 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA A 957 " --> pdb=" O SER A 953 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 958 " --> pdb=" O ARG A 954 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 959 " --> pdb=" O VAL A 955 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 973 through 986 Processing helix chain 'A' and resid 989 through 1003 removed outlier: 4.729A pdb=" N ILE A1002 " --> pdb=" O TRP A 998 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1029 removed outlier: 4.462A pdb=" N ALA A1029 " --> pdb=" O GLU A1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 113 through 128 Processing helix chain 'C' and resid 148 through 163 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 191 through 205 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 232 through 240 Processing helix chain 'C' and resid 261 through 271 Processing helix chain 'C' and resid 301 through 306 Proline residue: C 305 - end of helix Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 376 through 390 Processing helix chain 'C' and resid 395 through 397 No H-bonds generated for 'chain 'C' and resid 395 through 397' Processing sheet with id= A, first strand: chain 'B' and resid 586 through 592 removed outlier: 6.028A pdb=" N LEU B 556 " --> pdb=" O GLU B 587 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE B 589 " --> pdb=" O LEU B 556 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 558 " --> pdb=" O PHE B 589 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N TYR B 591 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR B 560 " --> pdb=" O TYR B 591 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 635 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL B 561 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 637 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 658 " --> pdb=" O LEU B 636 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ASN B 638 " --> pdb=" O ILE B 658 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ALA B 660 " --> pdb=" O ASN B 638 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 719 through 721 removed outlier: 7.827A pdb=" N VAL B 720 " --> pdb=" O ASN B 773 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 734 through 737 Processing sheet with id= D, first strand: chain 'B' and resid 842 through 845 Processing sheet with id= E, first strand: chain 'A' and resid 586 through 592 removed outlier: 6.028A pdb=" N LEU A 556 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE A 589 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 558 " --> pdb=" O PHE A 589 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N TYR A 591 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR A 560 " --> pdb=" O TYR A 591 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 635 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 561 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 637 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 658 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ASN A 638 " --> pdb=" O ILE A 658 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ALA A 660 " --> pdb=" O ASN A 638 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 719 through 721 removed outlier: 7.827A pdb=" N VAL A 720 " --> pdb=" O ASN A 773 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 734 through 737 Processing sheet with id= H, first strand: chain 'A' and resid 842 through 845 Processing sheet with id= I, first strand: chain 'C' and resid 169 through 171 removed outlier: 8.922A pdb=" N ALA C 170 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR C 135 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 136 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL C 310 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 277 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N THR C 312 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP C 279 " --> pdb=" O THR C 312 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 213 through 215 removed outlier: 6.225A pdb=" N GLU C 246 " --> pdb=" O PHE C 214 " (cutoff:3.500A) No H-bonds generated for sheet with id= J 862 hydrogen bonds defined for protein. 2445 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: 5.94 Time building geometry restraints manager: 8.76 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: 6350 1.34 - 1.46: 4374 1.46 - 1.59: 8671 1.59 - 1.71: 0 1.71 - 1.83: 175 Bond restraints: 19570 Sorted by residual: bond pdb=" O1A UDP A1101 " pdb=" PA UDP A1101 " ideal model delta sigma weight residual 1.482 1.525 -0.043 1.00e-02 1.00e+04 1.84e+01 bond pdb=" O1B UDP A1101 " pdb=" PB UDP A1101 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.00e-02 1.00e+04 1.64e+01 bond pdb=" CB ASN A 500 " pdb=" CG ASN A 500 " ideal model delta sigma weight residual 1.516 1.585 -0.069 2.50e-02 1.60e+03 7.71e+00 bond pdb=" CB ASN B 500 " pdb=" CG ASN B 500 " ideal model delta sigma weight residual 1.516 1.585 -0.069 2.50e-02 1.60e+03 7.64e+00 bond pdb=" CA ILE B 577 " pdb=" CB ILE B 577 " ideal model delta sigma weight residual 1.537 1.550 -0.014 5.00e-03 4.00e+04 7.44e+00 ... (remaining 19565 not shown) Histogram of bond angle deviations from ideal: 97.02 - 104.43: 362 104.43 - 111.84: 9217 111.84 - 119.25: 6767 119.25 - 126.66: 9931 126.66 - 134.07: 302 Bond angle restraints: 26579 Sorted by residual: angle pdb=" O1B UDP A1101 " pdb=" PB UDP A1101 " pdb=" O3A UDP A1101 " ideal model delta sigma weight residual 102.95 112.03 -9.08 1.00e+00 1.00e+00 8.25e+01 angle pdb=" O3A UDP A1101 " pdb=" PB UDP A1101 " pdb=" O3B UDP A1101 " ideal model delta sigma weight residual 112.01 102.99 9.02 1.00e+00 1.00e+00 8.13e+01 angle pdb=" CA LYS A 83 " pdb=" CB LYS A 83 " pdb=" CG LYS A 83 " ideal model delta sigma weight residual 114.10 131.00 -16.90 2.00e+00 2.50e-01 7.14e+01 angle pdb=" CA LYS B 83 " pdb=" CB LYS B 83 " pdb=" CG LYS B 83 " ideal model delta sigma weight residual 114.10 130.98 -16.88 2.00e+00 2.50e-01 7.13e+01 angle pdb=" CB ARG B 113 " pdb=" CG ARG B 113 " pdb=" CD ARG B 113 " ideal model delta sigma weight residual 111.30 127.73 -16.43 2.30e+00 1.89e-01 5.11e+01 ... (remaining 26574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 10475 17.80 - 35.61: 956 35.61 - 53.41: 255 53.41 - 71.21: 139 71.21 - 89.01: 18 Dihedral angle restraints: 11843 sinusoidal: 4750 harmonic: 7093 Sorted by residual: dihedral pdb=" CA GLN A 630 " pdb=" C GLN A 630 " pdb=" N ASP A 631 " pdb=" CA ASP A 631 " ideal model delta harmonic sigma weight residual 180.00 137.19 42.81 0 5.00e+00 4.00e-02 7.33e+01 dihedral pdb=" CA GLN B 630 " pdb=" C GLN B 630 " pdb=" N ASP B 631 " pdb=" CA ASP B 631 " ideal model delta harmonic sigma weight residual 180.00 137.21 42.79 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA ARG A 501 " pdb=" C ARG A 501 " pdb=" N LEU A 502 " pdb=" CA LEU A 502 " ideal model delta harmonic sigma weight residual -180.00 -137.67 -42.33 0 5.00e+00 4.00e-02 7.17e+01 ... (remaining 11840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2355 0.060 - 0.119: 516 0.119 - 0.179: 49 0.179 - 0.239: 1 0.239 - 0.298: 6 Chirality restraints: 2927 Sorted by residual: chirality pdb=" CA ARG A 501 " pdb=" N ARG A 501 " pdb=" C ARG A 501 " pdb=" CB ARG A 501 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA ARG B 501 " pdb=" N ARG B 501 " pdb=" C ARG B 501 " pdb=" CB ARG B 501 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ASN B 500 " pdb=" N ASN B 500 " pdb=" C ASN B 500 " pdb=" CB ASN B 500 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2924 not shown) Planarity restraints: 3469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1102 " -0.091 2.00e-02 2.50e+03 7.44e-02 6.93e+01 pdb=" C7 NAG A1102 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG A1102 " -0.069 2.00e-02 2.50e+03 pdb=" N2 NAG A1102 " 0.117 2.00e-02 2.50e+03 pdb=" O7 NAG A1102 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 861 " 0.024 2.00e-02 2.50e+03 2.65e-02 1.76e+01 pdb=" CG TRP B 861 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP B 861 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP B 861 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 861 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 861 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 861 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 861 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 861 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 861 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 861 " -0.024 2.00e-02 2.50e+03 2.65e-02 1.76e+01 pdb=" CG TRP A 861 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP A 861 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP A 861 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 861 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 861 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 861 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 861 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 861 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 861 " 0.001 2.00e-02 2.50e+03 ... (remaining 3466 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 434 2.59 - 3.17: 19231 3.17 - 3.74: 33627 3.74 - 4.32: 44993 4.32 - 4.90: 67239 Nonbonded interactions: 165524 Sorted by model distance: nonbonded pdb=" N GLU B 344 " pdb=" OE1 GLU B 344 " model vdw 2.011 2.520 nonbonded pdb=" N GLU A 344 " pdb=" OE1 GLU A 344 " model vdw 2.012 2.520 nonbonded pdb=" OE1 GLU C 66 " pdb=" OH TYR C 93 " model vdw 2.074 2.440 nonbonded pdb=" N GLN A 630 " pdb=" OE1 GLN A 630 " model vdw 2.077 2.520 nonbonded pdb=" N GLN B 630 " pdb=" OE1 GLN B 630 " model vdw 2.078 2.520 ... (remaining 165519 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 20 through 1039) selection = chain 'B' } 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: 1.670 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: 0.020 Extract box with map and model: 8.000 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 53.030 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.006 0.069 19570 Z= 0.386 Angle : 1.004 16.897 26579 Z= 0.554 Chirality : 0.049 0.298 2927 Planarity : 0.006 0.074 3469 Dihedral : 16.733 89.013 7267 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 28.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 5.09 % Allowed : 1.42 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.15 (0.17), residues: 2409 helix: 0.06 (0.14), residues: 1299 sheet: -1.21 (0.43), residues: 165 loop : -1.79 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.005 TRP A 861 HIS 0.008 0.002 HIS B 629 PHE 0.015 0.002 PHE C 133 TYR 0.021 0.002 TYR B 398 ARG 0.016 0.001 ARG A 877 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 160 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7787 (mmm) REVERT: B 46 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7180 (pt0) REVERT: B 237 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7770 (mm-30) REVERT: B 320 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8332 (pp) REVERT: B 401 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8670 (ppp) REVERT: B 466 TYR cc_start: 0.8453 (t80) cc_final: 0.7828 (t80) REVERT: B 606 MET cc_start: 0.5429 (OUTLIER) cc_final: 0.5209 (tpp) REVERT: B 877 ARG cc_start: 0.4429 (OUTLIER) cc_final: 0.3309 (ptm-80) REVERT: B 893 MET cc_start: 0.3023 (ppp) cc_final: 0.2813 (ppp) REVERT: B 1036 MET cc_start: -0.0531 (OUTLIER) cc_final: -0.2498 (ttp) REVERT: B 1038 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6682 (mmtt) REVERT: A 45 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7710 (mmt) REVERT: A 756 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8050 (mmm) REVERT: A 861 TRP cc_start: 0.8022 (m-90) cc_final: 0.7475 (m-90) REVERT: C 75 MET cc_start: 0.8907 (tpt) cc_final: 0.8638 (tpp) outliers start: 104 outliers final: 10 residues processed: 208 average time/residue: 0.3805 time to fit residues: 113.8487 Evaluate side-chains 122 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 792 ARG Chi-restraints excluded: chain B residue 877 ARG Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 877 ARG Chi-restraints excluded: chain A residue 1038 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 101 optimal weight: 0.4980 chunk 62 optimal weight: 20.0000 chunk 123 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 HIS B 928 ASN A 144 GLN A 317 ASN A 708 HIS ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 282 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19570 Z= 0.214 Angle : 0.679 14.359 26579 Z= 0.348 Chirality : 0.044 0.192 2927 Planarity : 0.005 0.052 3469 Dihedral : 8.625 100.105 2743 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.47 % Allowed : 10.68 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.64 (0.18), residues: 2409 helix: 0.51 (0.14), residues: 1339 sheet: -1.33 (0.39), residues: 193 loop : -1.60 (0.23), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 48 HIS 0.009 0.001 HIS B 708 PHE 0.027 0.002 PHE B 673 TYR 0.027 0.002 TYR B 851 ARG 0.005 0.001 ARG A 501 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 GLN cc_start: 0.7750 (tp-100) cc_final: 0.7396 (pt0) REVERT: B 466 TYR cc_start: 0.8336 (t80) cc_final: 0.7724 (t80) REVERT: B 851 TYR cc_start: 0.6889 (p90) cc_final: 0.6429 (p90) REVERT: B 877 ARG cc_start: 0.4435 (OUTLIER) cc_final: 0.3414 (ptm160) REVERT: B 893 MET cc_start: 0.3325 (ppp) cc_final: 0.3038 (ppp) REVERT: B 1023 MET cc_start: 0.7004 (mpp) cc_final: 0.6523 (mtt) REVERT: A 736 LEU cc_start: 0.9108 (tp) cc_final: 0.8905 (tp) REVERT: A 792 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8360 (ttp80) REVERT: A 860 MET cc_start: 0.8669 (mtp) cc_final: 0.8428 (ttm) REVERT: A 861 TRP cc_start: 0.7988 (m-90) cc_final: 0.7572 (m-90) REVERT: C 75 MET cc_start: 0.8878 (tpt) cc_final: 0.8637 (tpp) REVERT: C 120 MET cc_start: 0.9066 (mmp) cc_final: 0.8756 (mmp) outliers start: 30 outliers final: 11 residues processed: 138 average time/residue: 0.3189 time to fit residues: 68.5491 Evaluate side-chains 114 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 877 ARG Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 877 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 60 optimal weight: 30.0000 chunk 219 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 HIS ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19570 Z= 0.340 Angle : 0.704 11.072 26579 Z= 0.368 Chirality : 0.044 0.163 2927 Planarity : 0.005 0.053 3469 Dihedral : 7.119 87.920 2696 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 24.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.11 % Allowed : 14.69 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: -0.72 (0.17), residues: 2409 helix: 0.44 (0.14), residues: 1333 sheet: -1.37 (0.42), residues: 163 loop : -1.62 (0.22), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 874 HIS 0.015 0.002 HIS B 708 PHE 0.025 0.002 PHE B 673 TYR 0.017 0.002 TYR B 398 ARG 0.006 0.001 ARG B 792 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 104 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8138 (mmm) cc_final: 0.7752 (mmm) REVERT: B 67 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7967 (pp20) REVERT: B 466 TYR cc_start: 0.8413 (t80) cc_final: 0.7784 (t80) REVERT: B 893 MET cc_start: 0.3297 (ppp) cc_final: 0.3041 (ppp) REVERT: A 67 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7448 (pt0) REVERT: A 736 LEU cc_start: 0.9155 (tp) cc_final: 0.8924 (tp) REVERT: A 756 MET cc_start: 0.7773 (mmm) cc_final: 0.7565 (mmm) REVERT: A 789 MET cc_start: 0.7462 (tpt) cc_final: 0.7112 (tpt) REVERT: A 923 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7437 (m-30) REVERT: C 75 MET cc_start: 0.8963 (tpt) cc_final: 0.8717 (tpp) REVERT: C 120 MET cc_start: 0.9141 (mmp) cc_final: 0.8826 (mmp) outliers start: 43 outliers final: 23 residues processed: 140 average time/residue: 0.3108 time to fit residues: 69.2320 Evaluate side-chains 122 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 1037 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 232 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 HIS A 144 GLN A 509 HIS ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19570 Z= 0.266 Angle : 0.643 11.382 26579 Z= 0.332 Chirality : 0.043 0.194 2927 Planarity : 0.005 0.052 3469 Dihedral : 6.701 88.371 2686 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.20 % Allowed : 17.24 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: -0.47 (0.18), residues: 2409 helix: 0.64 (0.14), residues: 1352 sheet: -1.28 (0.42), residues: 163 loop : -1.54 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 874 HIS 0.005 0.001 HIS B 708 PHE 0.022 0.002 PHE B 673 TYR 0.019 0.002 TYR B 851 ARG 0.005 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 103 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8270 (mmm) cc_final: 0.7980 (mmm) REVERT: B 67 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8087 (pp20) REVERT: B 466 TYR cc_start: 0.8381 (t80) cc_final: 0.7647 (t80) REVERT: B 893 MET cc_start: 0.3228 (ppp) cc_final: 0.2945 (ppp) REVERT: B 1014 MET cc_start: 0.7931 (mpp) cc_final: 0.7727 (mpp) REVERT: B 1023 MET cc_start: 0.4436 (mmt) cc_final: 0.3973 (tpp) REVERT: A 67 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: A 406 LYS cc_start: 0.9499 (OUTLIER) cc_final: 0.9202 (tttt) REVERT: A 453 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7978 (ttp80) REVERT: A 736 LEU cc_start: 0.9203 (tp) cc_final: 0.8901 (tp) REVERT: A 756 MET cc_start: 0.7794 (mmm) cc_final: 0.7588 (mmm) REVERT: A 861 TRP cc_start: 0.7973 (m-10) cc_final: 0.7449 (m-90) REVERT: A 923 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7446 (m-30) REVERT: C 75 MET cc_start: 0.8899 (tpt) cc_final: 0.8639 (tpp) REVERT: C 110 MET cc_start: 0.5896 (tpp) cc_final: 0.5303 (tpp) REVERT: C 120 MET cc_start: 0.9100 (mmp) cc_final: 0.8774 (mmp) outliers start: 45 outliers final: 22 residues processed: 142 average time/residue: 0.2904 time to fit residues: 66.7643 Evaluate side-chains 123 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 1037 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 118 optimal weight: 0.4980 chunk 209 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 HIS ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19570 Z= 0.204 Angle : 0.609 10.474 26579 Z= 0.313 Chirality : 0.042 0.153 2927 Planarity : 0.005 0.059 3469 Dihedral : 6.367 86.423 2684 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.60 % Allowed : 18.61 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: -0.20 (0.18), residues: 2409 helix: 0.86 (0.14), residues: 1356 sheet: -1.16 (0.43), residues: 163 loop : -1.44 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1024 HIS 0.004 0.001 HIS A 568 PHE 0.021 0.001 PHE B 673 TYR 0.016 0.001 TYR B 851 ARG 0.004 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 100 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8401 (mmm) cc_final: 0.8126 (mmm) REVERT: B 67 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8118 (pp20) REVERT: B 466 TYR cc_start: 0.8325 (t80) cc_final: 0.7637 (t80) REVERT: B 893 MET cc_start: 0.3172 (ppp) cc_final: 0.2911 (ppp) REVERT: B 1023 MET cc_start: 0.4531 (mmt) cc_final: 0.4036 (tpp) REVERT: A 67 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7480 (pt0) REVERT: A 406 LYS cc_start: 0.9485 (OUTLIER) cc_final: 0.9135 (tttt) REVERT: A 408 MET cc_start: 0.8438 (pmm) cc_final: 0.8014 (pmm) REVERT: A 453 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8004 (ttp80) REVERT: A 574 MET cc_start: 0.8288 (ppp) cc_final: 0.7931 (ppp) REVERT: A 665 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7838 (p90) REVERT: A 736 LEU cc_start: 0.9205 (tp) cc_final: 0.8921 (tp) REVERT: A 861 TRP cc_start: 0.7929 (m-10) cc_final: 0.7439 (m-90) REVERT: A 923 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7158 (m-30) REVERT: C 75 MET cc_start: 0.8863 (tpt) cc_final: 0.8599 (tpp) REVERT: C 110 MET cc_start: 0.6012 (tpp) cc_final: 0.5430 (tpp) REVERT: C 120 MET cc_start: 0.9111 (mmp) cc_final: 0.8775 (mmp) outliers start: 53 outliers final: 30 residues processed: 148 average time/residue: 0.2842 time to fit residues: 68.9283 Evaluate side-chains 129 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 93 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 1037 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 427 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 233 optimal weight: 20.0000 chunk 193 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN B 264 ASN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 HIS ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19570 Z= 0.237 Angle : 0.628 10.535 26579 Z= 0.323 Chirality : 0.042 0.153 2927 Planarity : 0.005 0.062 3469 Dihedral : 6.291 86.579 2684 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.69 % Allowed : 19.69 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: -0.22 (0.18), residues: 2409 helix: 0.87 (0.14), residues: 1336 sheet: -1.43 (0.41), residues: 169 loop : -1.39 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 874 HIS 0.006 0.001 HIS A 568 PHE 0.028 0.002 PHE A 902 TYR 0.014 0.001 TYR C 225 ARG 0.003 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 98 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8464 (mmm) cc_final: 0.8141 (mmm) REVERT: B 67 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8154 (pp20) REVERT: B 224 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7751 (t80) REVERT: B 466 TYR cc_start: 0.8307 (t80) cc_final: 0.7687 (t80) REVERT: B 486 MET cc_start: 0.3469 (tpp) cc_final: 0.3196 (tpp) REVERT: B 893 MET cc_start: 0.3260 (ppp) cc_final: 0.3021 (ppp) REVERT: B 934 MET cc_start: 0.4574 (ppp) cc_final: 0.4125 (ppp) REVERT: B 1019 LEU cc_start: 0.8294 (tp) cc_final: 0.8026 (tp) REVERT: B 1023 MET cc_start: 0.4415 (mmt) cc_final: 0.3881 (tpp) REVERT: A 67 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7553 (pt0) REVERT: A 406 LYS cc_start: 0.9499 (OUTLIER) cc_final: 0.9158 (tttt) REVERT: A 453 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7972 (ttp80) REVERT: A 545 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.6766 (p90) REVERT: A 574 MET cc_start: 0.8363 (ppp) cc_final: 0.8090 (ppp) REVERT: A 665 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7837 (p90) REVERT: A 736 LEU cc_start: 0.9188 (tp) cc_final: 0.8920 (tp) REVERT: A 860 MET cc_start: 0.8557 (mtm) cc_final: 0.8305 (mtm) REVERT: A 861 TRP cc_start: 0.7969 (m-10) cc_final: 0.7438 (m-90) REVERT: A 923 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: C 75 MET cc_start: 0.8889 (tpt) cc_final: 0.8601 (tpp) REVERT: C 110 MET cc_start: 0.5850 (tpp) cc_final: 0.5172 (tpp) REVERT: C 120 MET cc_start: 0.9134 (mmp) cc_final: 0.8803 (mmp) outliers start: 55 outliers final: 37 residues processed: 148 average time/residue: 0.2843 time to fit residues: 68.4440 Evaluate side-chains 140 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 95 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain B residue 1037 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain D residue 418 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 232 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 ASN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19570 Z= 0.159 Angle : 0.607 10.760 26579 Z= 0.306 Chirality : 0.042 0.326 2927 Planarity : 0.005 0.065 3469 Dihedral : 5.943 81.388 2684 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.20 % Allowed : 20.76 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2409 helix: 1.01 (0.14), residues: 1351 sheet: -1.33 (0.41), residues: 167 loop : -1.43 (0.23), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1024 HIS 0.005 0.001 HIS A 364 PHE 0.023 0.001 PHE A 902 TYR 0.015 0.001 TYR C 286 ARG 0.004 0.000 ARG B 792 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 103 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8441 (mmm) cc_final: 0.8124 (mmm) REVERT: B 67 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8192 (pp20) REVERT: B 224 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7526 (t80) REVERT: B 466 TYR cc_start: 0.8271 (t80) cc_final: 0.7598 (t80) REVERT: B 486 MET cc_start: 0.3411 (tpp) cc_final: 0.3092 (tpp) REVERT: B 851 TYR cc_start: 0.7272 (p90) cc_final: 0.6748 (p90) REVERT: B 893 MET cc_start: 0.3316 (ppp) cc_final: 0.2995 (ppp) REVERT: B 934 MET cc_start: 0.4509 (ppp) cc_final: 0.4007 (ppp) REVERT: B 1023 MET cc_start: 0.4390 (mmt) cc_final: 0.3903 (tpp) REVERT: A 67 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7502 (pt0) REVERT: A 606 MET cc_start: 0.7892 (mmm) cc_final: 0.7643 (mmp) REVERT: A 665 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7768 (p90) REVERT: A 736 LEU cc_start: 0.9153 (tp) cc_final: 0.8891 (tp) REVERT: A 860 MET cc_start: 0.8563 (mtm) cc_final: 0.8324 (mtm) REVERT: C 75 MET cc_start: 0.8807 (tpt) cc_final: 0.8529 (tpp) REVERT: C 110 MET cc_start: 0.5926 (tpp) cc_final: 0.5352 (tpp) REVERT: C 120 MET cc_start: 0.9080 (mmp) cc_final: 0.8750 (mmp) REVERT: C 128 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8034 (pm20) outliers start: 45 outliers final: 28 residues processed: 142 average time/residue: 0.2861 time to fit residues: 66.0845 Evaluate side-chains 128 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 95 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 143 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 chunk 138 optimal weight: 0.9980 chunk 69 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 chunk 211 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 897 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19570 Z= 0.161 Angle : 0.605 13.630 26579 Z= 0.302 Chirality : 0.041 0.191 2927 Planarity : 0.004 0.066 3469 Dihedral : 5.746 77.999 2684 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.11 % Allowed : 20.81 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2409 helix: 1.01 (0.14), residues: 1352 sheet: -1.29 (0.41), residues: 167 loop : -1.44 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1024 HIS 0.005 0.001 HIS B 545 PHE 0.022 0.001 PHE A 902 TYR 0.015 0.001 TYR B1027 ARG 0.004 0.000 ARG B 792 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 99 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8446 (mmm) cc_final: 0.8111 (mmm) REVERT: B 67 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8182 (pp20) REVERT: B 101 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: B 224 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7559 (t80) REVERT: B 466 TYR cc_start: 0.8264 (t80) cc_final: 0.7596 (t80) REVERT: B 851 TYR cc_start: 0.7189 (p90) cc_final: 0.6463 (p90) REVERT: B 893 MET cc_start: 0.3449 (ppp) cc_final: 0.3083 (ppp) REVERT: B 934 MET cc_start: 0.4503 (ppp) cc_final: 0.3977 (ppp) REVERT: B 1023 MET cc_start: 0.4408 (mmt) cc_final: 0.3910 (tpp) REVERT: A 67 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: A 545 HIS cc_start: 0.7152 (OUTLIER) cc_final: 0.6793 (p90) REVERT: A 665 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7779 (p90) REVERT: A 736 LEU cc_start: 0.9140 (tp) cc_final: 0.8860 (tp) REVERT: C 75 MET cc_start: 0.8806 (tpt) cc_final: 0.8552 (tpp) REVERT: C 110 MET cc_start: 0.5941 (tpp) cc_final: 0.5334 (tpp) REVERT: C 120 MET cc_start: 0.9073 (mmp) cc_final: 0.8747 (mmp) REVERT: C 128 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8138 (pm20) outliers start: 43 outliers final: 29 residues processed: 136 average time/residue: 0.2658 time to fit residues: 60.4620 Evaluate side-chains 133 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 97 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 222 optimal weight: 0.6980 chunk 203 optimal weight: 0.0970 chunk 216 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 215 optimal weight: 0.3980 chunk 142 optimal weight: 0.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19570 Z= 0.162 Angle : 0.620 13.422 26579 Z= 0.306 Chirality : 0.042 0.175 2927 Planarity : 0.004 0.066 3469 Dihedral : 5.644 74.662 2684 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.15 % Allowed : 21.11 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: -0.04 (0.18), residues: 2409 helix: 1.05 (0.14), residues: 1350 sheet: -1.28 (0.41), residues: 167 loop : -1.42 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1024 HIS 0.005 0.001 HIS B 701 PHE 0.023 0.001 PHE A 902 TYR 0.012 0.001 TYR C 286 ARG 0.003 0.000 ARG B 792 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 101 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8421 (mmm) cc_final: 0.8077 (mmm) REVERT: B 67 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8167 (pp20) REVERT: B 101 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: B 224 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7548 (t80) REVERT: B 466 TYR cc_start: 0.8267 (t80) cc_final: 0.7561 (t80) REVERT: B 851 TYR cc_start: 0.7181 (p90) cc_final: 0.6439 (p90) REVERT: B 893 MET cc_start: 0.3406 (ppp) cc_final: 0.3011 (ppp) REVERT: B 934 MET cc_start: 0.4581 (ppp) cc_final: 0.4054 (ppp) REVERT: B 1019 LEU cc_start: 0.8289 (tp) cc_final: 0.8052 (tp) REVERT: B 1023 MET cc_start: 0.4420 (mmt) cc_final: 0.3897 (tpp) REVERT: A 67 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: A 545 HIS cc_start: 0.7133 (OUTLIER) cc_final: 0.6756 (p90) REVERT: A 606 MET cc_start: 0.7849 (mmm) cc_final: 0.7511 (mmp) REVERT: A 639 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.7767 (mtm) REVERT: A 665 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7778 (p90) REVERT: A 736 LEU cc_start: 0.9122 (tp) cc_final: 0.8838 (tp) REVERT: C 75 MET cc_start: 0.8785 (tpt) cc_final: 0.8521 (tpp) REVERT: C 110 MET cc_start: 0.5936 (tpp) cc_final: 0.5321 (tpp) REVERT: C 120 MET cc_start: 0.9071 (mmp) cc_final: 0.8756 (mmp) outliers start: 44 outliers final: 33 residues processed: 137 average time/residue: 0.2879 time to fit residues: 65.4344 Evaluate side-chains 134 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 94 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 191 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19570 Z= 0.164 Angle : 0.620 12.383 26579 Z= 0.305 Chirality : 0.042 0.372 2927 Planarity : 0.004 0.064 3469 Dihedral : 5.514 69.459 2684 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.06 % Allowed : 21.11 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: 0.07 (0.18), residues: 2409 helix: 1.13 (0.14), residues: 1338 sheet: -1.19 (0.39), residues: 187 loop : -1.32 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1024 HIS 0.004 0.001 HIS B 258 PHE 0.020 0.001 PHE B 673 TYR 0.015 0.001 TYR B 851 ARG 0.004 0.000 ARG B 792 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 99 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8444 (mmm) cc_final: 0.8088 (mmm) REVERT: B 67 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8169 (pp20) REVERT: B 101 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: B 466 TYR cc_start: 0.8296 (t80) cc_final: 0.7629 (t80) REVERT: B 639 MET cc_start: 0.6798 (mpp) cc_final: 0.6391 (mpp) REVERT: B 851 TYR cc_start: 0.7028 (p90) cc_final: 0.6555 (p90) REVERT: B 893 MET cc_start: 0.3316 (ppp) cc_final: 0.2940 (ppp) REVERT: B 934 MET cc_start: 0.4641 (ppp) cc_final: 0.4121 (ppp) REVERT: B 1019 LEU cc_start: 0.8314 (tp) cc_final: 0.8089 (tp) REVERT: B 1023 MET cc_start: 0.4461 (mmt) cc_final: 0.3939 (tpp) REVERT: A 67 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7610 (pt0) REVERT: A 545 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6809 (p90) REVERT: A 606 MET cc_start: 0.7897 (mmm) cc_final: 0.7548 (mmp) REVERT: A 639 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.7802 (mtm) REVERT: A 665 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7740 (p90) REVERT: A 736 LEU cc_start: 0.9087 (tp) cc_final: 0.8804 (tp) REVERT: C 75 MET cc_start: 0.8774 (tpt) cc_final: 0.8504 (tpp) REVERT: C 90 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8417 (mp) REVERT: C 110 MET cc_start: 0.5933 (tpp) cc_final: 0.5295 (tpp) REVERT: C 120 MET cc_start: 0.9092 (mmp) cc_final: 0.8774 (mmp) outliers start: 42 outliers final: 33 residues processed: 135 average time/residue: 0.2682 time to fit residues: 60.6589 Evaluate side-chains 134 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 94 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 501 ARG Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 80 optimal weight: 40.0000 chunk 196 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 GLN A 196 ASN ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.070584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.050833 restraints weight = 129166.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.050447 restraints weight = 92295.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.050389 restraints weight = 65152.874| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19570 Z= 0.271 Angle : 0.678 12.345 26579 Z= 0.341 Chirality : 0.043 0.253 2927 Planarity : 0.005 0.059 3469 Dihedral : 5.876 73.462 2684 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.25 % Allowed : 21.16 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: -0.09 (0.18), residues: 2409 helix: 1.02 (0.14), residues: 1332 sheet: -1.34 (0.39), residues: 191 loop : -1.38 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 208 HIS 0.010 0.001 HIS A 568 PHE 0.022 0.002 PHE B 673 TYR 0.015 0.002 TYR A 398 ARG 0.007 0.001 ARG B 485 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3241.48 seconds wall clock time: 61 minutes 42.46 seconds (3702.46 seconds total)