Starting phenix.real_space_refine on Fri Nov 17 12:17:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeh_33773/11_2023/7yeh_33773_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeh_33773/11_2023/7yeh_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_33773/11_2023/7yeh_33773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeh_33773/11_2023/7yeh_33773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeh_33773/11_2023/7yeh_33773_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yeh_33773/11_2023/7yeh_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 10.02, per 1000 atoms: 0.52 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 3.3 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: 4.77 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: 6.14 Time building geometry restraints manager: 8.67 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 - 17.44: 10408 17.44 - 34.88: 973 34.88 - 52.32: 246 52.32 - 69.76: 139 69.76 - 87.19: 21 Dihedral angle restraints: 11787 sinusoidal: 4694 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 11784 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.840 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 51.530 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.940 ------------------------------------------------------------------------------- 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 : 16.653 87.194 7211 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 *********************** 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 : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 10 residues processed: 208 average time/residue: 0.4043 time to fit residues: 122.2955 Evaluate side-chains 110 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 2.203 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3410 time to fit residues: 7.9742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 20.0000 chunk 182 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 123 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 188 optimal weight: 0.0270 chunk 73 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 overall best weight: 2.3844 ------------------------------------------------------------------------------- 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 ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19570 Z= 0.234 Angle : 0.691 13.788 26579 Z= 0.356 Chirality : 0.044 0.193 2927 Planarity : 0.005 0.052 3469 Dihedral : 6.199 35.182 2627 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.93 % Allowed : 10.38 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.73 (0.18), residues: 2409 helix: 0.44 (0.14), residues: 1329 sheet: -1.29 (0.41), residues: 183 loop : -1.65 (0.23), residues: 897 *********************** 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 137 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 132 average time/residue: 0.3227 time to fit residues: 66.9614 Evaluate side-chains 108 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 2.027 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2323 time to fit residues: 6.2058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 60 optimal weight: 30.0000 chunk 219 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 HIS ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 HIS ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19570 Z= 0.248 Angle : 0.646 11.539 26579 Z= 0.333 Chirality : 0.043 0.174 2927 Planarity : 0.005 0.054 3469 Dihedral : 5.741 25.582 2627 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.37 % Allowed : 14.10 % Favored : 84.52 % 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: -0.55 (0.18), residues: 2409 helix: 0.58 (0.14), residues: 1344 sheet: -1.34 (0.43), residues: 163 loop : -1.58 (0.22), residues: 902 *********************** 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 136 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 129 average time/residue: 0.3046 time to fit residues: 63.5344 Evaluate side-chains 104 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 2.243 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1921 time to fit residues: 6.1961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 8.9990 chunk 164 optimal weight: 0.0030 chunk 113 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 chunk 62 optimal weight: 50.0000 overall best weight: 3.5996 ------------------------------------------------------------------------------- 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 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN A 509 HIS ** 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** ** A1000 GLN ** 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 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19570 Z= 0.260 Angle : 0.651 11.205 26579 Z= 0.333 Chirality : 0.043 0.176 2927 Planarity : 0.005 0.056 3469 Dihedral : 5.553 24.876 2627 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.52 % Allowed : 17.53 % Favored : 80.95 % 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: -0.37 (0.18), residues: 2409 helix: 0.72 (0.14), residues: 1340 sheet: -1.27 (0.43), residues: 163 loop : -1.46 (0.22), residues: 906 *********************** 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 135 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 10 residues processed: 132 average time/residue: 0.2954 time to fit residues: 64.4292 Evaluate side-chains 105 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1925 time to fit residues: 6.2841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** 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** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 897 GLN B 911 HIS ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1031 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 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19570 Z= 0.384 Angle : 0.731 10.029 26579 Z= 0.380 Chirality : 0.045 0.185 2927 Planarity : 0.005 0.053 3469 Dihedral : 5.807 27.149 2627 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 27.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.11 % Allowed : 19.59 % Favored : 78.31 % 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: -0.87 (0.17), residues: 2409 helix: 0.32 (0.14), residues: 1339 sheet: -1.25 (0.43), residues: 156 loop : -1.75 (0.21), residues: 914 *********************** 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 137 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 94 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 23 residues processed: 130 average time/residue: 0.2763 time to fit residues: 60.2102 Evaluate side-chains 114 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 2.190 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1787 time to fit residues: 10.7166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 233 optimal weight: 30.0000 chunk 193 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.0370 overall best weight: 0.9260 ------------------------------------------------------------------------------- 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 317 ASN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN B 581 HIS ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 GLN ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19570 Z= 0.172 Angle : 0.629 11.809 26579 Z= 0.315 Chirality : 0.042 0.192 2927 Planarity : 0.005 0.061 3469 Dihedral : 5.318 25.592 2627 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.52 % Allowed : 20.03 % Favored : 78.45 % 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: -0.29 (0.18), residues: 2409 helix: 0.83 (0.14), residues: 1340 sheet: -1.33 (0.41), residues: 167 loop : -1.48 (0.22), residues: 902 *********************** 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 132 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 10 residues processed: 128 average time/residue: 0.2834 time to fit residues: 60.4612 Evaluate side-chains 106 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 2.154 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1876 time to fit residues: 6.3415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 196 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 232 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 ASN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** 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: 0.8018 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19570 Z= 0.171 Angle : 0.626 11.599 26579 Z= 0.310 Chirality : 0.042 0.380 2927 Planarity : 0.004 0.065 3469 Dihedral : 5.055 23.912 2627 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.32 % Allowed : 20.71 % Favored : 77.96 % 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: -0.21 (0.18), residues: 2409 helix: 0.88 (0.14), residues: 1353 sheet: -1.36 (0.41), residues: 167 loop : -1.45 (0.22), residues: 889 *********************** 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 130 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 2.311 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 8 residues processed: 127 average time/residue: 0.2949 time to fit residues: 61.4553 Evaluate side-chains 102 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 2.392 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2946 time to fit residues: 6.7694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 30.0000 chunk 138 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 182 optimal weight: 0.3980 chunk 211 optimal weight: 8.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19570 Z= 0.185 Angle : 0.647 13.789 26579 Z= 0.318 Chirality : 0.042 0.292 2927 Planarity : 0.004 0.065 3469 Dihedral : 5.020 23.943 2627 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.64 % Allowed : 21.11 % Favored : 78.26 % 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: -0.18 (0.18), residues: 2409 helix: 0.90 (0.14), residues: 1352 sheet: -1.32 (0.41), residues: 167 loop : -1.43 (0.22), residues: 890 *********************** 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 109 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 2.120 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 106 average time/residue: 0.2852 time to fit residues: 49.6884 Evaluate side-chains 97 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 2.126 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2193 time to fit residues: 4.9257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 222 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 216 optimal weight: 0.0980 chunk 130 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 215 optimal weight: 0.1980 chunk 142 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19570 Z= 0.212 Angle : 0.653 11.889 26579 Z= 0.323 Chirality : 0.043 0.312 2927 Planarity : 0.004 0.063 3469 Dihedral : 5.017 24.840 2627 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.24 % Allowed : 21.94 % Favored : 77.82 % 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: -0.13 (0.18), residues: 2409 helix: 0.93 (0.14), residues: 1346 sheet: -1.31 (0.41), residues: 167 loop : -1.36 (0.22), residues: 896 *********************** 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 101 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 2.206 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 101 average time/residue: 0.2999 time to fit residues: 50.5913 Evaluate side-chains 92 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 2.356 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1801 time to fit residues: 3.3830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 7.9990 chunk 139 optimal weight: 0.0050 chunk 108 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 overall best weight: 2.0000 ------------------------------------------------------------------------------- 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 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 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1000 GLN ** 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: 0.8046 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 : 0.003 0.046 19570 Z= 0.191 Angle : 0.653 12.129 26579 Z= 0.320 Chirality : 0.042 0.279 2927 Planarity : 0.004 0.065 3469 Dihedral : 4.974 25.347 2627 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.29 % Allowed : 22.14 % Favored : 77.57 % 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: -0.11 (0.18), residues: 2409 helix: 0.96 (0.14), residues: 1342 sheet: -1.13 (0.40), residues: 187 loop : -1.41 (0.22), residues: 880 ********************** 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 103 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 2.319 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 101 average time/residue: 0.2882 time to fit residues: 48.3303 Evaluate side-chains 98 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 2.004 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1951 time to fit residues: 3.8310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 196 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.071741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.051664 restraints weight = 131366.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.051797 restraints weight = 79238.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.051761 restraints weight = 56969.515| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19570 Z= 0.187 Angle : 0.644 12.237 26579 Z= 0.315 Chirality : 0.042 0.258 2927 Planarity : 0.004 0.064 3469 Dihedral : 4.902 25.243 2627 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.05 % Allowed : 22.33 % 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: -0.05 (0.18), residues: 2409 helix: 1.01 (0.14), residues: 1342 sheet: -1.10 (0.40), residues: 187 loop : -1.39 (0.22), residues: 880 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3084.06 seconds wall clock time: 60 minutes 47.94 seconds (3647.94 seconds total)