Starting phenix.real_space_refine on Fri Jan 19 17:38:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dte_30852/01_2024/7dte_30852.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dte_30852/01_2024/7dte_30852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dte_30852/01_2024/7dte_30852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dte_30852/01_2024/7dte_30852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dte_30852/01_2024/7dte_30852.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dte_30852/01_2024/7dte_30852.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.121 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 62 5.49 5 S 82 5.16 5 C 7451 2.51 5 N 2062 2.21 5 O 2471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A ASP 517": "OD1" <-> "OD2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ASP 523": "OD1" <-> "OD2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ASP 608": "OD1" <-> "OD2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A TYR 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A ASP 740": "OD1" <-> "OD2" Residue "A ASP 760": "OD1" <-> "OD2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ASP 845": "OD1" <-> "OD2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 901": "OD1" <-> "OD2" Residue "A TYR 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 914": "NH1" <-> "NH2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B ASP 101": "OD1" <-> "OD2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ASP 64": "OD1" <-> "OD2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D ASP 161": "OD1" <-> "OD2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ARG 190": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12130 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7473 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 897} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1401 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 554 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1387 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 52 Chain: "F" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 693 Classifications: {'RNA': 33} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 13, 'rna3p_pyr': 19} Link IDs: {'rna2p': 1, 'rna3p': 31} Chain: "G" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 620 Classifications: {'RNA': 29} Modifications used: {'rna3p_pur': 16, 'rna3p_pyr': 13} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2459 SG CYS A 301 61.099 83.925 53.740 1.00 20.61 S ATOM 2500 SG CYS A 306 60.078 87.463 51.962 1.00 18.78 S ATOM 2532 SG CYS A 310 59.093 83.980 50.572 1.00 19.77 S ATOM 3940 SG CYS A 487 62.495 86.092 74.086 1.00 17.16 S ATOM 5193 SG CYS A 645 62.385 89.584 73.101 1.00 24.14 S ATOM 5199 SG CYS A 646 63.789 86.453 70.853 1.00 21.71 S Time building chain proxies: 6.56, per 1000 atoms: 0.54 Number of scatterers: 12130 At special positions: 0 Unit cell: (91.84, 131.2, 160.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 82 16.00 P 62 15.00 O 2471 8.00 N 2062 7.00 C 7451 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.29 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 6 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2644 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 13 sheets defined 54.7% alpha, 12.9% beta 27 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 4.56 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.861A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.886A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.500A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 242 through 248 removed outlier: 4.138A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 removed outlier: 4.484A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.541A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.642A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.870A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.715A pdb=" N ASP A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 385 removed outlier: 3.626A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.557A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.216A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.735A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.917A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.807A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.862A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.633A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.501A pdb=" N THR A 850 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 867 removed outlier: 3.910A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.691A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 915 removed outlier: 3.998A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 915 " --> pdb=" O THR A 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 915' Processing helix chain 'A' and resid 918 through 924 Processing helix chain 'B' and resid 9 through 27 removed outlier: 3.863A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 95 removed outlier: 3.945A pdb=" N LYS B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.664A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.856A pdb=" N TYR B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.696A pdb=" N LEU B 180 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 61 removed outlier: 4.076A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'D' and resid 10 through 27 removed outlier: 4.066A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 82 removed outlier: 3.556A pdb=" N LEU D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.835A pdb=" N THR D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.604A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.654A pdb=" N ASN D 179 " --> pdb=" O ASN D 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.144A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.144A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 114 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.842A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 339 through 343 Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 348 Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 390 removed outlier: 6.419A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 390 removed outlier: 6.419A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.320A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AB2, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB3, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AB4, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.754A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 5.16 Time building geometry restraints manager: 5.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3515 1.33 - 1.45: 2487 1.45 - 1.57: 6252 1.57 - 1.69: 122 1.69 - 1.81: 128 Bond restraints: 12504 Sorted by residual: bond pdb=" C SER B 177 " pdb=" N PRO B 178 " ideal model delta sigma weight residual 1.334 1.347 -0.014 8.40e-03 1.42e+04 2.63e+00 bond pdb=" CB VAL A 605 " pdb=" CG2 VAL A 605 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.06e+00 bond pdb=" CG LEU A 731 " pdb=" CD2 LEU A 731 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" O5' A F 19 " pdb=" C5' A F 19 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.86e+00 bond pdb=" O5' G F -1 " pdb=" C5' G F -1 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.73e+00 ... (remaining 12499 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.53: 584 106.53 - 113.42: 6953 113.42 - 120.31: 4787 120.31 - 127.19: 4716 127.19 - 134.08: 209 Bond angle restraints: 17249 Sorted by residual: angle pdb=" N SER D 85 " pdb=" CA SER D 85 " pdb=" C SER D 85 " ideal model delta sigma weight residual 114.56 109.02 5.54 1.27e+00 6.20e-01 1.91e+01 angle pdb=" N VAL A 320 " pdb=" CA VAL A 320 " pdb=" C VAL A 320 " ideal model delta sigma weight residual 112.96 108.78 4.18 1.00e+00 1.00e+00 1.75e+01 angle pdb=" N TRP D 182 " pdb=" CA TRP D 182 " pdb=" C TRP D 182 " ideal model delta sigma weight residual 109.81 118.17 -8.36 2.21e+00 2.05e-01 1.43e+01 angle pdb=" N THR A 120 " pdb=" CA THR A 120 " pdb=" C THR A 120 " ideal model delta sigma weight residual 110.35 114.62 -4.27 1.36e+00 5.41e-01 9.86e+00 angle pdb=" O3' C F 18 " pdb=" C3' C F 18 " pdb=" C2' C F 18 " ideal model delta sigma weight residual 109.50 113.73 -4.23 1.50e+00 4.44e-01 7.96e+00 ... (remaining 17244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 7282 34.69 - 69.37: 229 69.37 - 104.06: 31 104.06 - 138.74: 0 138.74 - 173.43: 1 Dihedral angle restraints: 7543 sinusoidal: 3463 harmonic: 4080 Sorted by residual: dihedral pdb=" C4' C F 18 " pdb=" C3' C F 18 " pdb=" C2' C F 18 " pdb=" C1' C F 18 " ideal model delta sinusoidal sigma weight residual -35.00 36.58 -71.58 1 8.00e+00 1.56e-02 1.03e+02 dihedral pdb=" C5' C F 18 " pdb=" C4' C F 18 " pdb=" C3' C F 18 " pdb=" O3' C F 18 " ideal model delta sinusoidal sigma weight residual 147.00 78.93 68.07 1 8.00e+00 1.56e-02 9.40e+01 dihedral pdb=" O4' C F 18 " pdb=" C4' C F 18 " pdb=" C3' C F 18 " pdb=" C2' C F 18 " ideal model delta sinusoidal sigma weight residual 24.00 -37.31 61.31 1 8.00e+00 1.56e-02 7.80e+01 ... (remaining 7540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1647 0.055 - 0.110: 321 0.110 - 0.164: 33 0.164 - 0.219: 2 0.219 - 0.274: 2 Chirality restraints: 2005 Sorted by residual: chirality pdb=" C3' C F 18 " pdb=" C4' C F 18 " pdb=" O3' C F 18 " pdb=" C2' C F 18 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C2' C F 18 " pdb=" C3' C F 18 " pdb=" O2' C F 18 " pdb=" C1' C F 18 " both_signs ideal model delta sigma weight residual False -2.52 -2.74 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C3' G F -1 " pdb=" C4' G F -1 " pdb=" O3' G F -1 " pdb=" C2' G F -1 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2002 not shown) Planarity restraints: 1982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 118 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C ARG A 118 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG A 118 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 119 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 177 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.25e+00 pdb=" N PRO B 178 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 182 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.02e+00 pdb=" N PRO D 183 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " 0.028 5.00e-02 4.00e+02 ... (remaining 1979 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 86 2.57 - 3.15: 9712 3.15 - 3.73: 18923 3.73 - 4.32: 27476 4.32 - 4.90: 45052 Nonbonded interactions: 101249 Sorted by model distance: nonbonded pdb=" O2 C F 18 " pdb=" N7 A F 19 " model vdw 1.985 3.120 nonbonded pdb=" O4 U F -2 " pdb=" O6 G F -1 " model vdw 2.193 3.040 nonbonded pdb=" ND2 ASN B 43 " pdb=" O4' A F 17 " model vdw 2.204 2.520 nonbonded pdb=" ND2 ASN B 43 " pdb=" O5' A F 17 " model vdw 2.213 2.520 nonbonded pdb=" OE2 GLU A 254 " pdb=" OH TYR A 286 " model vdw 2.222 2.440 ... (remaining 101244 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 'B' and (resid 6 through 18 or (resid 19 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 191)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 7.800 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 40.430 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 0.049 12504 Z= 0.421 Angle : 0.606 9.592 17249 Z= 0.342 Chirality : 0.043 0.274 2005 Planarity : 0.004 0.052 1982 Dihedral : 16.337 173.428 4899 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.42 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -2.94 (0.19), residues: 1366 helix: -1.06 (0.18), residues: 687 sheet: -3.08 (0.34), residues: 131 loop : -2.73 (0.22), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.021 0.002 PHE A 920 TYR 0.015 0.002 TYR A 788 ARG 0.004 0.000 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.190 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8156 (tpt90) cc_final: 0.7949 (tpt170) REVERT: A 54 CYS cc_start: 0.8106 (t) cc_final: 0.7756 (t) REVERT: A 110 MET cc_start: 0.6997 (mmp) cc_final: 0.6718 (mmp) REVERT: A 223 ILE cc_start: 0.8847 (mm) cc_final: 0.8604 (mp) REVERT: A 450 ILE cc_start: 0.8967 (tp) cc_final: 0.8730 (tp) REVERT: A 519 MET cc_start: 0.8919 (mtp) cc_final: 0.8706 (mtt) REVERT: A 555 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7722 (mtm180) REVERT: A 825 ASP cc_start: 0.7003 (m-30) cc_final: 0.6719 (m-30) REVERT: B 67 MET cc_start: 0.6362 (ttt) cc_final: 0.6123 (tmm) REVERT: B 70 MET cc_start: 0.6791 (mmp) cc_final: 0.6423 (tmm) REVERT: B 104 ASN cc_start: 0.8050 (t0) cc_final: 0.7829 (t0) REVERT: B 139 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7705 (ttpt) REVERT: B 165 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7682 (tttm) REVERT: D 104 ASN cc_start: 0.8200 (m110) cc_final: 0.7963 (m110) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 1.2956 time to fit residues: 263.5503 Evaluate side-chains 139 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 81 GLN A 99 HIS A 356 ASN A 534 ASN A 613 HIS A 713 ASN A 725 HIS A 790 ASN B 108 ASN B 140 ASN B 168 GLN C 31 GLN C 36 HIS D 100 ASN D 108 ASN D 168 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12504 Z= 0.197 Angle : 0.534 8.552 17249 Z= 0.284 Chirality : 0.039 0.356 2005 Planarity : 0.004 0.041 1982 Dihedral : 14.273 167.223 2394 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.22 % Allowed : 11.25 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.22), residues: 1366 helix: 0.27 (0.20), residues: 693 sheet: -2.25 (0.37), residues: 125 loop : -2.18 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 509 HIS 0.007 0.001 HIS C 36 PHE 0.014 0.001 PHE A 694 TYR 0.013 0.001 TYR A 831 ARG 0.003 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7818 (t) cc_final: 0.7522 (t) REVERT: A 223 ILE cc_start: 0.8952 (mm) cc_final: 0.8749 (mt) REVERT: A 277 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7478 (mm-30) REVERT: A 394 THR cc_start: 0.9087 (p) cc_final: 0.8884 (p) REVERT: A 450 ILE cc_start: 0.8882 (tp) cc_final: 0.8682 (tp) REVERT: A 668 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7939 (ttp) REVERT: A 825 ASP cc_start: 0.6952 (m-30) cc_final: 0.6696 (m-30) REVERT: B 62 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.6233 (tmm) REVERT: B 67 MET cc_start: 0.6367 (ttt) cc_final: 0.6128 (tmm) REVERT: B 70 MET cc_start: 0.6367 (mmp) cc_final: 0.6119 (tmm) REVERT: B 104 ASN cc_start: 0.7849 (t0) cc_final: 0.7561 (t0) REVERT: B 105 ASN cc_start: 0.7978 (t0) cc_final: 0.7431 (m-40) REVERT: B 139 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7728 (ttpt) REVERT: B 165 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7638 (tttm) REVERT: D 104 ASN cc_start: 0.8159 (m110) cc_final: 0.7920 (m110) outliers start: 26 outliers final: 14 residues processed: 166 average time/residue: 1.1147 time to fit residues: 203.4573 Evaluate side-chains 160 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.0010 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 137 optimal weight: 30.0000 chunk 113 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 43 optimal weight: 0.0020 chunk 102 optimal weight: 3.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 492 GLN A 909 ASN D 100 ASN D 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12504 Z= 0.139 Angle : 0.473 7.387 17249 Z= 0.250 Chirality : 0.037 0.247 2005 Planarity : 0.003 0.035 1982 Dihedral : 13.919 144.132 2394 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.96 % Allowed : 13.81 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.56 (0.23), residues: 1366 helix: 0.98 (0.20), residues: 705 sheet: -1.56 (0.39), residues: 137 loop : -1.92 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 182 HIS 0.005 0.001 HIS A 309 PHE 0.012 0.001 PHE A 753 TYR 0.013 0.001 TYR A 788 ARG 0.001 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 163 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.8955 (mm) cc_final: 0.8736 (mt) REVERT: A 277 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7439 (mm-30) REVERT: A 825 ASP cc_start: 0.6911 (m-30) cc_final: 0.6637 (m-30) REVERT: B 105 ASN cc_start: 0.7865 (t0) cc_final: 0.7440 (m-40) REVERT: B 165 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7604 (tttm) REVERT: D 68 THR cc_start: 0.7938 (t) cc_final: 0.7657 (p) outliers start: 23 outliers final: 7 residues processed: 176 average time/residue: 1.0908 time to fit residues: 210.6134 Evaluate side-chains 145 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 112 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.4980 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 0.0770 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN C 19 GLN D 100 ASN D 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12504 Z= 0.217 Angle : 0.508 7.887 17249 Z= 0.266 Chirality : 0.039 0.165 2005 Planarity : 0.003 0.032 1982 Dihedral : 13.902 132.134 2394 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.90 % Allowed : 15.35 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.30 (0.23), residues: 1366 helix: 1.10 (0.20), residues: 706 sheet: -1.25 (0.41), residues: 138 loop : -1.73 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 290 HIS 0.007 0.001 HIS A 309 PHE 0.035 0.002 PHE A 920 TYR 0.016 0.001 TYR A 788 ARG 0.003 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 141 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: A 223 ILE cc_start: 0.8974 (mm) cc_final: 0.8753 (mt) REVERT: A 277 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: A 411 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8553 (mtmm) REVERT: A 825 ASP cc_start: 0.6921 (m-30) cc_final: 0.6633 (m-30) REVERT: B 105 ASN cc_start: 0.7906 (t0) cc_final: 0.7462 (m-40) REVERT: B 165 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7631 (tttm) REVERT: D 68 THR cc_start: 0.7990 (t) cc_final: 0.7680 (p) outliers start: 34 outliers final: 15 residues processed: 161 average time/residue: 1.1530 time to fit residues: 203.0111 Evaluate side-chains 154 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.0770 chunk 115 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 492 GLN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN C 19 GLN D 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12504 Z= 0.159 Angle : 0.472 7.489 17249 Z= 0.248 Chirality : 0.037 0.162 2005 Planarity : 0.003 0.029 1982 Dihedral : 13.802 105.339 2394 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.81 % Allowed : 15.77 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.03 (0.23), residues: 1366 helix: 1.32 (0.20), residues: 706 sheet: -1.04 (0.42), residues: 138 loop : -1.63 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 598 HIS 0.007 0.001 HIS A 309 PHE 0.029 0.001 PHE A 920 TYR 0.014 0.001 TYR A 788 ARG 0.003 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7441 (pm20) REVERT: A 223 ILE cc_start: 0.8968 (mm) cc_final: 0.8734 (mt) REVERT: A 277 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: A 411 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8535 (mtmm) REVERT: A 825 ASP cc_start: 0.6931 (m-30) cc_final: 0.6613 (m-30) REVERT: A 855 MET cc_start: 0.6918 (mmm) cc_final: 0.6717 (mmm) REVERT: A 899 MET cc_start: 0.8204 (tpp) cc_final: 0.7917 (mmt) REVERT: B 105 ASN cc_start: 0.7845 (t0) cc_final: 0.7427 (m-40) REVERT: B 165 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7648 (tttm) REVERT: D 68 THR cc_start: 0.7964 (t) cc_final: 0.7655 (p) outliers start: 33 outliers final: 17 residues processed: 161 average time/residue: 1.1528 time to fit residues: 203.4882 Evaluate side-chains 152 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 112 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 75 HIS A 138 ASN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN D 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12504 Z= 0.325 Angle : 0.552 8.405 17249 Z= 0.288 Chirality : 0.041 0.157 2005 Planarity : 0.004 0.034 1982 Dihedral : 13.839 82.405 2394 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.41 % Allowed : 15.77 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.17 (0.23), residues: 1366 helix: 1.11 (0.20), residues: 715 sheet: -0.97 (0.42), residues: 138 loop : -1.62 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.007 0.001 HIS A 309 PHE 0.034 0.002 PHE A 920 TYR 0.017 0.002 TYR A 788 ARG 0.003 0.000 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 135 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.8961 (mm) cc_final: 0.8740 (mt) REVERT: A 277 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: A 315 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8517 (m) REVERT: A 411 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8556 (mtmm) REVERT: A 726 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7569 (mtp180) REVERT: A 895 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8301 (tp) REVERT: A 899 MET cc_start: 0.8318 (tpp) cc_final: 0.7963 (mmt) REVERT: A 902 MET cc_start: 0.7533 (mtp) cc_final: 0.7259 (mtt) REVERT: B 105 ASN cc_start: 0.7943 (t0) cc_final: 0.7498 (m-40) REVERT: B 165 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7653 (tttm) REVERT: D 68 THR cc_start: 0.7978 (t) cc_final: 0.7682 (p) outliers start: 40 outliers final: 20 residues processed: 161 average time/residue: 1.1045 time to fit residues: 195.0935 Evaluate side-chains 157 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12504 Z= 0.191 Angle : 0.491 9.957 17249 Z= 0.255 Chirality : 0.038 0.164 2005 Planarity : 0.003 0.031 1982 Dihedral : 13.766 73.683 2394 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.30 % Allowed : 17.39 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.23), residues: 1366 helix: 1.36 (0.20), residues: 706 sheet: -0.90 (0.42), residues: 138 loop : -1.53 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 598 HIS 0.006 0.001 HIS A 309 PHE 0.028 0.001 PHE A 920 TYR 0.014 0.001 TYR A 788 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.8931 (mm) cc_final: 0.8699 (mt) REVERT: A 277 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7459 (mm-30) REVERT: A 411 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8545 (mtmm) REVERT: A 899 MET cc_start: 0.8312 (tpp) cc_final: 0.7998 (mmt) REVERT: A 902 MET cc_start: 0.7536 (mtp) cc_final: 0.7220 (mtt) REVERT: B 105 ASN cc_start: 0.7914 (t0) cc_final: 0.7451 (m110) REVERT: B 165 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7652 (tttm) REVERT: D 173 SER cc_start: 0.7070 (t) cc_final: 0.6703 (m) outliers start: 27 outliers final: 17 residues processed: 152 average time/residue: 1.1601 time to fit residues: 193.0220 Evaluate side-chains 151 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 0.0070 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.0050 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 0.0010 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 492 GLN A 790 ASN D 73 GLN D 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12504 Z= 0.122 Angle : 0.456 11.196 17249 Z= 0.235 Chirality : 0.036 0.159 2005 Planarity : 0.003 0.027 1982 Dihedral : 13.608 73.586 2394 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.88 % Allowed : 18.16 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.43 (0.23), residues: 1366 helix: 1.70 (0.20), residues: 700 sheet: -0.76 (0.42), residues: 137 loop : -1.40 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.005 0.001 HIS A 309 PHE 0.023 0.001 PHE A 920 TYR 0.012 0.001 TYR A 788 ARG 0.003 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.8963 (mm) cc_final: 0.8712 (mt) REVERT: A 411 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8560 (mtmm) REVERT: A 695 ASN cc_start: 0.8390 (t0) cc_final: 0.8152 (t0) REVERT: A 825 ASP cc_start: 0.6897 (m-30) cc_final: 0.6579 (m-30) REVERT: A 902 MET cc_start: 0.7441 (mtp) cc_final: 0.7172 (mtt) REVERT: A 906 MET cc_start: 0.6869 (mmm) cc_final: 0.5928 (tpp) REVERT: B 105 ASN cc_start: 0.7797 (t0) cc_final: 0.7400 (m110) REVERT: B 165 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7665 (tttm) REVERT: D 68 THR cc_start: 0.7949 (t) cc_final: 0.7622 (p) REVERT: D 173 SER cc_start: 0.7044 (t) cc_final: 0.6651 (m) outliers start: 22 outliers final: 13 residues processed: 150 average time/residue: 1.2136 time to fit residues: 199.7976 Evaluate side-chains 148 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 111 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 132 optimal weight: 0.0870 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 492 GLN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12504 Z= 0.226 Angle : 0.504 9.833 17249 Z= 0.260 Chirality : 0.039 0.153 2005 Planarity : 0.003 0.030 1982 Dihedral : 13.559 73.700 2394 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.96 % Allowed : 19.18 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.33 (0.23), residues: 1366 helix: 1.56 (0.20), residues: 700 sheet: -0.78 (0.43), residues: 138 loop : -1.36 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 290 HIS 0.007 0.001 HIS A 309 PHE 0.029 0.002 PHE A 920 TYR 0.016 0.001 TYR A 788 ARG 0.003 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.8953 (mm) cc_final: 0.8712 (mt) REVERT: A 411 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8529 (mtmm) REVERT: A 726 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7404 (mtp180) REVERT: A 902 MET cc_start: 0.7428 (mtp) cc_final: 0.7102 (mtt) REVERT: B 105 ASN cc_start: 0.7933 (t0) cc_final: 0.7513 (m110) REVERT: B 165 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7668 (tttm) REVERT: B 174 MET cc_start: 0.7230 (tpt) cc_final: 0.6998 (tpp) outliers start: 23 outliers final: 13 residues processed: 148 average time/residue: 1.2254 time to fit residues: 197.7328 Evaluate side-chains 146 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain D residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.0370 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 139 optimal weight: 20.0000 chunk 128 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 138 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12504 Z= 0.287 Angle : 0.541 11.472 17249 Z= 0.280 Chirality : 0.040 0.160 2005 Planarity : 0.003 0.032 1982 Dihedral : 13.518 73.786 2394 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.13 % Allowed : 18.76 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.23), residues: 1366 helix: 1.41 (0.20), residues: 702 sheet: -0.81 (0.42), residues: 138 loop : -1.37 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.008 0.001 HIS A 309 PHE 0.030 0.002 PHE A 920 TYR 0.018 0.002 TYR A 788 ARG 0.004 0.000 ARG D 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.8923 (mm) cc_final: 0.8690 (mt) REVERT: A 411 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8557 (mtmm) REVERT: A 726 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7477 (mtp180) REVERT: A 902 MET cc_start: 0.7496 (mtp) cc_final: 0.7183 (mtt) REVERT: A 906 MET cc_start: 0.7065 (mmm) cc_final: 0.6049 (tpp) REVERT: B 105 ASN cc_start: 0.7952 (t0) cc_final: 0.7501 (m110) REVERT: B 165 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7662 (tttm) REVERT: B 174 MET cc_start: 0.7284 (tpt) cc_final: 0.7072 (tpp) REVERT: D 68 THR cc_start: 0.7968 (t) cc_final: 0.7666 (p) outliers start: 25 outliers final: 16 residues processed: 151 average time/residue: 1.1572 time to fit residues: 191.1702 Evaluate side-chains 151 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 790 ASN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.156056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.113028 restraints weight = 12037.128| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.26 r_work: 0.2888 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12504 Z= 0.153 Angle : 0.479 10.952 17249 Z= 0.248 Chirality : 0.037 0.162 2005 Planarity : 0.003 0.029 1982 Dihedral : 13.417 73.633 2394 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.53 % Allowed : 19.27 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.45 (0.23), residues: 1366 helix: 1.64 (0.20), residues: 697 sheet: -0.74 (0.43), residues: 138 loop : -1.24 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 182 HIS 0.007 0.001 HIS A 309 PHE 0.024 0.001 PHE A 920 TYR 0.014 0.001 TYR A 788 ARG 0.004 0.000 ARG D 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4087.77 seconds wall clock time: 73 minutes 53.05 seconds (4433.05 seconds total)