Starting phenix.real_space_refine on Sat Mar 16 18:17:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzh_24760/03_2024/7rzh_24760.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzh_24760/03_2024/7rzh_24760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzh_24760/03_2024/7rzh_24760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzh_24760/03_2024/7rzh_24760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzh_24760/03_2024/7rzh_24760.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzh_24760/03_2024/7rzh_24760.pdb" } resolution = 3.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 9866 2.51 5 N 2559 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 577": "OE1" <-> "OE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 636": "OD1" <-> "OD2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A ASP 747": "OD1" <-> "OD2" Residue "A TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 862": "NH1" <-> "NH2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A PHE 882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 892": "NH1" <-> "NH2" Residue "A ASP 947": "OD1" <-> "OD2" Residue "A PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 426": "OD1" <-> "OD2" Residue "B GLU 428": "OE1" <-> "OE2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 653": "OE1" <-> "OE2" Residue "B GLU 692": "OE1" <-> "OE2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B GLU 746": "OE1" <-> "OE2" Residue "B ARG 782": "NH1" <-> "NH2" Residue "B GLU 804": "OE1" <-> "OE2" Residue "B TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 853": "OE1" <-> "OE2" Residue "B TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 862": "NH1" <-> "NH2" Residue "B GLU 871": "OE1" <-> "OE2" Residue "B ARG 892": "NH1" <-> "NH2" Residue "B TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 921": "OD1" <-> "OD2" Residue "B PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15300 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7637 Classifications: {'peptide': 932} Link IDs: {'PTRANS': 49, 'TRANS': 882} Chain breaks: 1 Chain: "B" Number of atoms: 7663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 935, 7663 Classifications: {'peptide': 935} Link IDs: {'PTRANS': 48, 'TRANS': 886} Chain breaks: 1 Time building chain proxies: 8.20, per 1000 atoms: 0.54 Number of scatterers: 15300 At special positions: 0 Unit cell: (114.925, 137.693, 169.135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 2832 8.00 N 2559 7.00 C 9866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.26 Conformation dependent library (CDL) restraints added in 3.1 seconds 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 10 sheets defined 51.4% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 105 through 116 removed outlier: 3.573A pdb=" N HIS A 112 " --> pdb=" O HIS A 108 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU A 116 " --> pdb=" O HIS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.646A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 196 removed outlier: 3.873A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 209 removed outlier: 3.764A pdb=" N GLY A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 236 through 248 Processing helix chain 'A' and resid 263 through 275 removed outlier: 3.786A pdb=" N LEU A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.700A pdb=" N TYR A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 removed outlier: 3.595A pdb=" N TYR A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 386 Processing helix chain 'A' and resid 386 through 405 Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.622A pdb=" N PHE A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 442 removed outlier: 3.860A pdb=" N HIS A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.554A pdb=" N ILE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 486 removed outlier: 4.117A pdb=" N GLU A 486 " --> pdb=" O LYS A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 506 through 516 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.682A pdb=" N ALA A 583 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 584 " --> pdb=" O PRO A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 615 removed outlier: 4.685A pdb=" N GLU A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N TYR A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 Processing helix chain 'A' and resid 655 through 673 Processing helix chain 'A' and resid 677 through 691 removed outlier: 3.581A pdb=" N LEU A 689 " --> pdb=" O TYR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'A' and resid 708 through 722 Proline residue: A 717 - end of helix removed outlier: 4.388A pdb=" N ARG A 722 " --> pdb=" O GLN A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 754 Processing helix chain 'A' and resid 801 through 823 removed outlier: 4.069A pdb=" N GLU A 817 " --> pdb=" O GLN A 813 " (cutoff:3.500A) Proline residue: A 818 - end of helix removed outlier: 3.631A pdb=" N ASN A 821 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 877 Processing helix chain 'A' and resid 878 through 894 Processing helix chain 'A' and resid 899 through 914 removed outlier: 3.707A pdb=" N GLU A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 910 " --> pdb=" O LYS A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 931 removed outlier: 4.210A pdb=" N THR A 923 " --> pdb=" O ASP A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 943 Processing helix chain 'A' and resid 994 through 1002 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 134 removed outlier: 3.856A pdb=" N SER B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 171 removed outlier: 3.644A pdb=" N PHE B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 169 " --> pdb=" O PHE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 195 removed outlier: 3.819A pdb=" N ARG B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.645A pdb=" N GLN B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 248 Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.750A pdb=" N LEU B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU B 277 " --> pdb=" O LYS B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 380 through 386 Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 407 through 424 removed outlier: 3.731A pdb=" N PHE B 411 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 444 removed outlier: 3.722A pdb=" N HIS B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR B 443 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 453 removed outlier: 4.675A pdb=" N GLU B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 471 Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 581 through 585 removed outlier: 3.567A pdb=" N TYR B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 608 removed outlier: 4.345A pdb=" N GLU B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 Processing helix chain 'B' and resid 637 through 651 removed outlier: 3.811A pdb=" N LEU B 641 " --> pdb=" O LYS B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 675 removed outlier: 3.818A pdb=" N ARG B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 691 Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 708 through 722 Proline residue: B 717 - end of helix removed outlier: 4.042A pdb=" N ARG B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 754 Processing helix chain 'B' and resid 801 through 822 removed outlier: 4.041A pdb=" N GLU B 817 " --> pdb=" O GLN B 813 " (cutoff:3.500A) Proline residue: B 818 - end of helix Processing helix chain 'B' and resid 855 through 877 Processing helix chain 'B' and resid 878 through 894 Processing helix chain 'B' and resid 899 through 913 removed outlier: 3.869A pdb=" N TYR B 907 " --> pdb=" O GLU B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 931 removed outlier: 3.678A pdb=" N ALA B 926 " --> pdb=" O ASN B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 943 Processing helix chain 'B' and resid 994 through 1002 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 3.864A pdb=" N ARG A 65 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.665A pdb=" N VAL A 377 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 372 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.665A pdb=" N VAL A 377 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN A 499 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 549 through 553 removed outlier: 6.783A pdb=" N LEU A 550 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE A 561 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 552 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP A 560 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N GLY A 731 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 775 through 782 removed outlier: 6.209A pdb=" N GLY A 775 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N SER A 955 " --> pdb=" O GLY A 775 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE A 777 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N HIS A 957 " --> pdb=" O PHE A 777 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR A 779 " --> pdb=" O HIS A 957 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 959 " --> pdb=" O TYR A 779 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN A 781 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS A 952 " --> pdb=" O GLN A 796 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLN A 844 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 847 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 836 " --> pdb=" O ARG A 847 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 849 " --> pdb=" O PHE A 834 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 851 " --> pdb=" O ILE A 832 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 832 " --> pdb=" O GLN A 851 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.382A pdb=" N LYS B 74 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N VAL B 258 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU B 76 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 88 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE B 151 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 90 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR B 149 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 365 removed outlier: 3.794A pdb=" N ILE B 375 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN B 312 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR B 302 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN B 499 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 549 through 553 removed outlier: 7.439A pdb=" N LEU B 559 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASP B 553 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS B 558 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU B 729 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP B 560 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 628 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 621 " --> pdb=" O TYR B 628 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 776 through 782 removed outlier: 6.089A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR B 779 " --> pdb=" O HIS B 957 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU B 959 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 850 " --> pdb=" O ILE B 791 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE B 832 " --> pdb=" O GLN B 851 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 776 through 782 removed outlier: 6.089A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR B 779 " --> pdb=" O HIS B 957 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU B 959 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 850 " --> pdb=" O ILE B 791 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 847 " --> pdb=" O GLY B 836 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY B 836 " --> pdb=" O ARG B 847 " (cutoff:3.500A) 781 hydrogen bonds defined for protein. 2247 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.54 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2955 1.33 - 1.45: 3776 1.45 - 1.57: 8864 1.57 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 15681 Sorted by residual: bond pdb=" N VAL B 305 " pdb=" CA VAL B 305 " ideal model delta sigma weight residual 1.458 1.492 -0.035 7.70e-03 1.69e+04 2.01e+01 bond pdb=" N ASP B 586 " pdb=" CA ASP B 586 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 1.98e+01 bond pdb=" N VAL B 283 " pdb=" CA VAL B 283 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.60e-03 1.73e+04 1.96e+01 bond pdb=" N VAL B 785 " pdb=" CA VAL B 785 " ideal model delta sigma weight residual 1.456 1.498 -0.041 9.50e-03 1.11e+04 1.90e+01 bond pdb=" N LYS A 854 " pdb=" CA LYS A 854 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.84e+01 ... (remaining 15676 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.61: 543 106.61 - 113.57: 8056 113.57 - 120.54: 7548 120.54 - 127.51: 4940 127.51 - 134.47: 118 Bond angle restraints: 21205 Sorted by residual: angle pdb=" N PHE B 115 " pdb=" CA PHE B 115 " pdb=" C PHE B 115 " ideal model delta sigma weight residual 113.72 106.21 7.51 1.30e+00 5.92e-01 3.34e+01 angle pdb=" CA ASP A 91 " pdb=" C ASP A 91 " pdb=" O ASP A 91 " ideal model delta sigma weight residual 121.33 115.36 5.97 1.08e+00 8.57e-01 3.06e+01 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" O GLY A 221 " ideal model delta sigma weight residual 122.29 117.96 4.33 8.10e-01 1.52e+00 2.85e+01 angle pdb=" N LYS A 281 " pdb=" CA LYS A 281 " pdb=" C LYS A 281 " ideal model delta sigma weight residual 113.16 106.80 6.36 1.24e+00 6.50e-01 2.63e+01 angle pdb=" N PRO A 587 " pdb=" CA PRO A 587 " pdb=" C PRO A 587 " ideal model delta sigma weight residual 113.53 106.49 7.04 1.39e+00 5.18e-01 2.57e+01 ... (remaining 21200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 8568 17.86 - 35.72: 675 35.72 - 53.58: 206 53.58 - 71.43: 32 71.43 - 89.29: 8 Dihedral angle restraints: 9489 sinusoidal: 3980 harmonic: 5509 Sorted by residual: dihedral pdb=" C THR B 118 " pdb=" N THR B 118 " pdb=" CA THR B 118 " pdb=" CB THR B 118 " ideal model delta harmonic sigma weight residual -122.00 -138.28 16.28 0 2.50e+00 1.60e-01 4.24e+01 dihedral pdb=" C TYR A 326 " pdb=" N TYR A 326 " pdb=" CA TYR A 326 " pdb=" CB TYR A 326 " ideal model delta harmonic sigma weight residual -122.60 -134.96 12.36 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" C ASN B 282 " pdb=" N ASN B 282 " pdb=" CA ASN B 282 " pdb=" CB ASN B 282 " ideal model delta harmonic sigma weight residual -122.60 -134.39 11.79 0 2.50e+00 1.60e-01 2.22e+01 ... (remaining 9486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1331 0.093 - 0.187: 794 0.187 - 0.280: 145 0.280 - 0.373: 7 0.373 - 0.467: 2 Chirality restraints: 2279 Sorted by residual: chirality pdb=" CA THR B 118 " pdb=" N THR B 118 " pdb=" C THR B 118 " pdb=" CB THR B 118 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA TYR A 326 " pdb=" N TYR A 326 " pdb=" C TYR A 326 " pdb=" CB TYR A 326 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA ARG A 229 " pdb=" N ARG A 229 " pdb=" C ARG A 229 " pdb=" CB ARG A 229 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 2276 not shown) Planarity restraints: 2742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 114 " -0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C LEU B 114 " 0.074 2.00e-02 2.50e+03 pdb=" O LEU B 114 " -0.028 2.00e-02 2.50e+03 pdb=" N PHE B 115 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 91 " 0.014 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C ASP A 91 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP A 91 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL A 92 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 941 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C LYS B 941 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS B 941 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 942 " -0.014 2.00e-02 2.50e+03 ... (remaining 2739 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.14: 5 2.14 - 2.83: 4139 2.83 - 3.52: 21983 3.52 - 4.21: 35908 4.21 - 4.90: 62002 Nonbonded interactions: 124037 Sorted by model distance: nonbonded pdb=" NH2 ARG B 62 " pdb=" CG2 ILE B 78 " model vdw 1.444 3.540 nonbonded pdb=" CE1 PHE A 115 " pdb=" CD2 TYR A 127 " model vdw 1.853 3.640 nonbonded pdb=" CZ PHE B 317 " pdb=" CG2 VAL B 476 " model vdw 1.993 3.760 nonbonded pdb=" OE1 GLU B 529 " pdb=" NZ LYS B 644 " model vdw 2.081 2.520 nonbonded pdb=" CD2 LEU B 771 " pdb=" CA HIS B 952 " model vdw 2.090 3.890 ... (remaining 124032 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 57 through 959 or resid 991 through 1009)) selection = (chain 'B' and resid 57 through 1009) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.600 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 43.160 Find NCS groups from input model: 1.040 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5423 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 : 0.012 0.045 15681 Z= 0.807 Angle : 1.501 8.149 21205 Z= 1.176 Chirality : 0.107 0.467 2279 Planarity : 0.004 0.043 2742 Dihedral : 14.190 89.294 5929 Min Nonbonded Distance : 1.444 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.58 % Favored : 97.26 % Rotamer: Outliers : 5.29 % Allowed : 8.71 % Favored : 86.01 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.19), residues: 1859 helix: 3.45 (0.17), residues: 861 sheet: 2.11 (0.28), residues: 322 loop : -0.14 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 560 HIS 0.011 0.001 HIS B 93 PHE 0.020 0.002 PHE B 130 TYR 0.014 0.002 TYR B 779 ARG 0.005 0.001 ARG B 402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 435 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 THR cc_start: 0.5699 (m) cc_final: 0.4873 (m) REVERT: A 371 MET cc_start: 0.2235 (mmm) cc_final: 0.1883 (mmm) REVERT: A 385 LEU cc_start: 0.7020 (mm) cc_final: 0.6786 (mm) REVERT: A 672 ASN cc_start: 0.7436 (t0) cc_final: 0.7127 (t0) REVERT: A 963 MET cc_start: 0.3184 (ttm) cc_final: 0.2827 (tmm) REVERT: B 61 LYS cc_start: 0.3613 (OUTLIER) cc_final: 0.3041 (tmtt) REVERT: B 199 TRP cc_start: 0.5883 (t-100) cc_final: 0.5491 (t-100) REVERT: B 215 PHE cc_start: 0.6409 (t80) cc_final: 0.5953 (t80) REVERT: B 279 GLU cc_start: 0.5509 (tp30) cc_final: 0.5277 (tp30) REVERT: B 307 ILE cc_start: 0.4184 (mt) cc_final: 0.3552 (tt) REVERT: B 687 ARG cc_start: 0.7101 (ptp-170) cc_final: 0.6634 (tmt-80) REVERT: B 706 ASP cc_start: 0.6694 (p0) cc_final: 0.6254 (p0) outliers start: 88 outliers final: 13 residues processed: 501 average time/residue: 0.2902 time to fit residues: 212.5806 Evaluate side-chains 250 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 236 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 759 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 GLN A 340 HIS A 534 ASN A 638 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 ASN ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 146 HIS B 312 ASN B 418 ASN B 514 GLN B 515 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 GLN B 922 ASN B 993 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5729 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15681 Z= 0.223 Angle : 0.714 14.371 21205 Z= 0.369 Chirality : 0.045 0.245 2279 Planarity : 0.005 0.052 2742 Dihedral : 5.371 46.992 2057 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 4.02 % Allowed : 16.16 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.19), residues: 1859 helix: 1.79 (0.16), residues: 894 sheet: 1.65 (0.27), residues: 351 loop : -0.17 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 513 HIS 0.005 0.001 HIS B 340 PHE 0.044 0.002 PHE A 715 TYR 0.030 0.002 TYR A 500 ARG 0.007 0.001 ARG B 674 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 247 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6637 (mm) REVERT: A 455 LEU cc_start: 0.5569 (OUTLIER) cc_final: 0.5344 (pt) REVERT: A 963 MET cc_start: 0.3594 (ttm) cc_final: 0.3136 (tmm) REVERT: B 199 TRP cc_start: 0.5980 (t-100) cc_final: 0.5606 (t-100) REVERT: B 227 GLU cc_start: -0.1664 (OUTLIER) cc_final: -0.2513 (tp30) REVERT: B 279 GLU cc_start: 0.5665 (tp30) cc_final: 0.5201 (tp30) REVERT: B 307 ILE cc_start: 0.4366 (mt) cc_final: 0.3737 (tt) REVERT: B 337 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6952 (tp) REVERT: B 688 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.5447 (tp) REVERT: B 706 ASP cc_start: 0.6917 (p0) cc_final: 0.6714 (p0) REVERT: B 744 MET cc_start: 0.7449 (ppp) cc_final: 0.7226 (ppp) REVERT: B 1011 HIS cc_start: 0.3804 (OUTLIER) cc_final: 0.3521 (t-170) outliers start: 67 outliers final: 28 residues processed: 293 average time/residue: 0.2522 time to fit residues: 112.7255 Evaluate side-chains 231 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 197 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 955 SER Chi-restraints excluded: chain B residue 1011 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.0670 chunk 52 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 GLN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 ASN B 922 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15681 Z= 0.233 Angle : 0.675 10.349 21205 Z= 0.346 Chirality : 0.044 0.200 2279 Planarity : 0.004 0.053 2742 Dihedral : 5.100 47.358 2043 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.60 % Allowed : 18.20 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 1859 helix: 1.29 (0.16), residues: 894 sheet: 1.31 (0.28), residues: 344 loop : -0.31 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 355 HIS 0.006 0.001 HIS A 885 PHE 0.048 0.002 PHE A 715 TYR 0.022 0.002 TYR A 779 ARG 0.014 0.001 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 202 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.2029 (mmm) cc_final: 0.1649 (mmm) REVERT: A 672 ASN cc_start: 0.7546 (t0) cc_final: 0.7324 (m-40) REVERT: A 793 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7822 (pt) REVERT: A 963 MET cc_start: 0.3698 (ttm) cc_final: 0.3098 (tmm) REVERT: B 119 LYS cc_start: 0.7718 (tptt) cc_final: 0.7224 (tppt) REVERT: B 227 GLU cc_start: -0.1753 (OUTLIER) cc_final: -0.2659 (tp30) REVERT: B 240 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7368 (mt-10) REVERT: B 279 GLU cc_start: 0.5851 (tp30) cc_final: 0.5464 (tp30) REVERT: B 307 ILE cc_start: 0.4283 (mt) cc_final: 0.3676 (tt) REVERT: B 324 LYS cc_start: 0.6337 (OUTLIER) cc_final: 0.4995 (ptpt) REVERT: B 688 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.5434 (tp) REVERT: B 706 ASP cc_start: 0.7171 (p0) cc_final: 0.6855 (p0) REVERT: B 1011 HIS cc_start: 0.4113 (OUTLIER) cc_final: 0.3757 (t-170) outliers start: 60 outliers final: 30 residues processed: 244 average time/residue: 0.2319 time to fit residues: 88.5853 Evaluate side-chains 211 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 176 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 955 SER Chi-restraints excluded: chain B residue 996 THR Chi-restraints excluded: chain B residue 1011 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 18 optimal weight: 30.0000 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 169 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN A 672 ASN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15681 Z= 0.216 Angle : 0.641 10.536 21205 Z= 0.330 Chirality : 0.043 0.182 2279 Planarity : 0.004 0.054 2742 Dihedral : 5.057 48.132 2041 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.84 % Allowed : 18.80 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1859 helix: 1.15 (0.16), residues: 896 sheet: 1.01 (0.28), residues: 343 loop : -0.33 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 199 HIS 0.007 0.001 HIS A 112 PHE 0.034 0.002 PHE B 998 TYR 0.021 0.002 TYR A 779 ARG 0.006 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 198 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 793 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7916 (pt) REVERT: B 119 LYS cc_start: 0.7792 (tptt) cc_final: 0.7315 (tppt) REVERT: B 227 GLU cc_start: -0.1684 (OUTLIER) cc_final: -0.2672 (tp30) REVERT: B 240 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7375 (mt-10) REVERT: B 279 GLU cc_start: 0.5822 (tp30) cc_final: 0.5449 (tp30) REVERT: B 307 ILE cc_start: 0.4200 (mt) cc_final: 0.3400 (tt) REVERT: B 324 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.5124 (ptpt) REVERT: B 337 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7481 (tp) REVERT: B 706 ASP cc_start: 0.7174 (p0) cc_final: 0.6855 (p0) REVERT: B 799 MET cc_start: 0.8211 (tmm) cc_final: 0.7988 (ttp) REVERT: B 908 TRP cc_start: 0.4333 (t-100) cc_final: 0.3426 (t60) REVERT: B 1011 HIS cc_start: 0.4554 (OUTLIER) cc_final: 0.3978 (t-170) outliers start: 64 outliers final: 42 residues processed: 242 average time/residue: 0.2345 time to fit residues: 88.7393 Evaluate side-chains 225 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 178 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 955 SER Chi-restraints excluded: chain B residue 996 THR Chi-restraints excluded: chain B residue 1011 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15681 Z= 0.315 Angle : 0.762 14.759 21205 Z= 0.394 Chirality : 0.047 0.215 2279 Planarity : 0.005 0.057 2742 Dihedral : 5.618 56.598 2041 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.92 % Allowed : 18.92 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 1859 helix: 0.59 (0.16), residues: 878 sheet: 0.55 (0.27), residues: 342 loop : -0.58 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 908 HIS 0.011 0.002 HIS A 885 PHE 0.029 0.003 PHE B 130 TYR 0.030 0.003 TYR A 779 ARG 0.009 0.001 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 183 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 TYR cc_start: 0.5699 (m-80) cc_final: 0.5498 (m-10) REVERT: A 454 TYR cc_start: 0.2864 (t80) cc_final: 0.2572 (t80) REVERT: A 632 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7401 (mttp) REVERT: B 119 LYS cc_start: 0.7953 (tptt) cc_final: 0.7377 (mmmt) REVERT: B 227 GLU cc_start: -0.1750 (OUTLIER) cc_final: -0.2797 (tp30) REVERT: B 240 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7367 (mt-10) REVERT: B 279 GLU cc_start: 0.6228 (tp30) cc_final: 0.5712 (tp30) REVERT: B 324 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6696 (pttm) REVERT: B 337 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7476 (tp) REVERT: B 574 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7987 (mt) REVERT: B 687 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6512 (tmt170) REVERT: B 706 ASP cc_start: 0.7282 (p0) cc_final: 0.6581 (p0) REVERT: B 798 ASP cc_start: 0.5405 (OUTLIER) cc_final: 0.5150 (m-30) REVERT: B 907 TYR cc_start: 0.5686 (OUTLIER) cc_final: 0.4996 (m-10) outliers start: 82 outliers final: 50 residues processed: 245 average time/residue: 0.2379 time to fit residues: 90.6006 Evaluate side-chains 224 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 166 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 715 PHE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 907 TYR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 955 SER Chi-restraints excluded: chain B residue 996 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 179 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 83 optimal weight: 0.3980 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 332 HIS ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15681 Z= 0.206 Angle : 0.650 11.109 21205 Z= 0.333 Chirality : 0.043 0.209 2279 Planarity : 0.004 0.054 2742 Dihedral : 5.318 55.197 2040 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.62 % Allowed : 19.88 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 1859 helix: 0.81 (0.16), residues: 873 sheet: 0.56 (0.27), residues: 348 loop : -0.57 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 908 HIS 0.007 0.001 HIS A 112 PHE 0.030 0.002 PHE B 998 TYR 0.017 0.002 TYR A 779 ARG 0.008 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 186 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.3734 (pmm) cc_final: 0.2487 (mmp) REVERT: A 205 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6564 (tm-30) REVERT: A 494 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6851 (pt0) REVERT: A 637 LYS cc_start: 0.3289 (OUTLIER) cc_final: 0.2675 (ptmt) REVERT: A 793 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7772 (pt) REVERT: B 119 LYS cc_start: 0.7903 (tptt) cc_final: 0.7369 (mmmt) REVERT: B 227 GLU cc_start: -0.1875 (OUTLIER) cc_final: -0.2579 (tp30) REVERT: B 240 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7333 (mt-10) REVERT: B 279 GLU cc_start: 0.6196 (tp30) cc_final: 0.5786 (tp30) REVERT: B 291 HIS cc_start: 0.5533 (p-80) cc_final: 0.4530 (t70) REVERT: B 324 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6774 (pttm) REVERT: B 337 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7534 (tp) REVERT: B 574 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8028 (mt) REVERT: B 589 HIS cc_start: 0.5897 (OUTLIER) cc_final: 0.5568 (m90) REVERT: B 687 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6510 (tmt170) REVERT: B 706 ASP cc_start: 0.7190 (p0) cc_final: 0.6863 (p0) REVERT: B 915 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7212 (mt0) outliers start: 77 outliers final: 48 residues processed: 248 average time/residue: 0.2514 time to fit residues: 95.7613 Evaluate side-chains 225 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 167 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 589 HIS Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 955 SER Chi-restraints excluded: chain B residue 996 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 101 optimal weight: 0.4980 chunk 151 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 HIS ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 GLN A 994 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 15681 Z= 0.347 Angle : 0.805 12.843 21205 Z= 0.411 Chirality : 0.047 0.217 2279 Planarity : 0.006 0.074 2742 Dihedral : 5.830 59.502 2040 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.86 % Allowed : 20.06 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 1859 helix: 0.24 (0.16), residues: 864 sheet: -0.01 (0.26), residues: 348 loop : -0.92 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 908 HIS 0.009 0.002 HIS A 730 PHE 0.040 0.003 PHE A 715 TYR 0.026 0.003 TYR A 779 ARG 0.008 0.001 ARG A 961 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 163 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.3462 (pmm) cc_final: 0.2301 (mmp) REVERT: A 632 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7460 (mtmt) REVERT: A 637 LYS cc_start: 0.3613 (OUTLIER) cc_final: 0.3116 (ptmt) REVERT: A 793 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7940 (pt) REVERT: A 806 MET cc_start: 0.7390 (mmm) cc_final: 0.7154 (mmp) REVERT: A 1005 PHE cc_start: 0.7129 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: B 90 LEU cc_start: 0.5707 (OUTLIER) cc_final: 0.5250 (tt) REVERT: B 119 LYS cc_start: 0.7819 (tptt) cc_final: 0.7271 (tppt) REVERT: B 227 GLU cc_start: -0.1243 (OUTLIER) cc_final: -0.2462 (tp30) REVERT: B 240 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7240 (mt-10) REVERT: B 279 GLU cc_start: 0.6547 (tp30) cc_final: 0.6042 (tp30) REVERT: B 291 HIS cc_start: 0.5816 (p-80) cc_final: 0.4885 (t70) REVERT: B 324 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6606 (pttm) REVERT: B 337 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7580 (tp) REVERT: B 574 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8001 (mt) REVERT: B 589 HIS cc_start: 0.6013 (OUTLIER) cc_final: 0.5379 (m90) REVERT: B 687 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6519 (tmt170) REVERT: B 706 ASP cc_start: 0.7282 (p0) cc_final: 0.6514 (p0) REVERT: B 907 TYR cc_start: 0.5607 (OUTLIER) cc_final: 0.4983 (m-10) REVERT: B 915 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7450 (mt0) outliers start: 81 outliers final: 52 residues processed: 226 average time/residue: 0.2456 time to fit residues: 86.0035 Evaluate side-chains 215 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 150 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 589 HIS Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 715 PHE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 907 TYR Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 955 SER Chi-restraints excluded: chain B residue 996 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15681 Z= 0.217 Angle : 0.693 12.184 21205 Z= 0.352 Chirality : 0.043 0.210 2279 Planarity : 0.005 0.059 2742 Dihedral : 5.375 49.598 2039 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.14 % Allowed : 21.32 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 1859 helix: 0.51 (0.16), residues: 868 sheet: 0.00 (0.26), residues: 355 loop : -0.93 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 513 HIS 0.005 0.001 HIS B 681 PHE 0.051 0.002 PHE A 715 TYR 0.021 0.002 TYR B 149 ARG 0.004 0.000 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 170 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.3415 (pmm) cc_final: 0.2271 (mmp) REVERT: A 620 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6955 (mt) REVERT: A 637 LYS cc_start: 0.3534 (OUTLIER) cc_final: 0.3027 (ptmt) REVERT: A 793 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7852 (pt) REVERT: B 90 LEU cc_start: 0.5577 (OUTLIER) cc_final: 0.5105 (tt) REVERT: B 119 LYS cc_start: 0.7749 (tptt) cc_final: 0.7244 (tppt) REVERT: B 227 GLU cc_start: -0.1532 (OUTLIER) cc_final: -0.2386 (tp30) REVERT: B 240 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7137 (mt-10) REVERT: B 279 GLU cc_start: 0.6533 (tp30) cc_final: 0.6052 (tp30) REVERT: B 291 HIS cc_start: 0.5697 (p-80) cc_final: 0.4743 (t70) REVERT: B 521 LYS cc_start: 0.5939 (OUTLIER) cc_final: 0.5208 (pttm) REVERT: B 574 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8054 (mt) REVERT: B 589 HIS cc_start: 0.5896 (OUTLIER) cc_final: 0.5381 (m90) REVERT: B 687 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6523 (tmt170) REVERT: B 706 ASP cc_start: 0.7136 (p0) cc_final: 0.6419 (p0) REVERT: B 915 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7247 (mt0) outliers start: 69 outliers final: 48 residues processed: 225 average time/residue: 0.2402 time to fit residues: 84.3530 Evaluate side-chains 211 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 153 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 589 HIS Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 715 PHE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 955 SER Chi-restraints excluded: chain B residue 996 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15681 Z= 0.182 Angle : 0.678 12.876 21205 Z= 0.337 Chirality : 0.043 0.236 2279 Planarity : 0.004 0.052 2742 Dihedral : 4.927 41.733 2035 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.07 % Favored : 96.88 % Rotamer: Outliers : 3.24 % Allowed : 22.22 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 1859 helix: 0.75 (0.17), residues: 872 sheet: 0.11 (0.27), residues: 361 loop : -0.75 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 695 HIS 0.011 0.001 HIS A 885 PHE 0.053 0.002 PHE A 715 TYR 0.023 0.002 TYR B 149 ARG 0.003 0.000 ARG A 961 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 176 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.3347 (pmm) cc_final: 0.2179 (mmp) REVERT: A 494 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6454 (pt0) REVERT: A 620 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6834 (mt) REVERT: B 90 LEU cc_start: 0.5623 (OUTLIER) cc_final: 0.5249 (tt) REVERT: B 119 LYS cc_start: 0.7905 (tptt) cc_final: 0.7375 (tppt) REVERT: B 227 GLU cc_start: -0.1627 (OUTLIER) cc_final: -0.2413 (tp30) REVERT: B 240 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7172 (mt-10) REVERT: B 279 GLU cc_start: 0.6481 (tp30) cc_final: 0.5999 (tp30) REVERT: B 291 HIS cc_start: 0.5633 (p-80) cc_final: 0.4749 (t70) REVERT: B 687 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6480 (tmt170) REVERT: B 706 ASP cc_start: 0.6991 (p0) cc_final: 0.6362 (p0) REVERT: B 744 MET cc_start: 0.7769 (ppp) cc_final: 0.7442 (ppp) REVERT: B 866 PHE cc_start: 0.6096 (t80) cc_final: 0.4682 (t80) REVERT: B 870 MET cc_start: 0.5986 (mmm) cc_final: 0.5462 (mmm) outliers start: 54 outliers final: 39 residues processed: 214 average time/residue: 0.2333 time to fit residues: 78.5763 Evaluate side-chains 203 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 159 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 955 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.9980 chunk 176 optimal weight: 0.0980 chunk 107 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 185 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 113 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15681 Z= 0.176 Angle : 0.675 13.285 21205 Z= 0.335 Chirality : 0.043 0.228 2279 Planarity : 0.004 0.048 2742 Dihedral : 4.812 41.198 2035 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.28 % Favored : 96.66 % Rotamer: Outliers : 2.76 % Allowed : 22.88 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.19), residues: 1859 helix: 0.81 (0.17), residues: 875 sheet: 0.20 (0.27), residues: 359 loop : -0.71 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 695 HIS 0.010 0.001 HIS A 885 PHE 0.048 0.002 PHE A 715 TYR 0.021 0.001 TYR B 149 ARG 0.005 0.000 ARG A 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 164 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.3282 (pmm) cc_final: 0.2148 (mmp) REVERT: A 494 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.5721 (pp20) REVERT: A 620 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6969 (mt) REVERT: A 744 MET cc_start: 0.5625 (ppp) cc_final: 0.5082 (ppp) REVERT: A 806 MET cc_start: 0.6994 (mmm) cc_final: 0.6461 (mmt) REVERT: B 90 LEU cc_start: 0.5571 (OUTLIER) cc_final: 0.5253 (tt) REVERT: B 227 GLU cc_start: -0.1559 (OUTLIER) cc_final: -0.2365 (tp30) REVERT: B 240 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7122 (mt-10) REVERT: B 279 GLU cc_start: 0.6368 (tp30) cc_final: 0.5935 (tp30) REVERT: B 291 HIS cc_start: 0.5614 (p-80) cc_final: 0.4756 (t70) REVERT: B 687 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6495 (tmt170) REVERT: B 706 ASP cc_start: 0.7020 (p0) cc_final: 0.6407 (p0) outliers start: 46 outliers final: 36 residues processed: 199 average time/residue: 0.2342 time to fit residues: 73.2213 Evaluate side-chains 199 residues out of total 1665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 955 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.2980 chunk 157 optimal weight: 7.9990 chunk 45 optimal weight: 0.4980 chunk 136 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 0.0470 chunk 147 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.148657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.127616 restraints weight = 48197.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.127971 restraints weight = 29998.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.129002 restraints weight = 25191.655| |-----------------------------------------------------------------------------| r_work (final): 0.4634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15681 Z= 0.206 Angle : 0.690 14.838 21205 Z= 0.344 Chirality : 0.043 0.221 2279 Planarity : 0.004 0.051 2742 Dihedral : 4.877 41.713 2035 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 2.76 % Allowed : 22.82 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 1859 helix: 0.72 (0.17), residues: 873 sheet: 0.21 (0.27), residues: 361 loop : -0.77 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 908 HIS 0.011 0.001 HIS A 885 PHE 0.049 0.002 PHE A 715 TYR 0.021 0.002 TYR B 149 ARG 0.002 0.000 ARG A 961 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3065.83 seconds wall clock time: 56 minutes 43.80 seconds (3403.80 seconds total)