Starting phenix.real_space_refine on Thu Apr 11 16:28:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8p_12088/04_2024/7b8p_12088.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8p_12088/04_2024/7b8p_12088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8p_12088/04_2024/7b8p_12088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8p_12088/04_2024/7b8p_12088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8p_12088/04_2024/7b8p_12088.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8p_12088/04_2024/7b8p_12088.pdb" } resolution = 3.54 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= 0.005 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 135 5.16 5 C 15000 2.51 5 N 3774 2.21 5 O 4293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A ASP 189": "OD1" <-> "OD2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 264": "OD1" <-> "OD2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A ASP 429": "OD1" <-> "OD2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "A ASP 600": "OD1" <-> "OD2" Residue "A PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 678": "OD1" <-> "OD2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A GLU 767": "OE1" <-> "OE2" Residue "A TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 836": "OE1" <-> "OE2" Residue "A TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A GLU 952": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 156": "OD1" <-> "OD2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B ASP 189": "OD1" <-> "OD2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 264": "OD1" <-> "OD2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B ASP 597": "OD1" <-> "OD2" Residue "B ASP 600": "OD1" <-> "OD2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 678": "OD1" <-> "OD2" Residue "B TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 723": "OD1" <-> "OD2" Residue "B PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "B GLU 767": "OE1" <-> "OE2" Residue "B TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 836": "OE1" <-> "OE2" Residue "B TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 857": "OE1" <-> "OE2" Residue "B PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 945": "OE1" <-> "OE2" Residue "B GLU 952": "OE1" <-> "OE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C ASP 189": "OD1" <-> "OD2" Residue "C TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 407": "OD1" <-> "OD2" Residue "C ASP 429": "OD1" <-> "OD2" Residue "C PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 518": "OD1" <-> "OD2" Residue "C PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 582": "OE1" <-> "OE2" Residue "C ASP 597": "OD1" <-> "OD2" Residue "C ASP 600": "OD1" <-> "OD2" Residue "C PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 678": "OD1" <-> "OD2" Residue "C TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 723": "OD1" <-> "OD2" Residue "C PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "C GLU 767": "OE1" <-> "OE2" Residue "C TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 836": "OE1" <-> "OE2" Residue "C TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 857": "OE1" <-> "OE2" Residue "C PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 945": "OE1" <-> "OE2" Residue "C GLU 952": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23202 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7734 Classifications: {'peptide': 1015} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 968} Chain breaks: 1 Chain: "B" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7734 Classifications: {'peptide': 1015} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 968} Chain breaks: 1 Chain: "C" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7734 Classifications: {'peptide': 1015} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 968} Chain breaks: 1 Time building chain proxies: 11.75, per 1000 atoms: 0.51 Number of scatterers: 23202 At special positions: 0 Unit cell: (119.7, 112.35, 138.6, 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 135 16.00 O 4293 8.00 N 3774 7.00 C 15000 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: 9.10 Conformation dependent library (CDL) restraints added in 4.5 seconds 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 24 sheets defined 59.0% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.951A pdb=" N ARG A 7 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 27 removed outlier: 3.611A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.855A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.515A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 329 through 360 Processing helix chain 'A' and resid 361 through 370 Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 370 through 387 removed outlier: 3.736A pdb=" N ILE A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 423 removed outlier: 4.328A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 453 removed outlier: 6.281A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.777A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'A' and resid 461 through 496 removed outlier: 4.089A pdb=" N GLN A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 512 through 534 removed outlier: 3.768A pdb=" N HIS A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 556 Processing helix chain 'A' and resid 580 through 595 Processing helix chain 'A' and resid 635 through 646 removed outlier: 3.651A pdb=" N ASP A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 698 Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 747 removed outlier: 3.596A pdb=" N VAL A 737 " --> pdb=" O LYS A 733 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER A 747 " --> pdb=" O THR A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 771 Processing helix chain 'A' and resid 773 through 778 removed outlier: 3.973A pdb=" N ILE A 777 " --> pdb=" O GLN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 841 Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 863 through 884 removed outlier: 3.574A pdb=" N LEU A 867 " --> pdb=" O GLN A 863 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 868 " --> pdb=" O MET A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 894 Processing helix chain 'A' and resid 895 through 911 Processing helix chain 'A' and resid 915 through 946 removed outlier: 3.784A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 982 removed outlier: 4.610A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 986 through 1007 removed outlier: 4.168A pdb=" N GLN A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1022 removed outlier: 4.121A pdb=" N VAL A1014 " --> pdb=" O PHE A1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.951A pdb=" N ARG B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 27 removed outlier: 3.612A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.855A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.514A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 314 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 329 through 360 Processing helix chain 'B' and resid 361 through 370 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.736A pdb=" N ILE B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 423 removed outlier: 4.327A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 453 removed outlier: 6.281A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 3.777A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 461 through 496 removed outlier: 4.089A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 512 through 534 removed outlier: 3.767A pdb=" N HIS B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 580 through 595 Processing helix chain 'B' and resid 635 through 646 removed outlier: 3.651A pdb=" N ASP B 642 " --> pdb=" O LYS B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 698 Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 747 removed outlier: 3.634A pdb=" N VAL B 737 " --> pdb=" O LYS B 733 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER B 747 " --> pdb=" O THR B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 Processing helix chain 'B' and resid 773 through 778 removed outlier: 3.973A pdb=" N ILE B 777 " --> pdb=" O GLN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 841 Processing helix chain 'B' and resid 852 through 862 Processing helix chain 'B' and resid 863 through 884 removed outlier: 3.574A pdb=" N LEU B 867 " --> pdb=" O GLN B 863 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 868 " --> pdb=" O MET B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 894 Processing helix chain 'B' and resid 895 through 911 Processing helix chain 'B' and resid 915 through 946 removed outlier: 3.783A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 982 removed outlier: 4.610A pdb=" N ARG B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Proline residue: B 964 - end of helix Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 986 through 1007 removed outlier: 4.168A pdb=" N GLN B 990 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1022 removed outlier: 4.122A pdb=" N VAL B1014 " --> pdb=" O PHE B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.951A pdb=" N ARG C 7 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 27 removed outlier: 3.612A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.855A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.515A pdb=" N ALA C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 329 through 360 Processing helix chain 'C' and resid 361 through 370 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 370 through 387 removed outlier: 3.736A pdb=" N ILE C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 423 removed outlier: 4.328A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA C 409 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 453 removed outlier: 6.281A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 3.775A pdb=" N PHE C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 461 through 496 removed outlier: 4.090A pdb=" N GLN C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 512 through 534 removed outlier: 3.767A pdb=" N HIS C 534 " --> pdb=" O LYS C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 556 Processing helix chain 'C' and resid 580 through 595 Processing helix chain 'C' and resid 635 through 646 removed outlier: 3.651A pdb=" N ASP C 642 " --> pdb=" O LYS C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 698 Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 747 removed outlier: 3.634A pdb=" N VAL C 737 " --> pdb=" O LYS C 733 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER C 747 " --> pdb=" O THR C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 771 Processing helix chain 'C' and resid 773 through 778 removed outlier: 3.973A pdb=" N ILE C 777 " --> pdb=" O GLN C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 841 Processing helix chain 'C' and resid 852 through 862 Processing helix chain 'C' and resid 863 through 884 removed outlier: 3.574A pdb=" N LEU C 867 " --> pdb=" O GLN C 863 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 868 " --> pdb=" O MET C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 894 Processing helix chain 'C' and resid 895 through 911 Processing helix chain 'C' and resid 915 through 946 removed outlier: 3.783A pdb=" N ILE C 936 " --> pdb=" O ASN C 932 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 982 removed outlier: 4.611A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 986 through 1007 removed outlier: 4.168A pdb=" N GLN C 990 " --> pdb=" O SER C 986 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1022 removed outlier: 4.121A pdb=" N VAL C1014 " --> pdb=" O PHE C1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.678A pdb=" N GLN A 42 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 821 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N MET A 706 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.678A pdb=" N GLN A 42 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.622A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.832A pdb=" N ILE A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR A 605 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 572 " --> pdb=" O MET A 656 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.776A pdb=" N LYS A 182 " --> pdb=" O GLN A 761 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE A 763 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET A 184 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLN A 765 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE A 186 " --> pdb=" O GLN A 765 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA8, first strand: chain 'A' and resid 796 through 803 removed outlier: 8.353A pdb=" N SER B 235 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A 718 " --> pdb=" O SER B 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 781 through 783 Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 821 " --> pdb=" O MET B 706 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.622A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.831A pdb=" N ILE B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 605 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 572 " --> pdb=" O MET B 656 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.776A pdb=" N LYS B 182 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE B 763 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET B 184 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN B 765 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE B 186 " --> pdb=" O GLN B 765 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AB7, first strand: chain 'B' and resid 796 through 803 removed outlier: 8.349A pdb=" N SER C 235 " --> pdb=" O ASP B 716 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE B 718 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 781 through 783 Processing sheet with id=AB9, first strand: chain 'C' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 821 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET C 706 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.622A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.831A pdb=" N ILE C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C 605 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER C 572 " --> pdb=" O MET C 656 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.776A pdb=" N LYS C 182 " --> pdb=" O GLN C 761 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE C 763 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET C 184 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN C 765 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE C 186 " --> pdb=" O GLN C 765 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 252 Processing sheet with id=AC6, first strand: chain 'C' and resid 781 through 783 1563 hydrogen bonds defined for protein. 4545 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: 9.90 Time building geometry restraints manager: 9.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7320 1.34 - 1.46: 4193 1.46 - 1.58: 11836 1.58 - 1.70: 6 1.70 - 1.81: 264 Bond restraints: 23619 Sorted by residual: bond pdb=" CA LEU B 198 " pdb=" C LEU B 198 " ideal model delta sigma weight residual 1.526 1.593 -0.067 1.36e-02 5.41e+03 2.44e+01 bond pdb=" CA LEU C 198 " pdb=" C LEU C 198 " ideal model delta sigma weight residual 1.526 1.593 -0.067 1.36e-02 5.41e+03 2.43e+01 bond pdb=" CA LEU A 198 " pdb=" C LEU A 198 " ideal model delta sigma weight residual 1.526 1.591 -0.066 1.36e-02 5.41e+03 2.34e+01 bond pdb=" CA VAL C 259 " pdb=" CB VAL C 259 " ideal model delta sigma weight residual 1.533 1.482 0.052 1.13e-02 7.83e+03 2.09e+01 bond pdb=" CA VAL A 259 " pdb=" CB VAL A 259 " ideal model delta sigma weight residual 1.533 1.482 0.051 1.13e-02 7.83e+03 2.07e+01 ... (remaining 23614 not shown) Histogram of bond angle deviations from ideal: 97.06 - 104.47: 514 104.47 - 111.87: 11710 111.87 - 119.27: 7886 119.27 - 126.67: 11668 126.67 - 134.08: 259 Bond angle restraints: 32037 Sorted by residual: angle pdb=" N LYS A 226 " pdb=" CA LYS A 226 " pdb=" C LYS A 226 " ideal model delta sigma weight residual 110.35 98.53 11.82 1.40e+00 5.10e-01 7.13e+01 angle pdb=" N LYS B 226 " pdb=" CA LYS B 226 " pdb=" C LYS B 226 " ideal model delta sigma weight residual 110.35 98.58 11.77 1.40e+00 5.10e-01 7.07e+01 angle pdb=" N LYS C 226 " pdb=" CA LYS C 226 " pdb=" C LYS C 226 " ideal model delta sigma weight residual 110.35 98.61 11.74 1.40e+00 5.10e-01 7.04e+01 angle pdb=" N LYS B 254 " pdb=" CA LYS B 254 " pdb=" C LYS B 254 " ideal model delta sigma weight residual 110.80 127.46 -16.66 2.13e+00 2.20e-01 6.12e+01 angle pdb=" N LYS C 254 " pdb=" CA LYS C 254 " pdb=" C LYS C 254 " ideal model delta sigma weight residual 110.80 127.45 -16.65 2.13e+00 2.20e-01 6.11e+01 ... (remaining 32032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 12519 15.70 - 31.41: 1336 31.41 - 47.11: 353 47.11 - 62.81: 93 62.81 - 78.52: 24 Dihedral angle restraints: 14325 sinusoidal: 5553 harmonic: 8772 Sorted by residual: dihedral pdb=" CA TYR B 49 " pdb=" C TYR B 49 " pdb=" N PRO B 50 " pdb=" CA PRO B 50 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR C 49 " pdb=" C TYR C 49 " pdb=" N PRO C 50 " pdb=" CA PRO C 50 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR A 49 " pdb=" C TYR A 49 " pdb=" N PRO A 50 " pdb=" CA PRO A 50 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 14322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3287 0.071 - 0.142: 457 0.142 - 0.212: 96 0.212 - 0.283: 9 0.283 - 0.354: 3 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA VAL B 707 " pdb=" N VAL B 707 " pdb=" C VAL B 707 " pdb=" CB VAL B 707 " both_signs ideal model delta sigma weight residual False 2.44 2.80 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA VAL C 707 " pdb=" N VAL C 707 " pdb=" C VAL C 707 " pdb=" CB VAL C 707 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA VAL A 707 " pdb=" N VAL A 707 " pdb=" C VAL A 707 " pdb=" CB VAL A 707 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 3849 not shown) Planarity restraints: 4032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 35 " -0.061 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO C 36 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO C 36 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 36 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 35 " 0.061 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO B 36 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 35 " 0.061 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO A 36 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 36 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 36 " 0.049 5.00e-02 4.00e+02 ... (remaining 4029 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 10123 2.92 - 3.41: 24347 3.41 - 3.91: 38792 3.91 - 4.40: 45193 4.40 - 4.90: 75260 Nonbonded interactions: 193715 Sorted by model distance: nonbonded pdb=" O GLU A 225 " pdb=" C LYS A 226 " model vdw 2.425 3.270 nonbonded pdb=" O GLU B 225 " pdb=" C LYS B 226 " model vdw 2.425 3.270 nonbonded pdb=" O GLU C 225 " pdb=" C LYS C 226 " model vdw 2.425 3.270 nonbonded pdb=" NZ LYS C 931 " pdb=" OD1 ASN C 932 " model vdw 2.466 2.520 nonbonded pdb=" NZ LYS B 931 " pdb=" OD1 ASN B 932 " model vdw 2.466 2.520 ... (remaining 193710 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' selection = chain 'B' selection = chain 'C' } 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: 0.840 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: 0.030 Extract box with map and model: 4.740 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 62.640 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.130 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 23619 Z= 0.371 Angle : 0.972 16.664 32037 Z= 0.648 Chirality : 0.053 0.354 3852 Planarity : 0.006 0.091 4032 Dihedral : 14.537 78.516 8649 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.75 % Allowed : 11.53 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.81 (0.14), residues: 3033 helix: -1.03 (0.11), residues: 1701 sheet: -2.78 (0.20), residues: 516 loop : -2.59 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 556 HIS 0.002 0.001 HIS C 360 PHE 0.015 0.001 PHE B 917 TYR 0.017 0.001 TYR C 49 ARG 0.005 0.000 ARG A 724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 559 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6127 (mm-30) REVERT: A 193 LEU cc_start: 0.8131 (tp) cc_final: 0.7474 (mp) REVERT: A 230 ILE cc_start: 0.9017 (mm) cc_final: 0.8754 (mt) REVERT: A 240 LEU cc_start: 0.8833 (mt) cc_final: 0.8407 (mt) REVERT: A 356 TYR cc_start: 0.7304 (t80) cc_final: 0.6764 (t80) REVERT: A 370 ILE cc_start: 0.9191 (tp) cc_final: 0.8955 (tp) REVERT: A 538 MET cc_start: 0.7943 (mmm) cc_final: 0.7199 (mmt) REVERT: A 743 THR cc_start: 0.8904 (p) cc_final: 0.8696 (p) REVERT: A 824 PHE cc_start: 0.6785 (t80) cc_final: 0.6352 (t80) REVERT: A 835 MET cc_start: 0.9207 (tpt) cc_final: 0.8987 (mmm) REVERT: A 964 PRO cc_start: 0.8897 (Cg_exo) cc_final: 0.8462 (Cg_endo) REVERT: A 1015 PHE cc_start: 0.8536 (m-10) cc_final: 0.8334 (m-80) REVERT: B 32 ILE cc_start: 0.8485 (pt) cc_final: 0.8243 (tt) REVERT: B 234 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8499 (tp) REVERT: B 395 MET cc_start: 0.8502 (mmp) cc_final: 0.8009 (mmp) REVERT: B 647 MET cc_start: 0.8341 (mmm) cc_final: 0.7809 (mmm) REVERT: B 824 PHE cc_start: 0.6754 (t80) cc_final: 0.6429 (t80) REVERT: B 835 MET cc_start: 0.9216 (tpt) cc_final: 0.8938 (tpt) REVERT: B 919 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8381 (mttp) REVERT: B 1015 PHE cc_start: 0.8562 (m-10) cc_final: 0.8193 (m-80) REVERT: C 42 GLN cc_start: 0.8638 (mt0) cc_final: 0.8378 (mt0) REVERT: C 68 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6440 (mm-30) REVERT: C 101 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7076 (mm-30) REVERT: C 352 PHE cc_start: 0.8485 (t80) cc_final: 0.8284 (t80) REVERT: C 356 TYR cc_start: 0.7234 (t80) cc_final: 0.6618 (t80) REVERT: C 370 ILE cc_start: 0.9211 (tp) cc_final: 0.8950 (tp) REVERT: C 393 LEU cc_start: 0.9202 (mt) cc_final: 0.8890 (mt) REVERT: C 395 MET cc_start: 0.8660 (mmp) cc_final: 0.8386 (mmp) REVERT: C 538 MET cc_start: 0.7947 (mmm) cc_final: 0.7676 (mmt) REVERT: C 695 MET cc_start: 0.8505 (tpp) cc_final: 0.8162 (mpp) REVERT: C 759 MET cc_start: 0.9033 (mmt) cc_final: 0.8751 (mmm) REVERT: C 835 MET cc_start: 0.9152 (tpt) cc_final: 0.8789 (tpt) outliers start: 19 outliers final: 1 residues processed: 570 average time/residue: 0.3674 time to fit residues: 322.7196 Evaluate side-chains 363 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 360 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain C residue 919 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 7.9990 chunk 229 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 chunk 275 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 273 GLN A 415 ASN A 574 GLN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 415 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 GLN C 239 GLN C 273 GLN C 415 ASN C 574 GLN ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23619 Z= 0.262 Angle : 0.589 7.835 32037 Z= 0.304 Chirality : 0.042 0.194 3852 Planarity : 0.004 0.056 4032 Dihedral : 4.114 32.994 3193 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.31 % Allowed : 15.29 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.10 (0.15), residues: 3033 helix: 0.45 (0.12), residues: 1710 sheet: -2.72 (0.21), residues: 486 loop : -1.68 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 708 HIS 0.002 0.001 HIS A 534 PHE 0.025 0.002 PHE C1015 TYR 0.016 0.002 TYR A 78 ARG 0.006 0.000 ARG B 724 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 366 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8273 (m) REVERT: A 370 ILE cc_start: 0.9206 (tp) cc_final: 0.8944 (tp) REVERT: A 426 SER cc_start: 0.8708 (m) cc_final: 0.8383 (p) REVERT: A 538 MET cc_start: 0.7994 (mmm) cc_final: 0.7650 (mmt) REVERT: A 539 MET cc_start: 0.8556 (tpp) cc_final: 0.8296 (mmm) REVERT: A 825 ASP cc_start: 0.6800 (m-30) cc_final: 0.6419 (m-30) REVERT: A 835 MET cc_start: 0.9279 (tpt) cc_final: 0.8825 (tpt) REVERT: B 68 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6767 (mm-30) REVERT: B 193 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8081 (mt) REVERT: B 527 MET cc_start: 0.7443 (ttt) cc_final: 0.7173 (mtp) REVERT: B 647 MET cc_start: 0.8276 (mmm) cc_final: 0.8002 (mmm) REVERT: B 745 MET cc_start: 0.6310 (mmm) cc_final: 0.6016 (mmm) REVERT: B 835 MET cc_start: 0.9226 (tpt) cc_final: 0.8640 (tpt) REVERT: B 1015 PHE cc_start: 0.8553 (m-10) cc_final: 0.8103 (m-80) REVERT: C 42 GLN cc_start: 0.8557 (mt0) cc_final: 0.8261 (mt0) REVERT: C 68 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6856 (mm-30) REVERT: C 101 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6849 (mm-30) REVERT: C 102 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7893 (tpp) REVERT: C 254 LYS cc_start: 0.7653 (tppt) cc_final: 0.7408 (tppt) REVERT: C 356 TYR cc_start: 0.7319 (t80) cc_final: 0.6642 (t80) REVERT: C 370 ILE cc_start: 0.9255 (tp) cc_final: 0.8985 (tp) REVERT: C 420 MET cc_start: 0.7511 (mtp) cc_final: 0.7200 (mtp) REVERT: C 538 MET cc_start: 0.8168 (mmm) cc_final: 0.7850 (mmt) REVERT: C 695 MET cc_start: 0.8436 (mpp) cc_final: 0.7931 (mpp) REVERT: C 745 MET cc_start: 0.6020 (mmm) cc_final: 0.5729 (mmm) REVERT: C 759 MET cc_start: 0.9000 (mmt) cc_final: 0.8760 (mmm) REVERT: C 839 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8673 (mt) REVERT: C 1015 PHE cc_start: 0.8632 (m-80) cc_final: 0.8241 (m-80) outliers start: 59 outliers final: 32 residues processed: 410 average time/residue: 0.3226 time to fit residues: 216.4038 Evaluate side-chains 358 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 322 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 152 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 275 optimal weight: 0.9990 chunk 297 optimal weight: 2.9990 chunk 245 optimal weight: 5.9990 chunk 273 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 GLN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23619 Z= 0.243 Angle : 0.549 7.180 32037 Z= 0.280 Chirality : 0.041 0.146 3852 Planarity : 0.004 0.055 4032 Dihedral : 3.907 16.959 3183 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.86 % Allowed : 16.20 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.26 (0.16), residues: 3033 helix: 1.08 (0.13), residues: 1716 sheet: -2.29 (0.21), residues: 510 loop : -1.25 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 708 HIS 0.002 0.001 HIS B 360 PHE 0.020 0.002 PHE B 824 TYR 0.015 0.001 TYR C 78 ARG 0.006 0.000 ARG B 724 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 365 time to evaluate : 2.600 Fit side-chains REVERT: A 26 SER cc_start: 0.9134 (t) cc_final: 0.8872 (p) REVERT: A 68 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6434 (mm-30) REVERT: A 370 ILE cc_start: 0.9227 (tp) cc_final: 0.8948 (tp) REVERT: A 426 SER cc_start: 0.8612 (m) cc_final: 0.8249 (p) REVERT: A 538 MET cc_start: 0.7937 (mmm) cc_final: 0.7599 (mmt) REVERT: A 824 PHE cc_start: 0.6405 (t80) cc_final: 0.6152 (t80) REVERT: A 883 TYR cc_start: 0.7291 (m-10) cc_final: 0.7051 (m-10) REVERT: B 68 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6911 (mm-30) REVERT: B 348 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7384 (tmm) REVERT: B 395 MET cc_start: 0.8614 (mmp) cc_final: 0.8055 (mmp) REVERT: B 527 MET cc_start: 0.7564 (ttt) cc_final: 0.7242 (ttp) REVERT: B 838 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8647 (mp) REVERT: B 839 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8746 (mp) REVERT: B 1015 PHE cc_start: 0.8561 (m-10) cc_final: 0.8171 (m-80) REVERT: C 26 SER cc_start: 0.9069 (t) cc_final: 0.8753 (p) REVERT: C 42 GLN cc_start: 0.8466 (mt0) cc_final: 0.8212 (mt0) REVERT: C 157 TYR cc_start: 0.8748 (t80) cc_final: 0.8467 (t80) REVERT: C 370 ILE cc_start: 0.9319 (tp) cc_final: 0.9022 (tp) REVERT: C 538 MET cc_start: 0.8156 (mmm) cc_final: 0.7809 (mmt) REVERT: C 691 GLN cc_start: 0.8459 (tt0) cc_final: 0.8096 (tt0) REVERT: C 695 MET cc_start: 0.8440 (mpp) cc_final: 0.7889 (mpp) REVERT: C 759 MET cc_start: 0.8970 (mmt) cc_final: 0.8760 (mmm) REVERT: C 825 ASP cc_start: 0.6640 (m-30) cc_final: 0.6353 (m-30) REVERT: C 839 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8707 (mt) REVERT: C 1015 PHE cc_start: 0.8595 (m-80) cc_final: 0.8115 (m-80) outliers start: 73 outliers final: 49 residues processed: 423 average time/residue: 0.3610 time to fit residues: 251.4245 Evaluate side-chains 370 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 317 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 942 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 272 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 143 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 292 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN A 805 GLN B 42 GLN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23619 Z= 0.223 Angle : 0.539 8.219 32037 Z= 0.273 Chirality : 0.041 0.160 3852 Planarity : 0.004 0.053 4032 Dihedral : 3.874 16.495 3183 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.98 % Allowed : 17.49 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.16), residues: 3033 helix: 1.37 (0.13), residues: 1710 sheet: -1.93 (0.23), residues: 489 loop : -0.98 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 512 HIS 0.002 0.001 HIS A 360 PHE 0.030 0.001 PHE B 824 TYR 0.011 0.001 TYR B 49 ARG 0.005 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 350 time to evaluate : 2.712 Fit side-chains REVERT: A 26 SER cc_start: 0.9111 (t) cc_final: 0.8839 (p) REVERT: A 91 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8280 (m) REVERT: A 370 ILE cc_start: 0.9259 (tp) cc_final: 0.8960 (tp) REVERT: A 405 ILE cc_start: 0.8535 (mt) cc_final: 0.8332 (mt) REVERT: A 426 SER cc_start: 0.8645 (m) cc_final: 0.8280 (p) REVERT: A 538 MET cc_start: 0.7907 (mmm) cc_final: 0.7593 (mmt) REVERT: A 592 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: A 839 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8651 (mp) REVERT: A 876 PHE cc_start: 0.8873 (t80) cc_final: 0.8483 (t80) REVERT: B 68 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6930 (mm-30) REVERT: B 348 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7378 (tmm) REVERT: B 363 ARG cc_start: 0.7910 (ttm110) cc_final: 0.7703 (mtt90) REVERT: B 527 MET cc_start: 0.7515 (ttt) cc_final: 0.7201 (ttp) REVERT: B 592 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7597 (tt0) REVERT: B 1015 PHE cc_start: 0.8542 (m-10) cc_final: 0.8187 (m-80) REVERT: C 26 SER cc_start: 0.9041 (t) cc_final: 0.8744 (p) REVERT: C 42 GLN cc_start: 0.8438 (mt0) cc_final: 0.8223 (mt0) REVERT: C 370 ILE cc_start: 0.9309 (tp) cc_final: 0.9009 (tp) REVERT: C 538 MET cc_start: 0.8114 (mmm) cc_final: 0.7813 (mmt) REVERT: C 592 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: C 695 MET cc_start: 0.8479 (tpp) cc_final: 0.7858 (mpp) REVERT: C 839 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8705 (mt) outliers start: 76 outliers final: 53 residues processed: 410 average time/residue: 0.3212 time to fit residues: 213.6327 Evaluate side-chains 386 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 326 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 691 GLN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 243 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 chunk 202 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 23619 Z= 0.303 Angle : 0.569 8.487 32037 Z= 0.287 Chirality : 0.042 0.177 3852 Planarity : 0.004 0.053 4032 Dihedral : 3.963 17.575 3183 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.69 % Allowed : 17.69 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.15 (0.16), residues: 3033 helix: 1.36 (0.13), residues: 1707 sheet: -2.09 (0.22), residues: 531 loop : -0.89 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 512 HIS 0.002 0.001 HIS B 360 PHE 0.035 0.002 PHE C1015 TYR 0.011 0.001 TYR C 883 ARG 0.006 0.000 ARG A 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 338 time to evaluate : 2.588 Fit side-chains REVERT: A 26 SER cc_start: 0.9079 (t) cc_final: 0.8833 (p) REVERT: A 363 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7419 (mtt90) REVERT: A 370 ILE cc_start: 0.9264 (tp) cc_final: 0.8970 (tp) REVERT: A 391 ASN cc_start: 0.8804 (p0) cc_final: 0.8603 (p0) REVERT: A 405 ILE cc_start: 0.8563 (mt) cc_final: 0.8347 (mt) REVERT: A 426 SER cc_start: 0.8641 (m) cc_final: 0.8277 (p) REVERT: A 538 MET cc_start: 0.7923 (mmm) cc_final: 0.7631 (mmt) REVERT: A 592 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: A 656 MET cc_start: 0.8267 (tpt) cc_final: 0.7998 (tpt) REVERT: A 839 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8625 (mp) REVERT: B 68 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6976 (mm-30) REVERT: B 348 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7331 (tmm) REVERT: B 363 ARG cc_start: 0.7965 (ttm110) cc_final: 0.7668 (mtt90) REVERT: B 391 ASN cc_start: 0.8806 (p0) cc_final: 0.8587 (p0) REVERT: B 527 MET cc_start: 0.7554 (ttt) cc_final: 0.7246 (ttp) REVERT: B 538 MET cc_start: 0.7755 (mmm) cc_final: 0.7483 (mmt) REVERT: B 592 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: B 839 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8790 (mp) REVERT: B 1015 PHE cc_start: 0.8521 (m-10) cc_final: 0.8196 (m-80) REVERT: C 26 SER cc_start: 0.9105 (t) cc_final: 0.8811 (p) REVERT: C 363 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7635 (mtt90) REVERT: C 370 ILE cc_start: 0.9339 (tp) cc_final: 0.9047 (tp) REVERT: C 538 MET cc_start: 0.8137 (mmm) cc_final: 0.7814 (mmt) REVERT: C 592 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: C 656 MET cc_start: 0.8327 (tpp) cc_final: 0.7999 (tpp) REVERT: C 695 MET cc_start: 0.8452 (tpp) cc_final: 0.7783 (mpp) REVERT: C 839 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8692 (mt) REVERT: C 1015 PHE cc_start: 0.8680 (m-80) cc_final: 0.8204 (m-80) outliers start: 94 outliers final: 66 residues processed: 412 average time/residue: 0.3219 time to fit residues: 215.6590 Evaluate side-chains 395 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 320 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 692 ASP Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 942 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 7.9990 chunk 263 optimal weight: 0.9990 chunk 57 optimal weight: 0.0370 chunk 171 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 293 optimal weight: 0.7980 chunk 243 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 23619 Z= 0.237 Angle : 0.547 9.398 32037 Z= 0.274 Chirality : 0.041 0.176 3852 Planarity : 0.004 0.053 4032 Dihedral : 3.922 16.399 3183 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.45 % Allowed : 18.55 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.39 (0.16), residues: 3033 helix: 1.51 (0.13), residues: 1701 sheet: -1.96 (0.22), residues: 525 loop : -0.71 (0.24), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 512 HIS 0.002 0.001 HIS C 360 PHE 0.039 0.002 PHE A1015 TYR 0.012 0.001 TYR A 883 ARG 0.006 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 337 time to evaluate : 2.648 Fit side-chains REVERT: A 26 SER cc_start: 0.9098 (t) cc_final: 0.8879 (p) REVERT: A 363 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7411 (mtt90) REVERT: A 370 ILE cc_start: 0.9306 (tp) cc_final: 0.8981 (tp) REVERT: A 391 ASN cc_start: 0.8769 (p0) cc_final: 0.8522 (p0) REVERT: A 405 ILE cc_start: 0.8552 (mt) cc_final: 0.8327 (mt) REVERT: A 426 SER cc_start: 0.8675 (m) cc_final: 0.8292 (p) REVERT: A 538 MET cc_start: 0.7876 (mmm) cc_final: 0.7410 (mmt) REVERT: A 541 ILE cc_start: 0.8970 (mt) cc_final: 0.8754 (tt) REVERT: A 592 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: A 656 MET cc_start: 0.8253 (tpt) cc_final: 0.7751 (tpt) REVERT: A 839 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8670 (mp) REVERT: A 876 PHE cc_start: 0.8848 (t80) cc_final: 0.8531 (t80) REVERT: B 26 SER cc_start: 0.9162 (t) cc_final: 0.8860 (p) REVERT: B 68 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6896 (mm-30) REVERT: B 348 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.6968 (mtt) REVERT: B 363 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7708 (mtt90) REVERT: B 391 ASN cc_start: 0.8770 (p0) cc_final: 0.8563 (p0) REVERT: B 527 MET cc_start: 0.7551 (ttt) cc_final: 0.7220 (ttp) REVERT: B 592 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: B 656 MET cc_start: 0.8395 (tpp) cc_final: 0.7688 (tpt) REVERT: B 839 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8795 (mp) REVERT: B 893 MET cc_start: 0.7167 (mmp) cc_final: 0.6942 (mtp) REVERT: B 1015 PHE cc_start: 0.8528 (m-10) cc_final: 0.8177 (m-80) REVERT: C 26 SER cc_start: 0.9069 (t) cc_final: 0.8788 (p) REVERT: C 363 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7684 (mtt90) REVERT: C 370 ILE cc_start: 0.9335 (tp) cc_final: 0.9051 (tp) REVERT: C 538 MET cc_start: 0.8055 (mmm) cc_final: 0.7790 (mmt) REVERT: C 592 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: C 656 MET cc_start: 0.8326 (tpp) cc_final: 0.8067 (tpp) REVERT: C 695 MET cc_start: 0.8408 (tpp) cc_final: 0.7650 (mpp) REVERT: C 839 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8713 (mt) REVERT: C 848 TYR cc_start: 0.8520 (p90) cc_final: 0.8243 (p90) REVERT: C 1015 PHE cc_start: 0.8627 (m-80) cc_final: 0.8065 (m-80) outliers start: 88 outliers final: 67 residues processed: 404 average time/residue: 0.3170 time to fit residues: 208.5782 Evaluate side-chains 398 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 321 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 942 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 246 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 292 optimal weight: 0.8980 chunk 182 optimal weight: 0.0010 chunk 178 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23619 Z= 0.167 Angle : 0.529 10.192 32037 Z= 0.264 Chirality : 0.040 0.210 3852 Planarity : 0.004 0.054 4032 Dihedral : 3.839 22.375 3183 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.53 % Allowed : 19.14 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.76 (0.16), residues: 3033 helix: 1.75 (0.13), residues: 1695 sheet: -1.41 (0.22), residues: 525 loop : -0.69 (0.24), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 512 HIS 0.001 0.000 HIS C 360 PHE 0.043 0.001 PHE A1015 TYR 0.013 0.001 TYR A 883 ARG 0.005 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 358 time to evaluate : 2.543 Fit side-chains REVERT: A 363 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7356 (mtt90) REVERT: A 370 ILE cc_start: 0.9293 (tp) cc_final: 0.8984 (tp) REVERT: A 391 ASN cc_start: 0.8783 (p0) cc_final: 0.8478 (p0) REVERT: A 393 LEU cc_start: 0.9197 (mt) cc_final: 0.8911 (mt) REVERT: A 426 SER cc_start: 0.8659 (m) cc_final: 0.8273 (p) REVERT: A 538 MET cc_start: 0.7782 (mmm) cc_final: 0.7469 (mmt) REVERT: A 592 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: B 26 SER cc_start: 0.9127 (t) cc_final: 0.8852 (p) REVERT: B 68 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6889 (mm-30) REVERT: B 240 LEU cc_start: 0.8876 (mt) cc_final: 0.8478 (mp) REVERT: B 348 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7007 (mtt) REVERT: B 363 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7707 (mtt90) REVERT: B 391 ASN cc_start: 0.8718 (p0) cc_final: 0.8491 (p0) REVERT: B 393 LEU cc_start: 0.9150 (mt) cc_final: 0.8817 (mt) REVERT: B 527 MET cc_start: 0.7589 (ttt) cc_final: 0.7252 (ttp) REVERT: B 592 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: B 839 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8760 (mp) REVERT: B 853 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.7998 (mt) REVERT: B 1015 PHE cc_start: 0.8504 (m-10) cc_final: 0.8156 (m-80) REVERT: C 26 SER cc_start: 0.9022 (t) cc_final: 0.8772 (p) REVERT: C 240 LEU cc_start: 0.8943 (mt) cc_final: 0.8682 (mp) REVERT: C 363 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7608 (mtt90) REVERT: C 370 ILE cc_start: 0.9314 (tp) cc_final: 0.9028 (tp) REVERT: C 393 LEU cc_start: 0.9198 (mt) cc_final: 0.8975 (mt) REVERT: C 656 MET cc_start: 0.8340 (tpp) cc_final: 0.8061 (tpp) REVERT: C 695 MET cc_start: 0.8473 (tpp) cc_final: 0.7748 (mpp) REVERT: C 839 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8685 (mt) REVERT: C 1015 PHE cc_start: 0.8540 (m-80) cc_final: 0.7894 (m-80) outliers start: 90 outliers final: 62 residues processed: 430 average time/residue: 0.3233 time to fit residues: 226.9073 Evaluate side-chains 399 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 328 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1020 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 180 optimal weight: 0.4980 chunk 116 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 198 optimal weight: 0.1980 chunk 144 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23619 Z= 0.177 Angle : 0.538 10.255 32037 Z= 0.268 Chirality : 0.041 0.238 3852 Planarity : 0.004 0.053 4032 Dihedral : 3.818 22.549 3183 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.94 % Allowed : 20.16 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.80 (0.16), residues: 3033 helix: 1.79 (0.13), residues: 1695 sheet: -1.52 (0.21), residues: 567 loop : -0.53 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 512 HIS 0.001 0.000 HIS A 360 PHE 0.043 0.001 PHE A1015 TYR 0.017 0.001 TYR B 848 ARG 0.008 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 346 time to evaluate : 2.476 Fit side-chains REVERT: A 363 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7424 (mtt90) REVERT: A 370 ILE cc_start: 0.9300 (tp) cc_final: 0.8979 (tp) REVERT: A 391 ASN cc_start: 0.8774 (p0) cc_final: 0.8454 (p0) REVERT: A 393 LEU cc_start: 0.9203 (mt) cc_final: 0.8893 (mt) REVERT: A 426 SER cc_start: 0.8635 (m) cc_final: 0.8272 (p) REVERT: A 538 MET cc_start: 0.7850 (mmm) cc_final: 0.7589 (mmt) REVERT: A 592 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: B 26 SER cc_start: 0.9109 (t) cc_final: 0.8855 (p) REVERT: B 68 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6975 (mm-30) REVERT: B 240 LEU cc_start: 0.8894 (mt) cc_final: 0.8496 (mp) REVERT: B 348 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7013 (mtt) REVERT: B 363 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7660 (mtt90) REVERT: B 391 ASN cc_start: 0.8742 (p0) cc_final: 0.8512 (p0) REVERT: B 393 LEU cc_start: 0.9146 (mt) cc_final: 0.8807 (mt) REVERT: B 592 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: B 839 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8796 (mp) REVERT: B 853 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8030 (mt) REVERT: B 1015 PHE cc_start: 0.8501 (m-10) cc_final: 0.8182 (m-80) REVERT: C 26 SER cc_start: 0.9013 (t) cc_final: 0.8745 (p) REVERT: C 240 LEU cc_start: 0.8965 (mt) cc_final: 0.8701 (mp) REVERT: C 363 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7629 (mtt90) REVERT: C 370 ILE cc_start: 0.9319 (tp) cc_final: 0.9027 (tp) REVERT: C 393 LEU cc_start: 0.9210 (mt) cc_final: 0.8988 (mt) REVERT: C 656 MET cc_start: 0.8343 (tpp) cc_final: 0.8119 (tpp) REVERT: C 695 MET cc_start: 0.8430 (tpp) cc_final: 0.7753 (mpp) REVERT: C 839 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8695 (mt) REVERT: C 909 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8477 (m) REVERT: C 1015 PHE cc_start: 0.8570 (m-80) cc_final: 0.7939 (m-80) outliers start: 75 outliers final: 61 residues processed: 407 average time/residue: 0.3213 time to fit residues: 212.8496 Evaluate side-chains 399 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 328 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1020 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 272 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 245 optimal weight: 7.9990 chunk 257 optimal weight: 0.9980 chunk 271 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23619 Z= 0.232 Angle : 0.562 10.473 32037 Z= 0.279 Chirality : 0.041 0.196 3852 Planarity : 0.004 0.051 4032 Dihedral : 3.879 21.986 3183 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.18 % Allowed : 20.24 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.73 (0.16), residues: 3033 helix: 1.73 (0.13), residues: 1698 sheet: -1.55 (0.21), residues: 573 loop : -0.53 (0.25), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 512 HIS 0.002 0.001 HIS A 360 PHE 0.042 0.002 PHE A1015 TYR 0.014 0.001 TYR B 848 ARG 0.008 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 335 time to evaluate : 2.811 Fit side-chains REVERT: A 26 SER cc_start: 0.9043 (t) cc_final: 0.8674 (p) REVERT: A 101 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6451 (mm-30) REVERT: A 363 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7340 (mtt90) REVERT: A 370 ILE cc_start: 0.9308 (tp) cc_final: 0.9003 (tp) REVERT: A 391 ASN cc_start: 0.8777 (p0) cc_final: 0.8479 (p0) REVERT: A 393 LEU cc_start: 0.9255 (mt) cc_final: 0.8949 (mt) REVERT: A 426 SER cc_start: 0.8499 (m) cc_final: 0.8253 (p) REVERT: A 538 MET cc_start: 0.7901 (mmm) cc_final: 0.7565 (mmt) REVERT: A 539 MET cc_start: 0.8394 (mmm) cc_final: 0.8158 (tpp) REVERT: A 592 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: B 26 SER cc_start: 0.9121 (t) cc_final: 0.8876 (p) REVERT: B 68 GLU cc_start: 0.7220 (mm-30) cc_final: 0.7005 (mm-30) REVERT: B 83 ASP cc_start: 0.7742 (p0) cc_final: 0.7507 (p0) REVERT: B 348 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7002 (mtt) REVERT: B 363 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7700 (mtt90) REVERT: B 391 ASN cc_start: 0.8733 (p0) cc_final: 0.8518 (p0) REVERT: B 592 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: B 838 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8739 (mp) REVERT: B 839 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8763 (mp) REVERT: B 1015 PHE cc_start: 0.8513 (m-10) cc_final: 0.8175 (m-80) REVERT: C 26 SER cc_start: 0.9072 (t) cc_final: 0.8806 (p) REVERT: C 363 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7653 (mtt90) REVERT: C 370 ILE cc_start: 0.9298 (tp) cc_final: 0.9027 (tp) REVERT: C 391 ASN cc_start: 0.8598 (p0) cc_final: 0.8240 (p0) REVERT: C 656 MET cc_start: 0.8305 (tpp) cc_final: 0.7828 (tpt) REVERT: C 695 MET cc_start: 0.8472 (tpp) cc_final: 0.7794 (mpp) REVERT: C 839 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8687 (mt) REVERT: C 1015 PHE cc_start: 0.8561 (m-80) cc_final: 0.7905 (m-80) outliers start: 81 outliers final: 67 residues processed: 401 average time/residue: 0.3347 time to fit residues: 218.8339 Evaluate side-chains 406 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 330 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 942 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 178 optimal weight: 5.9990 chunk 287 optimal weight: 0.1980 chunk 175 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 277 optimal weight: 0.7980 chunk 240 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23619 Z= 0.211 Angle : 0.552 11.199 32037 Z= 0.274 Chirality : 0.041 0.181 3852 Planarity : 0.004 0.052 4032 Dihedral : 3.865 21.927 3183 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.98 % Allowed : 20.39 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.85 (0.16), residues: 3033 helix: 1.79 (0.13), residues: 1698 sheet: -1.45 (0.21), residues: 567 loop : -0.45 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 512 HIS 0.002 0.001 HIS A 360 PHE 0.042 0.001 PHE A1015 TYR 0.016 0.001 TYR A 705 ARG 0.009 0.000 ARG B 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 334 time to evaluate : 2.564 Fit side-chains REVERT: A 26 SER cc_start: 0.9076 (t) cc_final: 0.8723 (p) REVERT: A 101 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6402 (mm-30) REVERT: A 363 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7342 (mtt90) REVERT: A 370 ILE cc_start: 0.9330 (tp) cc_final: 0.9017 (tp) REVERT: A 391 ASN cc_start: 0.8770 (p0) cc_final: 0.8489 (p0) REVERT: A 393 LEU cc_start: 0.9250 (mt) cc_final: 0.8939 (mt) REVERT: A 426 SER cc_start: 0.8501 (m) cc_final: 0.8253 (p) REVERT: A 538 MET cc_start: 0.7880 (mmm) cc_final: 0.7581 (mmt) REVERT: A 539 MET cc_start: 0.8418 (mmm) cc_final: 0.8172 (tpp) REVERT: A 592 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: A 824 PHE cc_start: 0.6760 (t80) cc_final: 0.6302 (t80) REVERT: B 83 ASP cc_start: 0.7701 (p0) cc_final: 0.7469 (p0) REVERT: B 348 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7043 (mtt) REVERT: B 363 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7789 (mtt90) REVERT: B 391 ASN cc_start: 0.8693 (p0) cc_final: 0.8478 (p0) REVERT: B 592 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: B 838 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8739 (mp) REVERT: B 839 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8761 (mp) REVERT: B 1015 PHE cc_start: 0.8529 (m-10) cc_final: 0.8184 (m-80) REVERT: C 26 SER cc_start: 0.9078 (t) cc_final: 0.8820 (p) REVERT: C 363 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7534 (mtt90) REVERT: C 367 ILE cc_start: 0.9224 (mt) cc_final: 0.8980 (mm) REVERT: C 370 ILE cc_start: 0.9313 (tp) cc_final: 0.9079 (tp) REVERT: C 391 ASN cc_start: 0.8574 (p0) cc_final: 0.8227 (p0) REVERT: C 393 LEU cc_start: 0.9226 (mt) cc_final: 0.8924 (mt) REVERT: C 656 MET cc_start: 0.8319 (tpp) cc_final: 0.7821 (tpt) REVERT: C 695 MET cc_start: 0.8498 (tpp) cc_final: 0.7779 (mpp) REVERT: C 839 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8690 (mt) REVERT: C 848 TYR cc_start: 0.8411 (p90) cc_final: 0.8121 (p90) REVERT: C 1015 PHE cc_start: 0.8541 (m-80) cc_final: 0.7849 (m-80) outliers start: 76 outliers final: 64 residues processed: 397 average time/residue: 0.3222 time to fit residues: 207.5354 Evaluate side-chains 402 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 329 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 942 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 5.9990 chunk 256 optimal weight: 0.0970 chunk 73 optimal weight: 0.8980 chunk 221 optimal weight: 0.4980 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 240 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.105788 restraints weight = 32388.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.108675 restraints weight = 20476.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.109819 restraints weight = 12622.049| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 23619 Z= 0.158 Angle : 0.540 11.231 32037 Z= 0.267 Chirality : 0.040 0.176 3852 Planarity : 0.004 0.053 4032 Dihedral : 3.786 23.509 3183 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.55 % Allowed : 20.94 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.11 (0.16), residues: 3033 helix: 1.93 (0.13), residues: 1695 sheet: -1.12 (0.22), residues: 525 loop : -0.41 (0.25), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 512 HIS 0.001 0.000 HIS A 360 PHE 0.035 0.001 PHE B 824 TYR 0.018 0.001 TYR C 705 ARG 0.007 0.000 ARG B 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4745.98 seconds wall clock time: 87 minutes 54.53 seconds (5274.53 seconds total)