Starting phenix.real_space_refine on Sun Mar 17 06:30:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8c_34542/03_2024/8h8c_34542.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8c_34542/03_2024/8h8c_34542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8c_34542/03_2024/8h8c_34542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8c_34542/03_2024/8h8c_34542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8c_34542/03_2024/8h8c_34542.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8c_34542/03_2024/8h8c_34542.pdb" } resolution = 3.36 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= 0.006 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 24 5.16 5 C 10662 2.51 5 N 2938 2.21 5 O 3316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 161": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 209": "OD1" <-> "OD2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B ARG 564": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B GLU 611": "OE1" <-> "OE2" Residue "B GLU 736": "OE1" <-> "OE2" Residue "B ARG 746": "NH1" <-> "NH2" Residue "B ARG 770": "NH1" <-> "NH2" Residue "B GLU 776": "OE1" <-> "OE2" Residue "B GLU 779": "OE1" <-> "OE2" Residue "B ARG 783": "NH1" <-> "NH2" Residue "B ARG 787": "NH1" <-> "NH2" Residue "B GLU 837": "OE1" <-> "OE2" Residue "B ARG 840": "NH1" <-> "NH2" Residue "B GLU 841": "OE1" <-> "OE2" Residue "B ARG 859": "NH1" <-> "NH2" Residue "B GLU 905": "OE1" <-> "OE2" Residue "B ARG 931": "NH1" <-> "NH2" Residue "B ARG 943": "NH1" <-> "NH2" Residue "B ARG 952": "NH1" <-> "NH2" Residue "B GLU 962": "OE1" <-> "OE2" Residue "B GLU 973": "OE1" <-> "OE2" Residue "B ARG 980": "NH1" <-> "NH2" Residue "B ARG 1009": "NH1" <-> "NH2" Residue "B ARG 1042": "NH1" <-> "NH2" Residue "B GLU 1067": "OE1" <-> "OE2" Residue "B ARG 1070": "NH1" <-> "NH2" Residue "B ARG 1074": "NH1" <-> "NH2" Residue "B GLU 1083": "OE1" <-> "OE2" Residue "B ARG 1100": "NH1" <-> "NH2" Residue "C GLU 1146": "OE1" <-> "OE2" Residue "C GLU 1156": "OE1" <-> "OE2" Residue "C GLU 1163": "OE1" <-> "OE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A ARG 770": "NH1" <-> "NH2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ARG 783": "NH1" <-> "NH2" Residue "A ARG 787": "NH1" <-> "NH2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A GLU 837": "OE1" <-> "OE2" Residue "A ARG 840": "NH1" <-> "NH2" Residue "A GLU 841": "OE1" <-> "OE2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A GLU 860": "OE1" <-> "OE2" Residue "A GLU 897": "OE1" <-> "OE2" Residue "A ARG 931": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A ARG 980": "NH1" <-> "NH2" Residue "A GLU 991": "OE1" <-> "OE2" Residue "A ARG 1009": "NH1" <-> "NH2" Residue "A ARG 1042": "NH1" <-> "NH2" Residue "A GLU 1068": "OE1" <-> "OE2" Residue "A ARG 1070": "NH1" <-> "NH2" Residue "A ARG 1074": "NH1" <-> "NH2" Residue "A ARG 1100": "NH1" <-> "NH2" Residue "D GLU 1135": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16940 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 7860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7860 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 22, 'TRANS': 941} Chain breaks: 1 Chain: "C" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain breaks: 1 Chain: "A" Number of atoms: 7860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7860 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 22, 'TRANS': 941} Chain breaks: 1 Chain: "D" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain breaks: 1 Time building chain proxies: 8.94, per 1000 atoms: 0.53 Number of scatterers: 16940 At special positions: 0 Unit cell: (93.09, 118.32, 140.07, 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 24 16.00 O 3316 8.00 N 2938 7.00 C 10662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.46 Conformation dependent library (CDL) restraints added in 3.0 seconds 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3812 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 36 sheets defined 2.0% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'C' and resid 1139 through 1148 removed outlier: 3.751A pdb=" N ALA C1145 " --> pdb=" O GLN C1141 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C1148 " --> pdb=" O LEU C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1154 through 1162 removed outlier: 4.596A pdb=" N GLN C1160 " --> pdb=" O GLU C1156 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C1161 " --> pdb=" O VAL C1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1166 removed outlier: 4.103A pdb=" N LYS C1166 " --> pdb=" O GLU C1163 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1163 through 1166' Processing helix chain 'D' and resid 1139 through 1148 removed outlier: 3.514A pdb=" N ALA D1145 " --> pdb=" O GLN D1141 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU D1146 " --> pdb=" O GLN D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1154 through 1162 removed outlier: 4.333A pdb=" N GLN D1160 " --> pdb=" O GLU D1156 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE D1161 " --> pdb=" O VAL D1157 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D1162 " --> pdb=" O CYS D1158 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 165 through 170 removed outlier: 7.164A pdb=" N TRP B 177 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 268 through 270 removed outlier: 3.755A pdb=" N LEU B 275 " --> pdb=" O VAL B 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 288 through 291 removed outlier: 6.590A pdb=" N GLN B 288 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B 300 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG B 290 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE B 298 " --> pdb=" O CYS B 310 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 320 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 321 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 331 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 334 through 335 removed outlier: 6.657A pdb=" N ILE B 334 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 356 removed outlier: 7.022A pdb=" N GLU B 355 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA B 363 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 390 " --> pdb=" O TYR B 374 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 376 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ARG B 388 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 399 through 402 removed outlier: 3.601A pdb=" N GLU B 429 " --> pdb=" O ILE B 420 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 439 through 442 removed outlier: 3.556A pdb=" N GLN B 439 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLU B 449 " --> pdb=" O TYR B 461 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASN B 464 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 469 " --> pdb=" O ASN B 464 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 514 through 515 removed outlier: 5.687A pdb=" N VAL B 533 " --> pdb=" O TRP B 545 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG B 544 " --> pdb=" O HIS B 556 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HIS B 556 " --> pdb=" O ARG B 544 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP B 546 " --> pdb=" O VAL B 554 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL B 554 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG B 564 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 576 " --> pdb=" O ARG B 564 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER B 566 " --> pdb=" O ASN B 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 584 through 587 removed outlier: 4.066A pdb=" N ILE B 597 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR B 599 " --> pdb=" O TYR B 608 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR B 608 " --> pdb=" O TYR B 599 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 622 " --> pdb=" O ALA B 613 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ALA B 621 " --> pdb=" O TYR B 632 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.905A pdb=" N GLU B 654 " --> pdb=" O THR B 662 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 673 through 676 removed outlier: 6.627A pdb=" N GLU B 673 " --> pdb=" O THR B 685 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR B 685 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TRP B 675 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 696 through 697 removed outlier: 7.295A pdb=" N LYS B 696 " --> pdb=" O ILE B 704 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 715 through 717 removed outlier: 7.422A pdb=" N SER B 716 " --> pdb=" O GLN B 724 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 724 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN B 724 " --> pdb=" O PHE B 739 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 726 " --> pdb=" O ASN B 737 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS B 738 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 751 " --> pdb=" O HIS B 738 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 778 through 781 removed outlier: 3.806A pdb=" N GLU B 780 " --> pdb=" O SER B 789 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N SER B 789 " --> pdb=" O GLU B 780 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL B 788 " --> pdb=" O PHE B 800 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE B 800 " --> pdb=" O VAL B 788 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN B 790 " --> pdb=" O PHE B 798 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASP B 803 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 808 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ARG B 807 " --> pdb=" O TYR B 825 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N TYR B 825 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N SER B 809 " --> pdb=" O PHE B 823 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU B 822 " --> pdb=" O THR B 834 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 834 " --> pdb=" O GLU B 822 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLN B 824 " --> pdb=" O SER B 832 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER B 832 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 853 " --> pdb=" O LEU B 844 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL B 852 " --> pdb=" O TYR B 863 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N SER B 872 " --> pdb=" O TYR B 884 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 895 " --> pdb=" O SER B 902 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 926 through 927 removed outlier: 3.532A pdb=" N LYS B 942 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL B 941 " --> pdb=" O ARG B 952 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 943 " --> pdb=" O GLN B 950 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 950 " --> pdb=" O ARG B 943 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 962 " --> pdb=" O VAL B 953 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 971 through 974 removed outlier: 6.045A pdb=" N THR B 981 " --> pdb=" O PHE B 992 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 992 " --> pdb=" O THR B 981 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 983 " --> pdb=" O THR B 990 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR B 990 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLU B 995 " --> pdb=" O LEU B 999 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 999 " --> pdb=" O GLU B 995 " (cutoff:3.500A) removed outlier: 11.029A pdb=" N ARG B 998 " --> pdb=" O TYR B1013 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N TYR B1013 " --> pdb=" O ARG B 998 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU B1000 " --> pdb=" O TYR B1011 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B1021 " --> pdb=" O TYR B1032 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B1042 " --> pdb=" O GLU B1033 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP B1045 " --> pdb=" O ILE B1050 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE B1050 " --> pdb=" O ASP B1045 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1087 through 1088 Processing sheet with id=AB9, first strand: chain 'B' and resid 1125 through 1126 removed outlier: 3.598A pdb=" N ILE B1126 " --> pdb=" O ASN C1188 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN C1188 " --> pdb=" O ILE B1126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 166 through 170 removed outlier: 7.077A pdb=" N TRP A 177 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 268 through 270 removed outlier: 3.853A pdb=" N LEU A 275 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 288 through 291 removed outlier: 7.783A pdb=" N ILE A 298 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU A 309 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 354 through 356 removed outlier: 7.188A pdb=" N GLU A 355 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.806A pdb=" N GLU A 376 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 399 through 403 removed outlier: 3.539A pdb=" N THR A 418 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU A 428 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 450 " --> pdb=" O HIS A 441 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU A 449 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASN A 464 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 469 " --> pdb=" O ASN A 464 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 492 through 494 Processing sheet with id=AC8, first strand: chain 'A' and resid 514 through 515 removed outlier: 5.486A pdb=" N VAL A 533 " --> pdb=" O TRP A 545 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL A 554 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS A 556 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 575 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN A 574 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 586 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR A 599 " --> pdb=" O TYR A 608 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR A 608 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 611 " --> pdb=" O GLN A 624 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 622 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA A 621 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 642 " --> pdb=" O GLN A 633 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.663A pdb=" N GLU A 654 " --> pdb=" O THR A 662 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 673 through 676 removed outlier: 4.657A pdb=" N GLY A 684 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 696 through 697 removed outlier: 3.904A pdb=" N ARG A 705 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 725 through 726 removed outlier: 3.612A pdb=" N ASN A 737 " --> pdb=" O ILE A 726 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AD5, first strand: chain 'A' and resid 780 through 781 removed outlier: 3.797A pdb=" N GLU A 780 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 791 through 792 removed outlier: 3.543A pdb=" N THR A 796 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N SER A 809 " --> pdb=" O PHE A 823 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 823 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER A 832 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 844 " --> pdb=" O GLU A 853 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 853 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL A 852 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER A 872 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 926 through 927 removed outlier: 6.640A pdb=" N ARG A 931 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG A 943 " --> pdb=" O ARG A 931 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS A 933 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL A 941 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU A 962 " --> pdb=" O VAL A 953 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 971 through 973 removed outlier: 3.539A pdb=" N LYS A 982 " --> pdb=" O GLU A 973 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU A1000 " --> pdb=" O TYR A1011 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A1021 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A1042 " --> pdb=" O GLU A1033 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL A1066 " --> pdb=" O SER A1053 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 3.674A pdb=" N ILE A1126 " --> pdb=" O ASN D1188 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN D1188 " --> pdb=" O ILE A1126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 332 hydrogen bonds defined for protein. 897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.82 Time building geometry restraints manager: 6.02 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: 5682 1.34 - 1.46: 3863 1.46 - 1.58: 7765 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 17342 Sorted by residual: bond pdb=" CA THR B 208 " pdb=" CB THR B 208 " ideal model delta sigma weight residual 1.530 1.542 -0.011 9.80e-03 1.04e+04 1.36e+00 bond pdb=" CA PHE B 202 " pdb=" C PHE B 202 " ideal model delta sigma weight residual 1.531 1.516 0.015 1.46e-02 4.69e+03 1.12e+00 bond pdb=" C SER A 216 " pdb=" O SER A 216 " ideal model delta sigma weight residual 1.236 1.225 0.012 1.15e-02 7.56e+03 1.02e+00 bond pdb=" C ASP A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 1.340 1.368 -0.028 2.76e-02 1.31e+03 1.01e+00 bond pdb=" C ALA A 577 " pdb=" N TYR A 578 " ideal model delta sigma weight residual 1.333 1.360 -0.027 2.74e-02 1.33e+03 9.96e-01 ... (remaining 17337 not shown) Histogram of bond angle deviations from ideal: 100.84 - 107.47: 443 107.47 - 114.10: 9263 114.10 - 120.72: 6835 120.72 - 127.35: 6747 127.35 - 133.98: 174 Bond angle restraints: 23462 Sorted by residual: angle pdb=" N VAL A 241 " pdb=" CA VAL A 241 " pdb=" C VAL A 241 " ideal model delta sigma weight residual 110.53 115.21 -4.68 9.40e-01 1.13e+00 2.48e+01 angle pdb=" C GLU A 210 " pdb=" CA GLU A 210 " pdb=" CB GLU A 210 " ideal model delta sigma weight residual 115.89 109.32 6.57 1.32e+00 5.74e-01 2.48e+01 angle pdb=" C VAL A 241 " pdb=" CA VAL A 241 " pdb=" CB VAL A 241 " ideal model delta sigma weight residual 112.02 107.97 4.05 1.31e+00 5.83e-01 9.54e+00 angle pdb=" N ILE B 480 " pdb=" CA ILE B 480 " pdb=" C ILE B 480 " ideal model delta sigma weight residual 111.81 109.19 2.62 8.60e-01 1.35e+00 9.29e+00 angle pdb=" N HIS A 212 " pdb=" CA HIS A 212 " pdb=" C HIS A 212 " ideal model delta sigma weight residual 111.54 107.58 3.96 1.36e+00 5.41e-01 8.48e+00 ... (remaining 23457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9280 17.70 - 35.39: 693 35.39 - 53.09: 131 53.09 - 70.79: 34 70.79 - 88.48: 14 Dihedral angle restraints: 10152 sinusoidal: 4122 harmonic: 6030 Sorted by residual: dihedral pdb=" CB GLU A 538 " pdb=" CG GLU A 538 " pdb=" CD GLU A 538 " pdb=" OE1 GLU A 538 " ideal model delta sinusoidal sigma weight residual 0.00 88.48 -88.48 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU A 355 " pdb=" CG GLU A 355 " pdb=" CD GLU A 355 " pdb=" OE1 GLU A 355 " ideal model delta sinusoidal sigma weight residual 0.00 87.74 -87.74 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU B 149 " pdb=" CG GLU B 149 " pdb=" CD GLU B 149 " pdb=" OE1 GLU B 149 " ideal model delta sinusoidal sigma weight residual 0.00 -86.99 86.99 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 10149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1474 0.027 - 0.054: 612 0.054 - 0.082: 131 0.082 - 0.109: 138 0.109 - 0.136: 47 Chirality restraints: 2402 Sorted by residual: chirality pdb=" CA ILE B 256 " pdb=" N ILE B 256 " pdb=" C ILE B 256 " pdb=" CB ILE B 256 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CB THR B 836 " pdb=" CA THR B 836 " pdb=" OG1 THR B 836 " pdb=" CG2 THR B 836 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA VAL A 342 " pdb=" N VAL A 342 " pdb=" C VAL A 342 " pdb=" CB VAL A 342 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 2399 not shown) Planarity restraints: 3092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 153 " -0.026 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 154 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 453 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.30e+00 pdb=" N PRO A 454 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 454 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 454 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 625 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 626 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 626 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 626 " 0.020 5.00e-02 4.00e+02 ... (remaining 3089 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2146 2.76 - 3.29: 14611 3.29 - 3.83: 26232 3.83 - 4.36: 30263 4.36 - 4.90: 55006 Nonbonded interactions: 128258 Sorted by model distance: nonbonded pdb=" OD2 ASP A 656 " pdb=" OG1 THR A 662 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR A 742 " pdb=" O GLY A 745 " model vdw 2.267 2.440 nonbonded pdb=" OG1 THR B 742 " pdb=" O GLY B 745 " model vdw 2.287 2.440 nonbonded pdb=" OE2 GLU B1002 " pdb=" OH TYR B1011 " model vdw 2.291 2.440 nonbonded pdb=" OG SER A1055 " pdb=" OG SER A1063 " model vdw 2.293 2.440 ... (remaining 128253 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' } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.440 Check model and map are aligned: 0.280 Set scattering table: 0.140 Process input model: 44.810 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 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 : 0.002 0.028 17342 Z= 0.106 Angle : 0.470 9.051 23462 Z= 0.288 Chirality : 0.039 0.136 2402 Planarity : 0.003 0.040 3092 Dihedral : 13.151 88.482 6340 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 1.83 % Allowed : 9.47 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.15), residues: 2062 helix: -5.11 (0.20), residues: 44 sheet: -1.28 (0.33), residues: 248 loop : -3.19 (0.12), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 417 HIS 0.002 0.000 HIS A 248 PHE 0.004 0.000 PHE B 823 TYR 0.008 0.000 TYR A 409 ARG 0.001 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 370 time to evaluate : 1.766 Fit side-chains REVERT: B 591 TYR cc_start: 0.6106 (m-80) cc_final: 0.5747 (m-80) REVERT: B 608 TYR cc_start: 0.7324 (t80) cc_final: 0.7116 (t80) REVERT: B 700 MET cc_start: 0.7388 (tpt) cc_final: 0.7060 (tpt) REVERT: B 973 GLU cc_start: 0.5489 (mt-10) cc_final: 0.5285 (mt-10) REVERT: B 1011 TYR cc_start: 0.8145 (m-80) cc_final: 0.7845 (m-80) REVERT: B 1086 LEU cc_start: 0.6016 (mt) cc_final: 0.5584 (mt) REVERT: A 290 ARG cc_start: 0.5837 (ttt180) cc_final: 0.5622 (tmt170) REVERT: A 353 ARG cc_start: 0.7041 (mmt90) cc_final: 0.6796 (mmt-90) REVERT: A 460 GLN cc_start: 0.7356 (tt0) cc_final: 0.6968 (tt0) REVERT: A 727 LYS cc_start: 0.7128 (ttmt) cc_final: 0.6657 (tmtt) REVERT: A 1024 LEU cc_start: 0.5745 (mt) cc_final: 0.5535 (tp) REVERT: A 1068 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6867 (tm-30) REVERT: D 1173 ASP cc_start: 0.7457 (m-30) cc_final: 0.7021 (m-30) outliers start: 33 outliers final: 21 residues processed: 399 average time/residue: 0.3150 time to fit residues: 182.0549 Evaluate side-chains 249 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 228 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.4980 chunk 156 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 ASN B 198 HIS B 278 GLN B 294 ASN B 373 HIS B 510 GLN B 551 GLN B 585 GLN ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 HIS B 724 GLN B 733 ASN B 738 HIS B 755 GLN B 772 GLN B 869 ASN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 HIS B1071 ASN B1089 ASN B1121 ASN C1213 ASN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN A 251 ASN A 303 ASN A 373 HIS A 421 HIS A 510 GLN A 550 GLN A 574 ASN A 585 GLN A 640 GLN A 658 GLN A 692 HIS A 725 HIS A 738 HIS A 740 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 GLN A 786 GLN A 855 GLN A 940 GLN A1026 ASN A1078 GLN A1089 ASN D1148 GLN D1160 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17342 Z= 0.365 Angle : 0.709 14.123 23462 Z= 0.374 Chirality : 0.046 0.166 2402 Planarity : 0.005 0.052 3092 Dihedral : 5.576 55.808 2373 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.31 % Favored : 85.50 % Rotamer: Outliers : 4.37 % Allowed : 17.39 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.15), residues: 2062 helix: -4.18 (0.50), residues: 44 sheet: -0.73 (0.29), residues: 324 loop : -3.31 (0.11), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 274 HIS 0.009 0.002 HIS A 421 PHE 0.017 0.002 PHE B1131 TYR 0.027 0.002 TYR A1079 ARG 0.005 0.001 ARG A 830 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 229 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 PHE cc_start: 0.6438 (t80) cc_final: 0.6235 (t80) REVERT: B 263 ASP cc_start: 0.6704 (t70) cc_final: 0.6381 (p0) REVERT: B 290 ARG cc_start: 0.6850 (ttp-170) cc_final: 0.6403 (ttm-80) REVERT: B 355 GLU cc_start: 0.6778 (tp30) cc_final: 0.6526 (tp30) REVERT: B 409 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7459 (p90) REVERT: B 460 GLN cc_start: 0.7304 (mt0) cc_final: 0.7036 (mt0) REVERT: B 831 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8309 (tp) REVERT: B 886 TYR cc_start: 0.7975 (m-80) cc_final: 0.7728 (m-80) REVERT: A 153 ASP cc_start: 0.0602 (OUTLIER) cc_final: -0.1542 (t70) REVERT: A 215 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7679 (p) REVERT: A 240 GLN cc_start: 0.5651 (OUTLIER) cc_final: 0.5371 (tt0) REVERT: A 290 ARG cc_start: 0.6350 (ttt180) cc_final: 0.5976 (tpt-90) REVERT: A 353 ARG cc_start: 0.7168 (mmt90) cc_final: 0.6855 (mmt90) REVERT: A 397 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: A 408 SER cc_start: 0.7169 (p) cc_final: 0.6937 (m) REVERT: A 586 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8431 (mm) REVERT: A 611 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7215 (mt-10) REVERT: A 1024 LEU cc_start: 0.6432 (mt) cc_final: 0.5838 (tp) REVERT: D 1148 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7724 (mm-40) REVERT: D 1180 LYS cc_start: 0.6855 (pttt) cc_final: 0.6569 (ptpt) REVERT: D 1212 ILE cc_start: 0.5072 (OUTLIER) cc_final: 0.4598 (pt) outliers start: 79 outliers final: 48 residues processed: 294 average time/residue: 0.2991 time to fit residues: 131.3247 Evaluate side-chains 255 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 199 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1049 ASN Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1179 VAL Chi-restraints excluded: chain D residue 1207 THR Chi-restraints excluded: chain D residue 1212 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 187 optimal weight: 0.6980 chunk 202 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS B 639 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN A1026 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17342 Z= 0.211 Angle : 0.567 13.693 23462 Z= 0.299 Chirality : 0.043 0.154 2402 Planarity : 0.004 0.051 3092 Dihedral : 4.861 45.614 2367 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 4.32 % Allowed : 19.60 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.15), residues: 2062 helix: -3.85 (0.56), residues: 44 sheet: -0.52 (0.31), residues: 306 loop : -3.12 (0.12), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 177 HIS 0.014 0.001 HIS B 198 PHE 0.016 0.001 PHE A 202 TYR 0.019 0.001 TYR D1214 ARG 0.005 0.000 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 212 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 249 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.6197 (t80) REVERT: B 263 ASP cc_start: 0.6751 (t70) cc_final: 0.6387 (p0) REVERT: B 290 ARG cc_start: 0.6739 (ttp-170) cc_final: 0.6291 (ttm-80) REVERT: B 355 GLU cc_start: 0.6798 (tp30) cc_final: 0.6533 (tp30) REVERT: B 409 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.7161 (p90) REVERT: B 460 GLN cc_start: 0.7314 (mt0) cc_final: 0.7065 (mt0) REVERT: A 153 ASP cc_start: 0.0682 (OUTLIER) cc_final: 0.0473 (p0) REVERT: A 288 GLN cc_start: 0.5786 (mp10) cc_final: 0.5499 (mp10) REVERT: A 290 ARG cc_start: 0.6407 (ttt180) cc_final: 0.5868 (tpt-90) REVERT: A 353 ARG cc_start: 0.7129 (mmt90) cc_final: 0.6789 (mmt90) REVERT: A 397 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: A 401 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.7146 (t-90) REVERT: A 445 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6545 (tt) REVERT: A 586 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8344 (mm) REVERT: A 611 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7187 (mt-10) REVERT: D 1148 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7615 (mm-40) REVERT: D 1173 ASP cc_start: 0.7928 (m-30) cc_final: 0.7561 (m-30) REVERT: D 1180 LYS cc_start: 0.6773 (pttt) cc_final: 0.6342 (ptpt) REVERT: D 1212 ILE cc_start: 0.4980 (OUTLIER) cc_final: 0.4634 (pt) outliers start: 78 outliers final: 54 residues processed: 276 average time/residue: 0.2886 time to fit residues: 118.8968 Evaluate side-chains 259 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 197 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1049 ASN Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1179 VAL Chi-restraints excluded: chain D residue 1207 THR Chi-restraints excluded: chain D residue 1212 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 0.6980 chunk 140 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 ASN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 HIS ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 17342 Z= 0.565 Angle : 0.804 13.984 23462 Z= 0.431 Chirality : 0.049 0.182 2402 Planarity : 0.006 0.056 3092 Dihedral : 6.073 49.989 2364 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 16.97 % Favored : 82.98 % Rotamer: Outliers : 6.26 % Allowed : 20.32 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.15), residues: 2062 helix: -3.88 (0.55), residues: 44 sheet: -1.51 (0.30), residues: 298 loop : -3.30 (0.12), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 274 HIS 0.009 0.002 HIS A1059 PHE 0.023 0.003 PHE B1131 TYR 0.029 0.003 TYR B1018 ARG 0.006 0.001 ARG B1074 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 187 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.6037 (t80) REVERT: B 290 ARG cc_start: 0.7167 (ttp-170) cc_final: 0.6557 (ttm-80) REVERT: B 320 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6445 (mm-30) REVERT: B 355 GLU cc_start: 0.6887 (tp30) cc_final: 0.6544 (tp30) REVERT: B 409 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.6985 (p90) REVERT: B 886 TYR cc_start: 0.8225 (m-80) cc_final: 0.7867 (m-80) REVERT: B 1056 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.5343 (m-80) REVERT: B 1076 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7260 (tp40) REVERT: C 1163 GLU cc_start: 0.7647 (tt0) cc_final: 0.7417 (tt0) REVERT: A 288 GLN cc_start: 0.6012 (mp10) cc_final: 0.5705 (mp10) REVERT: A 290 ARG cc_start: 0.6999 (ttt180) cc_final: 0.6414 (tpt170) REVERT: A 291 TYR cc_start: 0.7253 (m-80) cc_final: 0.6693 (m-80) REVERT: A 320 GLU cc_start: 0.5994 (OUTLIER) cc_final: 0.5669 (mt-10) REVERT: A 334 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7497 (mp) REVERT: A 353 ARG cc_start: 0.7332 (mmt90) cc_final: 0.6977 (mmt-90) REVERT: A 397 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8134 (m-30) REVERT: A 401 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.7098 (t-90) REVERT: A 445 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7150 (tt) REVERT: A 586 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8487 (mm) REVERT: A 611 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7152 (mt-10) REVERT: A 654 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: A 719 ASP cc_start: 0.6858 (t0) cc_final: 0.6490 (t0) REVERT: A 790 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: D 1148 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7625 (mm-40) REVERT: D 1180 LYS cc_start: 0.7238 (pttt) cc_final: 0.6973 (ptpt) REVERT: D 1212 ILE cc_start: 0.6290 (OUTLIER) cc_final: 0.5964 (pt) outliers start: 113 outliers final: 78 residues processed: 283 average time/residue: 0.3077 time to fit residues: 131.2117 Evaluate side-chains 266 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 175 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 903 THR Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1049 ASN Chi-restraints excluded: chain B residue 1056 TYR Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1076 GLN Chi-restraints excluded: chain C residue 1206 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1179 VAL Chi-restraints excluded: chain D residue 1207 THR Chi-restraints excluded: chain D residue 1212 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN B 574 ASN ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A 441 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17342 Z= 0.263 Angle : 0.619 14.371 23462 Z= 0.331 Chirality : 0.044 0.164 2402 Planarity : 0.004 0.056 3092 Dihedral : 5.342 52.544 2361 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer: Outliers : 5.87 % Allowed : 21.59 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.15), residues: 2062 helix: -3.73 (0.57), residues: 44 sheet: -1.09 (0.30), residues: 322 loop : -3.22 (0.12), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 177 HIS 0.006 0.001 HIS B 766 PHE 0.013 0.002 PHE B 390 TYR 0.016 0.001 TYR B1018 ARG 0.004 0.000 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 191 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 242 TYR cc_start: 0.6062 (OUTLIER) cc_final: 0.5278 (t80) REVERT: B 249 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.6306 (t80) REVERT: B 290 ARG cc_start: 0.7011 (ttp-170) cc_final: 0.6367 (ttm-80) REVERT: B 355 GLU cc_start: 0.6904 (tp30) cc_final: 0.6566 (tp30) REVERT: B 409 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7295 (p90) REVERT: B 411 ASP cc_start: 0.7389 (m-30) cc_final: 0.6902 (t0) REVERT: B 460 GLN cc_start: 0.7296 (mt0) cc_final: 0.6985 (mt0) REVERT: B 886 TYR cc_start: 0.8155 (m-80) cc_final: 0.7870 (m-80) REVERT: B 998 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6575 (mtm180) REVERT: B 1107 ILE cc_start: 0.8056 (mt) cc_final: 0.7833 (mt) REVERT: A 290 ARG cc_start: 0.7043 (ttt180) cc_final: 0.6264 (tpt90) REVERT: A 291 TYR cc_start: 0.7159 (m-80) cc_final: 0.6626 (m-80) REVERT: A 334 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7403 (mp) REVERT: A 353 ARG cc_start: 0.7297 (mmt90) cc_final: 0.6814 (mmt90) REVERT: A 364 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7887 (tttt) REVERT: A 401 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.7063 (t-90) REVERT: A 445 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7065 (tt) REVERT: A 586 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8423 (mm) REVERT: A 611 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7121 (mt-10) REVERT: A 654 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7362 (mt-10) REVERT: A 719 ASP cc_start: 0.6741 (t0) cc_final: 0.6486 (t0) REVERT: A 790 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: A 835 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7451 (pm20) REVERT: A 942 LYS cc_start: 0.7805 (mttp) cc_final: 0.7290 (tttp) REVERT: D 1148 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7639 (mm-40) REVERT: D 1180 LYS cc_start: 0.7074 (pttt) cc_final: 0.6801 (ptpt) outliers start: 106 outliers final: 72 residues processed: 279 average time/residue: 0.3019 time to fit residues: 124.6382 Evaluate side-chains 263 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 179 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 903 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 998 ARG Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain C residue 1196 LEU Chi-restraints excluded: chain C residue 1206 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1179 VAL Chi-restraints excluded: chain D residue 1207 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 116 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 ASN B 639 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17342 Z= 0.384 Angle : 0.700 14.539 23462 Z= 0.373 Chirality : 0.046 0.171 2402 Planarity : 0.005 0.058 3092 Dihedral : 5.689 58.459 2358 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.41 % Favored : 82.59 % Rotamer: Outliers : 6.48 % Allowed : 21.26 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.15), residues: 2062 helix: -3.61 (0.58), residues: 44 sheet: -1.52 (0.29), residues: 344 loop : -3.25 (0.12), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 177 HIS 0.009 0.001 HIS A 444 PHE 0.018 0.002 PHE B1131 TYR 0.021 0.002 TYR A1018 ARG 0.005 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 181 time to evaluate : 1.889 Fit side-chains revert: symmetry clash REVERT: B 242 TYR cc_start: 0.6177 (OUTLIER) cc_final: 0.5284 (t80) REVERT: B 249 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6378 (t80) REVERT: B 290 ARG cc_start: 0.7122 (ttp-170) cc_final: 0.6425 (ttm-80) REVERT: B 355 GLU cc_start: 0.6859 (tp30) cc_final: 0.6500 (tp30) REVERT: B 409 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7321 (p90) REVERT: B 411 ASP cc_start: 0.7455 (m-30) cc_final: 0.6824 (t0) REVERT: B 460 GLN cc_start: 0.7277 (mt0) cc_final: 0.6986 (mt0) REVERT: B 470 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8381 (tp) REVERT: B 886 TYR cc_start: 0.8238 (m-80) cc_final: 0.8002 (m-80) REVERT: B 998 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.6386 (mtm180) REVERT: B 1049 ASN cc_start: 0.6901 (OUTLIER) cc_final: 0.6683 (p0) REVERT: B 1056 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.5517 (m-80) REVERT: B 1076 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6997 (tp40) REVERT: B 1107 ILE cc_start: 0.8246 (mt) cc_final: 0.8043 (mt) REVERT: A 182 ARG cc_start: 0.8384 (mmt180) cc_final: 0.7926 (mmt180) REVERT: A 290 ARG cc_start: 0.7147 (ttt180) cc_final: 0.6303 (tpt90) REVERT: A 291 TYR cc_start: 0.7347 (m-80) cc_final: 0.6826 (m-80) REVERT: A 334 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7405 (mp) REVERT: A 353 ARG cc_start: 0.7377 (mmt90) cc_final: 0.6972 (mmt-90) REVERT: A 364 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7995 (tttt) REVERT: A 397 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: A 401 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.7085 (t-90) REVERT: A 445 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7125 (tt) REVERT: A 586 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8458 (mm) REVERT: A 611 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7148 (mt-10) REVERT: A 654 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: A 719 ASP cc_start: 0.6807 (t0) cc_final: 0.6574 (t0) REVERT: A 727 LYS cc_start: 0.6843 (tmtt) cc_final: 0.6332 (tttt) REVERT: A 790 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: A 835 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7478 (pm20) REVERT: A 942 LYS cc_start: 0.7819 (mttp) cc_final: 0.7321 (tttp) REVERT: D 1180 LYS cc_start: 0.7202 (pttt) cc_final: 0.6908 (ptpt) outliers start: 117 outliers final: 79 residues processed: 278 average time/residue: 0.2980 time to fit residues: 123.6846 Evaluate side-chains 271 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 175 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 903 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 998 ARG Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1049 ASN Chi-restraints excluded: chain B residue 1056 TYR Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1076 GLN Chi-restraints excluded: chain C residue 1196 LEU Chi-restraints excluded: chain C residue 1206 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1179 VAL Chi-restraints excluded: chain D residue 1207 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 ASN ** B 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 ASN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 ASN ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17342 Z= 0.397 Angle : 0.704 14.499 23462 Z= 0.377 Chirality : 0.046 0.173 2402 Planarity : 0.005 0.060 3092 Dihedral : 5.747 44.648 2358 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.86 % Favored : 84.14 % Rotamer: Outliers : 6.64 % Allowed : 22.76 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.15), residues: 2062 helix: -3.55 (0.58), residues: 44 sheet: -1.35 (0.29), residues: 322 loop : -3.29 (0.12), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 177 HIS 0.007 0.001 HIS B 766 PHE 0.018 0.002 PHE B1131 TYR 0.019 0.002 TYR B1018 ARG 0.005 0.001 ARG B 859 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 180 time to evaluate : 2.038 Fit side-chains revert: symmetry clash REVERT: B 242 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5141 (t80) REVERT: B 249 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6484 (t80) REVERT: B 290 ARG cc_start: 0.7168 (ttp-170) cc_final: 0.6473 (ttm-80) REVERT: B 355 GLU cc_start: 0.6913 (tp30) cc_final: 0.6532 (tp30) REVERT: B 460 GLN cc_start: 0.7260 (mt0) cc_final: 0.6976 (mt0) REVERT: B 470 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8375 (tp) REVERT: B 998 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6328 (mtm180) REVERT: B 1056 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.5752 (m-80) REVERT: B 1076 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7403 (tp40) REVERT: B 1107 ILE cc_start: 0.8279 (mt) cc_final: 0.8066 (mt) REVERT: A 194 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: A 290 ARG cc_start: 0.7140 (ttt180) cc_final: 0.6434 (tpt170) REVERT: A 291 TYR cc_start: 0.7374 (m-80) cc_final: 0.6901 (m-80) REVERT: A 320 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5820 (mt-10) REVERT: A 334 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7341 (mp) REVERT: A 353 ARG cc_start: 0.7393 (mmt90) cc_final: 0.6955 (mmt-90) REVERT: A 364 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7989 (tttt) REVERT: A 397 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8030 (m-30) REVERT: A 401 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.7117 (t-90) REVERT: A 445 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7307 (tt) REVERT: A 586 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8437 (mm) REVERT: A 611 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7139 (mt-10) REVERT: A 654 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: A 719 ASP cc_start: 0.6799 (t0) cc_final: 0.6523 (t0) REVERT: A 758 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7855 (pt0) REVERT: A 790 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: A 835 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: A 942 LYS cc_start: 0.7847 (mttp) cc_final: 0.7378 (tttp) REVERT: D 1180 LYS cc_start: 0.7256 (pttt) cc_final: 0.6953 (ptpt) outliers start: 120 outliers final: 87 residues processed: 280 average time/residue: 0.2919 time to fit residues: 122.4134 Evaluate side-chains 281 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 176 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 903 THR Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 998 ARG Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1056 TYR Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1076 GLN Chi-restraints excluded: chain C residue 1196 LEU Chi-restraints excluded: chain C residue 1206 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 758 GLN Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1179 VAL Chi-restraints excluded: chain D residue 1183 LYS Chi-restraints excluded: chain D residue 1207 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 ASN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17342 Z= 0.225 Angle : 0.611 14.591 23462 Z= 0.325 Chirality : 0.044 0.176 2402 Planarity : 0.004 0.058 3092 Dihedral : 5.053 40.094 2355 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.89 % Favored : 85.11 % Rotamer: Outliers : 5.37 % Allowed : 24.14 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.15), residues: 2062 helix: -3.36 (0.60), residues: 46 sheet: -1.13 (0.31), residues: 308 loop : -3.15 (0.12), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 177 HIS 0.005 0.001 HIS B 766 PHE 0.015 0.001 PHE B 390 TYR 0.019 0.001 TYR B 181 ARG 0.004 0.000 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 189 time to evaluate : 1.852 Fit side-chains revert: symmetry clash REVERT: B 242 TYR cc_start: 0.6256 (OUTLIER) cc_final: 0.5176 (t80) REVERT: B 249 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6623 (t80) REVERT: B 290 ARG cc_start: 0.7144 (ttp-170) cc_final: 0.6420 (ttm-80) REVERT: B 355 GLU cc_start: 0.6843 (tp30) cc_final: 0.6485 (tp30) REVERT: B 411 ASP cc_start: 0.7319 (m-30) cc_final: 0.7028 (t70) REVERT: B 460 GLN cc_start: 0.7257 (mt0) cc_final: 0.6965 (mt0) REVERT: B 470 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8299 (tp) REVERT: B 1056 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.5416 (m-80) REVERT: B 1076 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7038 (tp40) REVERT: A 182 ARG cc_start: 0.8382 (mmt180) cc_final: 0.7928 (mmt180) REVERT: A 290 ARG cc_start: 0.7124 (ttt180) cc_final: 0.6437 (tpt170) REVERT: A 291 TYR cc_start: 0.7240 (m-80) cc_final: 0.6838 (m-80) REVERT: A 334 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7351 (mp) REVERT: A 353 ARG cc_start: 0.7353 (mmt90) cc_final: 0.6848 (mmt90) REVERT: A 397 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7905 (m-30) REVERT: A 401 HIS cc_start: 0.7519 (OUTLIER) cc_final: 0.7101 (t-90) REVERT: A 445 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7276 (tt) REVERT: A 586 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8379 (mm) REVERT: A 594 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7292 (ptp90) REVERT: A 654 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: A 719 ASP cc_start: 0.6684 (t0) cc_final: 0.6478 (t0) REVERT: A 727 LYS cc_start: 0.6722 (tmtt) cc_final: 0.6288 (tttt) REVERT: A 790 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: A 835 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: A 868 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8307 (mt0) REVERT: A 942 LYS cc_start: 0.7804 (mttp) cc_final: 0.7335 (tttp) REVERT: D 1180 LYS cc_start: 0.7083 (pttt) cc_final: 0.6790 (ptpt) outliers start: 97 outliers final: 74 residues processed: 265 average time/residue: 0.2977 time to fit residues: 117.0664 Evaluate side-chains 268 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 179 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 903 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1056 TYR Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1076 GLN Chi-restraints excluded: chain C residue 1196 LEU Chi-restraints excluded: chain C residue 1206 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1179 VAL Chi-restraints excluded: chain D residue 1183 LYS Chi-restraints excluded: chain D residue 1207 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 ASN B 885 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 288 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17342 Z= 0.332 Angle : 0.672 14.826 23462 Z= 0.359 Chirality : 0.045 0.172 2402 Planarity : 0.004 0.059 3092 Dihedral : 5.367 41.597 2355 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.34 % Favored : 83.66 % Rotamer: Outliers : 6.09 % Allowed : 23.98 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.15), residues: 2062 helix: -3.40 (0.59), residues: 46 sheet: -1.23 (0.31), residues: 302 loop : -3.17 (0.12), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 177 HIS 0.006 0.001 HIS B 766 PHE 0.026 0.002 PHE B1080 TYR 0.017 0.002 TYR A1018 ARG 0.004 0.000 ARG B1074 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 179 time to evaluate : 1.930 Fit side-chains revert: symmetry clash REVERT: B 242 TYR cc_start: 0.6318 (OUTLIER) cc_final: 0.5210 (t80) REVERT: B 249 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6659 (t80) REVERT: B 290 ARG cc_start: 0.7231 (ttp-170) cc_final: 0.6509 (ttm-80) REVERT: B 355 GLU cc_start: 0.6900 (tp30) cc_final: 0.6514 (tp30) REVERT: B 411 ASP cc_start: 0.7365 (m-30) cc_final: 0.7062 (t70) REVERT: B 460 GLN cc_start: 0.7266 (mt0) cc_final: 0.6967 (mt0) REVERT: B 470 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8362 (tp) REVERT: B 998 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6329 (mtm180) REVERT: B 1056 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.5678 (m-80) REVERT: B 1076 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7412 (tp40) REVERT: A 290 ARG cc_start: 0.7239 (ttt180) cc_final: 0.6464 (tpt90) REVERT: A 291 TYR cc_start: 0.7280 (m-80) cc_final: 0.6837 (m-80) REVERT: A 320 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5859 (mt-10) REVERT: A 334 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7332 (mp) REVERT: A 353 ARG cc_start: 0.7406 (mmt90) cc_final: 0.6929 (mmt90) REVERT: A 397 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: A 401 HIS cc_start: 0.7521 (OUTLIER) cc_final: 0.7123 (t-90) REVERT: A 445 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7302 (tt) REVERT: A 489 LYS cc_start: 0.7636 (mmmt) cc_final: 0.7400 (mptt) REVERT: A 586 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8428 (mm) REVERT: A 594 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7224 (ptp90) REVERT: A 654 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7305 (mt-10) REVERT: A 719 ASP cc_start: 0.6713 (t0) cc_final: 0.6499 (t0) REVERT: A 727 LYS cc_start: 0.6818 (tmtt) cc_final: 0.6406 (tttt) REVERT: A 790 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: A 835 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7459 (pm20) REVERT: A 868 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: A 920 MET cc_start: 0.7202 (tpt) cc_final: 0.6754 (ptm) REVERT: A 942 LYS cc_start: 0.7792 (mttp) cc_final: 0.7349 (tttp) REVERT: D 1180 LYS cc_start: 0.7209 (pttt) cc_final: 0.6920 (ptpt) outliers start: 110 outliers final: 85 residues processed: 268 average time/residue: 0.3033 time to fit residues: 121.4598 Evaluate side-chains 277 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 175 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 903 THR Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 998 ARG Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1056 TYR Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1076 GLN Chi-restraints excluded: chain C residue 1196 LEU Chi-restraints excluded: chain C residue 1206 ILE Chi-restraints excluded: chain C residue 1207 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1179 VAL Chi-restraints excluded: chain D residue 1207 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 92 optimal weight: 0.0570 chunk 136 optimal weight: 0.6980 chunk 205 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN B 885 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17342 Z= 0.144 Angle : 0.561 14.526 23462 Z= 0.297 Chirality : 0.043 0.165 2402 Planarity : 0.004 0.059 3092 Dihedral : 4.566 36.896 2355 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 3.54 % Allowed : 26.30 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.16), residues: 2062 helix: -3.01 (0.66), residues: 46 sheet: -0.90 (0.30), residues: 336 loop : -2.96 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 177 HIS 0.004 0.001 HIS A 725 PHE 0.021 0.001 PHE B1080 TYR 0.013 0.001 TYR B 409 ARG 0.004 0.000 ARG B 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 203 time to evaluate : 1.737 Fit side-chains revert: symmetry clash REVERT: B 242 TYR cc_start: 0.6231 (OUTLIER) cc_final: 0.5099 (t80) REVERT: B 249 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6761 (t80) REVERT: B 290 ARG cc_start: 0.6962 (ttp-170) cc_final: 0.6261 (ttm-80) REVERT: B 411 ASP cc_start: 0.7276 (m-30) cc_final: 0.6993 (t70) REVERT: B 460 GLN cc_start: 0.7299 (mt0) cc_final: 0.6947 (mt0) REVERT: B 1056 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.5259 (m-80) REVERT: B 1076 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7006 (tp40) REVERT: A 182 ARG cc_start: 0.8364 (mmt180) cc_final: 0.7940 (mmt180) REVERT: A 288 GLN cc_start: 0.5805 (mp-120) cc_final: 0.5247 (mp10) REVERT: A 290 ARG cc_start: 0.7069 (ttt180) cc_final: 0.6260 (tpt90) REVERT: A 291 TYR cc_start: 0.7038 (m-80) cc_final: 0.6810 (m-80) REVERT: A 334 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7385 (mp) REVERT: A 353 ARG cc_start: 0.7301 (mmt90) cc_final: 0.6748 (mmt-90) REVERT: A 397 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7728 (m-30) REVERT: A 401 HIS cc_start: 0.7524 (OUTLIER) cc_final: 0.7125 (t-90) REVERT: A 445 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7069 (tt) REVERT: A 727 LYS cc_start: 0.6635 (tmtt) cc_final: 0.6295 (tttt) REVERT: A 790 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7466 (tp40) REVERT: A 868 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8225 (mt0) REVERT: A 920 MET cc_start: 0.7104 (tpt) cc_final: 0.6612 (ptm) REVERT: A 942 LYS cc_start: 0.7736 (mttp) cc_final: 0.7340 (tttp) REVERT: D 1180 LYS cc_start: 0.6844 (pttt) cc_final: 0.6635 (ptpt) outliers start: 64 outliers final: 47 residues processed: 252 average time/residue: 0.3014 time to fit residues: 112.7920 Evaluate side-chains 243 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 187 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1056 TYR Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1076 GLN Chi-restraints excluded: chain C residue 1206 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 799 ASN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN A1089 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.177011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.149333 restraints weight = 22170.434| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.41 r_work: 0.3523 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17342 Z= 0.172 Angle : 0.582 14.338 23462 Z= 0.308 Chirality : 0.043 0.163 2402 Planarity : 0.004 0.058 3092 Dihedral : 4.574 37.821 2355 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer: Outliers : 3.54 % Allowed : 26.52 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.16), residues: 2062 helix: -2.76 (0.67), residues: 46 sheet: -0.55 (0.30), residues: 350 loop : -2.95 (0.13), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 177 HIS 0.004 0.001 HIS B 766 PHE 0.021 0.001 PHE B1080 TYR 0.014 0.001 TYR D1214 ARG 0.003 0.000 ARG B 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3718.19 seconds wall clock time: 67 minutes 37.65 seconds (4057.65 seconds total)