Starting phenix.real_space_refine on Wed Mar 20 21:09:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3g_21036/03_2024/6v3g_21036.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3g_21036/03_2024/6v3g_21036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3g_21036/03_2024/6v3g_21036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3g_21036/03_2024/6v3g_21036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3g_21036/03_2024/6v3g_21036.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3g_21036/03_2024/6v3g_21036.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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 192 5.16 5 C 18456 2.51 5 N 4680 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B GLU 479": "OE1" <-> "OE2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B GLU 569": "OE1" <-> "OE2" Residue "B GLU 576": "OE1" <-> "OE2" Residue "B ARG 707": "NH1" <-> "NH2" Residue "B ASP 812": "OD1" <-> "OD2" Residue "B ASP 817": "OD1" <-> "OD2" Residue "B PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 972": "NH1" <-> "NH2" Residue "B PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A ARG 707": "NH1" <-> "NH2" Residue "A ASP 812": "OD1" <-> "OD2" Residue "A ASP 817": "OD1" <-> "OD2" Residue "A PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 972": "NH1" <-> "NH2" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "C ARG 368": "NH1" <-> "NH2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C GLU 569": "OE1" <-> "OE2" Residue "C GLU 576": "OE1" <-> "OE2" Residue "C ARG 707": "NH1" <-> "NH2" Residue "C ASP 812": "OD1" <-> "OD2" Residue "C ASP 817": "OD1" <-> "OD2" Residue "C PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 972": "NH1" <-> "NH2" Residue "C PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D GLU 569": "OE1" <-> "OE2" Residue "D GLU 576": "OE1" <-> "OE2" Residue "D ARG 707": "NH1" <-> "NH2" Residue "D ASP 812": "OD1" <-> "OD2" Residue "D ASP 817": "OD1" <-> "OD2" Residue "D PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 972": "NH1" <-> "NH2" Residue "D PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28520 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 7130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 7130 Classifications: {'peptide': 895} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 866} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 7130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 7130 Classifications: {'peptide': 895} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 866} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 7130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 7130 Classifications: {'peptide': 895} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 866} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 7130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 7130 Classifications: {'peptide': 895} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 866} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 14.57, per 1000 atoms: 0.51 Number of scatterers: 28520 At special positions: 0 Unit cell: (144.3, 144.3, 135.2, 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 192 16.00 O 5192 8.00 N 4680 7.00 C 18456 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: 11.29 Conformation dependent library (CDL) restraints added in 5.3 seconds 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6800 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 20 sheets defined 49.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'B' and resid 22 through 34 removed outlier: 3.934A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.916A pdb=" N SER B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 134 removed outlier: 3.823A pdb=" N ARG B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 removed outlier: 3.639A pdb=" N ALA B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.529A pdb=" N LEU B 179 " --> pdb=" O TRP B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 188 removed outlier: 4.385A pdb=" N ASP B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 200 removed outlier: 4.631A pdb=" N TYR B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.765A pdb=" N ARG B 210 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 211 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 213 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 215 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.533A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 259 removed outlier: 3.529A pdb=" N SER B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.990A pdb=" N MET B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 318 removed outlier: 3.565A pdb=" N LEU B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 326 removed outlier: 3.797A pdb=" N GLU B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 removed outlier: 3.709A pdb=" N ASN B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 432 through 451 removed outlier: 3.892A pdb=" N GLU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.581A pdb=" N HIS B 468 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 500 removed outlier: 3.830A pdb=" N ILE B 494 " --> pdb=" O LYS B 490 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 510 removed outlier: 3.596A pdb=" N MET B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 533 removed outlier: 3.768A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 601 through 607 removed outlier: 3.626A pdb=" N VAL B 605 " --> pdb=" O ASP B 601 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 607 " --> pdb=" O LYS B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 610 No H-bonds generated for 'chain 'B' and resid 608 through 610' Processing helix chain 'B' and resid 621 through 626 removed outlier: 3.551A pdb=" N LYS B 626 " --> pdb=" O PRO B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 765 through 770 removed outlier: 5.434A pdb=" N GLU B 768 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 792 removed outlier: 3.781A pdb=" N LEU B 789 " --> pdb=" O SER B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 816 Processing helix chain 'B' and resid 817 through 830 Processing helix chain 'B' and resid 872 through 876 removed outlier: 3.587A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 removed outlier: 3.717A pdb=" N ASN B 887 " --> pdb=" O ASN B 884 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 888 " --> pdb=" O ASP B 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 884 through 888' Processing helix chain 'B' and resid 906 through 912 Processing helix chain 'B' and resid 919 through 930 removed outlier: 3.751A pdb=" N LEU B 923 " --> pdb=" O VAL B 919 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 942 Processing helix chain 'B' and resid 946 through 954 Processing helix chain 'B' and resid 995 through 1008 removed outlier: 3.917A pdb=" N THR B1006 " --> pdb=" O LYS B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1021 removed outlier: 3.671A pdb=" N ALA B1020 " --> pdb=" O LEU B1017 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS B1021 " --> pdb=" O ARG B1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1017 through 1021' Processing helix chain 'A' and resid 22 through 34 removed outlier: 3.933A pdb=" N SER A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.916A pdb=" N SER A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 134 removed outlier: 3.822A pdb=" N ARG A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.639A pdb=" N ALA A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.528A pdb=" N LEU A 179 " --> pdb=" O TRP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 removed outlier: 4.385A pdb=" N ASP A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 200 removed outlier: 4.632A pdb=" N TYR A 198 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.765A pdb=" N ARG A 210 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 211 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 213 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 215 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.532A pdb=" N ILE A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 259 removed outlier: 3.529A pdb=" N SER A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.990A pdb=" N MET A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 318 removed outlier: 3.565A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 326 removed outlier: 3.796A pdb=" N GLU A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.708A pdb=" N ASN A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 432 through 451 removed outlier: 3.892A pdb=" N GLU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.580A pdb=" N HIS A 468 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 removed outlier: 3.830A pdb=" N ILE A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 510 removed outlier: 3.596A pdb=" N MET A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.768A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 601 through 607 removed outlier: 3.625A pdb=" N VAL A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 610 No H-bonds generated for 'chain 'A' and resid 608 through 610' Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.550A pdb=" N LYS A 626 " --> pdb=" O PRO A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 759 through 764 Processing helix chain 'A' and resid 765 through 770 removed outlier: 5.433A pdb=" N GLU A 768 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.780A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 816 Processing helix chain 'A' and resid 817 through 830 Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.586A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.717A pdb=" N ASN A 887 " --> pdb=" O ASN A 884 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 888 " --> pdb=" O ASP A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 888' Processing helix chain 'A' and resid 906 through 912 Processing helix chain 'A' and resid 919 through 930 removed outlier: 3.752A pdb=" N LEU A 923 " --> pdb=" O VAL A 919 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 942 Processing helix chain 'A' and resid 946 through 954 Processing helix chain 'A' and resid 995 through 1008 removed outlier: 3.917A pdb=" N THR A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1021 removed outlier: 3.671A pdb=" N ALA A1020 " --> pdb=" O LEU A1017 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS A1021 " --> pdb=" O ARG A1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1017 through 1021' Processing helix chain 'C' and resid 22 through 34 removed outlier: 3.934A pdb=" N SER C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.916A pdb=" N SER C 106 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 134 removed outlier: 3.823A pdb=" N ARG C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 115 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL C 116 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 165 removed outlier: 3.638A pdb=" N ALA C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 175 through 179 removed outlier: 3.529A pdb=" N LEU C 179 " --> pdb=" O TRP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 188 removed outlier: 4.385A pdb=" N ASP C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 removed outlier: 4.632A pdb=" N TYR C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.765A pdb=" N ARG C 210 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 211 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C 213 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 215 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.533A pdb=" N ILE C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 259 removed outlier: 3.528A pdb=" N SER C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.990A pdb=" N MET C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 318 removed outlier: 3.565A pdb=" N LEU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 326 removed outlier: 3.797A pdb=" N GLU C 324 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 364 removed outlier: 3.709A pdb=" N ASN C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 432 through 451 removed outlier: 3.892A pdb=" N GLU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 removed outlier: 3.581A pdb=" N HIS C 468 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.830A pdb=" N ILE C 494 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 510 removed outlier: 3.596A pdb=" N MET C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 removed outlier: 3.768A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL C 532 " --> pdb=" O TYR C 528 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 601 through 607 removed outlier: 3.626A pdb=" N VAL C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 607 " --> pdb=" O LYS C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 610 No H-bonds generated for 'chain 'C' and resid 608 through 610' Processing helix chain 'C' and resid 621 through 626 removed outlier: 3.551A pdb=" N LYS C 626 " --> pdb=" O PRO C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 759 through 764 Processing helix chain 'C' and resid 765 through 770 removed outlier: 5.434A pdb=" N GLU C 768 " --> pdb=" O ARG C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 removed outlier: 3.781A pdb=" N LEU C 789 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 816 Processing helix chain 'C' and resid 817 through 830 Processing helix chain 'C' and resid 872 through 876 removed outlier: 3.587A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 removed outlier: 3.717A pdb=" N ASN C 887 " --> pdb=" O ASN C 884 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL C 888 " --> pdb=" O ASP C 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 884 through 888' Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 919 through 930 removed outlier: 3.752A pdb=" N LEU C 923 " --> pdb=" O VAL C 919 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 942 Processing helix chain 'C' and resid 946 through 954 Processing helix chain 'C' and resid 995 through 1008 removed outlier: 3.917A pdb=" N THR C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1021 removed outlier: 3.672A pdb=" N ALA C1020 " --> pdb=" O LEU C1017 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS C1021 " --> pdb=" O ARG C1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1017 through 1021' Processing helix chain 'D' and resid 22 through 34 removed outlier: 3.934A pdb=" N SER D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 101 through 106 removed outlier: 3.916A pdb=" N SER D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 134 removed outlier: 3.823A pdb=" N ARG D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL D 116 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.639A pdb=" N ALA D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 175 through 179 removed outlier: 3.530A pdb=" N LEU D 179 " --> pdb=" O TRP D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 188 removed outlier: 4.385A pdb=" N ASP D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 removed outlier: 4.631A pdb=" N TYR D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 removed outlier: 3.766A pdb=" N ARG D 210 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 211 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG D 213 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 215 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.532A pdb=" N ILE D 220 " --> pdb=" O GLN D 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 259 removed outlier: 3.528A pdb=" N SER D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.989A pdb=" N MET D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 318 removed outlier: 3.565A pdb=" N LEU D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 326 removed outlier: 3.797A pdb=" N GLU D 324 " --> pdb=" O PRO D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 364 removed outlier: 3.709A pdb=" N ASN D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 432 through 451 removed outlier: 3.892A pdb=" N GLU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 removed outlier: 3.581A pdb=" N HIS D 468 " --> pdb=" O ASN D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 500 removed outlier: 3.830A pdb=" N ILE D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 499 " --> pdb=" O ALA D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 510 removed outlier: 3.596A pdb=" N MET D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 533 removed outlier: 3.768A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU D 530 " --> pdb=" O LYS D 526 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL D 532 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 601 through 607 removed outlier: 3.626A pdb=" N VAL D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG D 607 " --> pdb=" O LYS D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 610 No H-bonds generated for 'chain 'D' and resid 608 through 610' Processing helix chain 'D' and resid 621 through 626 removed outlier: 3.550A pdb=" N LYS D 626 " --> pdb=" O PRO D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 740 through 742 No H-bonds generated for 'chain 'D' and resid 740 through 742' Processing helix chain 'D' and resid 759 through 764 Processing helix chain 'D' and resid 765 through 770 removed outlier: 5.435A pdb=" N GLU D 768 " --> pdb=" O ARG D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 792 removed outlier: 3.780A pdb=" N LEU D 789 " --> pdb=" O SER D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 816 Processing helix chain 'D' and resid 817 through 830 Processing helix chain 'D' and resid 872 through 876 removed outlier: 3.587A pdb=" N ASN D 875 " --> pdb=" O THR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.718A pdb=" N ASN D 887 " --> pdb=" O ASN D 884 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 888 " --> pdb=" O ASP D 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 884 through 888' Processing helix chain 'D' and resid 906 through 912 Processing helix chain 'D' and resid 919 through 930 removed outlier: 3.752A pdb=" N LEU D 923 " --> pdb=" O VAL D 919 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET D 924 " --> pdb=" O LEU D 920 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 932 through 942 Processing helix chain 'D' and resid 946 through 954 Processing helix chain 'D' and resid 995 through 1008 removed outlier: 3.917A pdb=" N THR D1006 " --> pdb=" O LYS D1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1021 removed outlier: 3.671A pdb=" N ALA D1020 " --> pdb=" O LEU D1017 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS D1021 " --> pdb=" O ARG D1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1017 through 1021' Processing sheet with id=AA1, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AA2, first strand: chain 'B' and resid 398 through 401 removed outlier: 4.517A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 535 through 540 removed outlier: 4.338A pdb=" N LEU B 594 " --> pdb=" O GLU B 569 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 567 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE B 598 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N MET B 565 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR B 570 " --> pdb=" O ARG B 578 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.494A pdb=" N VAL B 719 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL B 757 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 721 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 976 through 980 removed outlier: 6.497A pdb=" N PHE B1050 " --> pdb=" O PHE B1012 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA7, first strand: chain 'A' and resid 398 through 401 removed outlier: 4.517A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 535 through 540 removed outlier: 4.338A pdb=" N LEU A 594 " --> pdb=" O GLU A 569 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 567 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR A 570 " --> pdb=" O ARG A 578 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.494A pdb=" N VAL A 719 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL A 757 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL A 721 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 976 through 980 removed outlier: 6.498A pdb=" N PHE A1050 " --> pdb=" O PHE A1012 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AB3, first strand: chain 'C' and resid 398 through 401 removed outlier: 4.517A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 535 through 540 removed outlier: 4.338A pdb=" N LEU C 594 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 567 " --> pdb=" O PHE C 596 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR C 570 " --> pdb=" O ARG C 578 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.494A pdb=" N VAL C 719 " --> pdb=" O VAL C 755 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL C 757 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL C 721 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 976 through 980 removed outlier: 6.497A pdb=" N PHE C1050 " --> pdb=" O PHE C1012 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AB8, first strand: chain 'D' and resid 398 through 401 removed outlier: 4.517A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE D 456 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE D 484 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR D 458 " --> pdb=" O ILE D 484 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 535 through 540 removed outlier: 4.338A pdb=" N LEU D 594 " --> pdb=" O GLU D 569 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR D 570 " --> pdb=" O ARG D 578 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.494A pdb=" N VAL D 719 " --> pdb=" O VAL D 755 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL D 757 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL D 721 " --> pdb=" O VAL D 757 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 976 through 980 removed outlier: 6.497A pdb=" N PHE D1050 " --> pdb=" O PHE D1012 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3012 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: 10.16 Time building geometry restraints manager: 12.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6819 1.33 - 1.45: 6241 1.45 - 1.57: 15828 1.57 - 1.69: 0 1.69 - 1.81: 284 Bond restraints: 29172 Sorted by residual: bond pdb=" N ASN A 582 " pdb=" CA ASN A 582 " ideal model delta sigma weight residual 1.457 1.486 -0.029 9.10e-03 1.21e+04 1.03e+01 bond pdb=" N ASN B 582 " pdb=" CA ASN B 582 " ideal model delta sigma weight residual 1.457 1.486 -0.029 9.10e-03 1.21e+04 1.03e+01 bond pdb=" N ASN D 582 " pdb=" CA ASN D 582 " ideal model delta sigma weight residual 1.457 1.486 -0.029 9.10e-03 1.21e+04 1.03e+01 bond pdb=" N ASN C 582 " pdb=" CA ASN C 582 " ideal model delta sigma weight residual 1.457 1.486 -0.029 9.10e-03 1.21e+04 1.02e+01 bond pdb=" N ILE C 568 " pdb=" CA ILE C 568 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.11e-02 8.12e+03 9.99e+00 ... (remaining 29167 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.66: 496 105.66 - 112.81: 15363 112.81 - 119.97: 11235 119.97 - 127.12: 12200 127.12 - 134.27: 286 Bond angle restraints: 39580 Sorted by residual: angle pdb=" N GLN D 807 " pdb=" CA GLN D 807 " pdb=" C GLN D 807 " ideal model delta sigma weight residual 112.89 106.80 6.09 1.24e+00 6.50e-01 2.41e+01 angle pdb=" N GLN A 807 " pdb=" CA GLN A 807 " pdb=" C GLN A 807 " ideal model delta sigma weight residual 112.89 106.81 6.08 1.24e+00 6.50e-01 2.41e+01 angle pdb=" N GLN B 807 " pdb=" CA GLN B 807 " pdb=" C GLN B 807 " ideal model delta sigma weight residual 112.89 106.82 6.07 1.24e+00 6.50e-01 2.40e+01 angle pdb=" N GLN C 807 " pdb=" CA GLN C 807 " pdb=" C GLN C 807 " ideal model delta sigma weight residual 112.89 106.82 6.07 1.24e+00 6.50e-01 2.39e+01 angle pdb=" O ILE C 625 " pdb=" C ILE C 625 " pdb=" N LYS C 626 " ideal model delta sigma weight residual 121.87 125.76 -3.89 9.70e-01 1.06e+00 1.61e+01 ... (remaining 39575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 16283 15.93 - 31.86: 757 31.86 - 47.79: 164 47.79 - 63.72: 32 63.72 - 79.65: 16 Dihedral angle restraints: 17252 sinusoidal: 6760 harmonic: 10492 Sorted by residual: dihedral pdb=" CA ARG C 742 " pdb=" C ARG C 742 " pdb=" N ALA C 743 " pdb=" CA ALA C 743 " ideal model delta harmonic sigma weight residual 180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ARG B 742 " pdb=" C ARG B 742 " pdb=" N ALA B 743 " pdb=" CA ALA B 743 " ideal model delta harmonic sigma weight residual 180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ARG A 742 " pdb=" C ARG A 742 " pdb=" N ALA A 743 " pdb=" CA ALA A 743 " ideal model delta harmonic sigma weight residual -180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 17249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2905 0.054 - 0.108: 1053 0.108 - 0.161: 354 0.161 - 0.215: 168 0.215 - 0.269: 44 Chirality restraints: 4524 Sorted by residual: chirality pdb=" CA ILE C 484 " pdb=" N ILE C 484 " pdb=" C ILE C 484 " pdb=" CB ILE C 484 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ILE A 484 " pdb=" N ILE A 484 " pdb=" C ILE A 484 " pdb=" CB ILE A 484 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE B 484 " pdb=" N ILE B 484 " pdb=" C ILE B 484 " pdb=" CB ILE B 484 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 4521 not shown) Planarity restraints: 4984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 246 " -0.020 2.00e-02 2.50e+03 1.66e-02 6.86e+00 pdb=" CG TRP A 246 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 246 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 246 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 246 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 246 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 246 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 246 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 246 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 246 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 246 " 0.020 2.00e-02 2.50e+03 1.64e-02 6.75e+00 pdb=" CG TRP C 246 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 246 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 246 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 246 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 246 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 246 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 246 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 246 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 246 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 246 " -0.020 2.00e-02 2.50e+03 1.64e-02 6.74e+00 pdb=" CG TRP D 246 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP D 246 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 246 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 246 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 246 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 246 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 246 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 246 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 246 " -0.002 2.00e-02 2.50e+03 ... (remaining 4981 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3354 2.75 - 3.29: 28552 3.29 - 3.82: 46798 3.82 - 4.36: 56132 4.36 - 4.90: 92504 Nonbonded interactions: 227340 Sorted by model distance: nonbonded pdb=" N GLU C 819 " pdb=" OE1 GLU C 819 " model vdw 2.211 2.520 nonbonded pdb=" N GLU B 819 " pdb=" OE1 GLU B 819 " model vdw 2.212 2.520 nonbonded pdb=" N GLU D 819 " pdb=" OE1 GLU D 819 " model vdw 2.212 2.520 nonbonded pdb=" N GLU A 819 " pdb=" OE1 GLU A 819 " model vdw 2.212 2.520 nonbonded pdb=" N ASP B 621 " pdb=" OD1 ASP B 621 " model vdw 2.217 2.520 ... (remaining 227335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.060 Extract box with map and model: 5.090 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 73.630 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.140 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.008 0.080 29172 Z= 0.521 Angle : 1.052 8.322 39580 Z= 0.694 Chirality : 0.071 0.269 4524 Planarity : 0.006 0.052 4984 Dihedral : 10.567 79.651 10452 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.66 % Allowed : 4.95 % Favored : 92.39 % 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: -2.76 (0.13), residues: 3548 helix: -2.14 (0.11), residues: 1456 sheet: -2.15 (0.22), residues: 416 loop : -1.28 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 246 HIS 0.013 0.002 HIS A 379 PHE 0.030 0.003 PHE A1012 TYR 0.025 0.002 TYR D1015 ARG 0.009 0.001 ARG C1031 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 533 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.6227 (mpp) cc_final: 0.5948 (mpp) REVERT: B 491 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8624 (tp) REVERT: B 506 MET cc_start: 0.6557 (ttm) cc_final: 0.6079 (ttp) REVERT: B 627 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7881 (mtmm) REVERT: B 715 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8009 (pp) REVERT: B 795 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8891 (p0) REVERT: B 998 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.7988 (p0) REVERT: A 21 MET cc_start: 0.6220 (mpp) cc_final: 0.5950 (mpp) REVERT: A 491 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8633 (tp) REVERT: A 506 MET cc_start: 0.6560 (ttm) cc_final: 0.6088 (ttp) REVERT: A 627 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7878 (mtmm) REVERT: A 715 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8013 (pp) REVERT: A 795 ASN cc_start: 0.9121 (OUTLIER) cc_final: 0.8885 (p0) REVERT: A 998 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.7981 (p0) REVERT: C 21 MET cc_start: 0.6224 (mpp) cc_final: 0.5951 (mpp) REVERT: C 491 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8636 (tp) REVERT: C 506 MET cc_start: 0.6554 (ttm) cc_final: 0.6066 (ttp) REVERT: C 627 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7787 (mtmm) REVERT: C 715 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8004 (pp) REVERT: C 795 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8875 (p0) REVERT: C 998 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8135 (p0) REVERT: D 21 MET cc_start: 0.6227 (mpp) cc_final: 0.5955 (mpp) REVERT: D 491 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8648 (tp) REVERT: D 506 MET cc_start: 0.6548 (ttm) cc_final: 0.6069 (ttp) REVERT: D 627 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7804 (mtmm) REVERT: D 715 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8056 (pp) REVERT: D 795 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8899 (p0) REVERT: D 998 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.7950 (p0) outliers start: 84 outliers final: 14 residues processed: 613 average time/residue: 0.3887 time to fit residues: 379.5288 Evaluate side-chains 292 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 258 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 800 CYS Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 627 LYS Chi-restraints excluded: chain C residue 632 ARG Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 795 ASN Chi-restraints excluded: chain C residue 800 CYS Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 632 ARG Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 795 ASN Chi-restraints excluded: chain D residue 800 CYS Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 1.9990 chunk 269 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 279 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 323 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN B 379 HIS B 394 HIS B 501 GLN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 379 HIS A 394 HIS A 501 GLN ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN C 379 HIS C 394 HIS C 501 GLN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN D 379 HIS D 394 HIS D 501 GLN ** D 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29172 Z= 0.304 Angle : 0.701 7.932 39580 Z= 0.359 Chirality : 0.043 0.145 4524 Planarity : 0.005 0.066 4984 Dihedral : 6.566 55.711 3908 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.86 % Allowed : 11.90 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3548 helix: -0.84 (0.13), residues: 1484 sheet: -1.46 (0.24), residues: 456 loop : -0.81 (0.17), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 246 HIS 0.004 0.001 HIS A 394 PHE 0.026 0.002 PHE A 303 TYR 0.015 0.002 TYR B 928 ARG 0.007 0.001 ARG D 735 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 304 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.6527 (mpp) cc_final: 0.6178 (mpp) REVERT: B 213 ARG cc_start: 0.8527 (mtt180) cc_final: 0.8247 (mmt-90) REVERT: B 252 PHE cc_start: 0.9138 (t80) cc_final: 0.8539 (t80) REVERT: B 303 PHE cc_start: 0.8430 (t80) cc_final: 0.7477 (t80) REVERT: B 460 MET cc_start: 0.8215 (mmm) cc_final: 0.8013 (mmm) REVERT: B 821 ILE cc_start: 0.9100 (tp) cc_final: 0.8816 (tp) REVERT: A 21 MET cc_start: 0.6528 (mpp) cc_final: 0.6175 (mpp) REVERT: A 213 ARG cc_start: 0.8506 (mtt180) cc_final: 0.8248 (mmt-90) REVERT: A 252 PHE cc_start: 0.9123 (t80) cc_final: 0.8563 (t80) REVERT: A 303 PHE cc_start: 0.8408 (t80) cc_final: 0.7458 (t80) REVERT: A 821 ILE cc_start: 0.9082 (tp) cc_final: 0.8831 (tp) REVERT: C 21 MET cc_start: 0.6529 (mpp) cc_final: 0.6180 (mpp) REVERT: C 213 ARG cc_start: 0.8528 (mtt180) cc_final: 0.8229 (mmt-90) REVERT: C 252 PHE cc_start: 0.9093 (t80) cc_final: 0.8569 (t80) REVERT: C 303 PHE cc_start: 0.8445 (t80) cc_final: 0.7560 (t80) REVERT: D 21 MET cc_start: 0.6542 (mpp) cc_final: 0.6182 (mpp) REVERT: D 213 ARG cc_start: 0.8608 (mtt180) cc_final: 0.8226 (mmt-90) REVERT: D 252 PHE cc_start: 0.9089 (t80) cc_final: 0.8643 (t80) REVERT: D 303 PHE cc_start: 0.8435 (t80) cc_final: 0.7886 (t80) outliers start: 90 outliers final: 35 residues processed: 368 average time/residue: 0.3464 time to fit residues: 213.3949 Evaluate side-chains 298 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 263 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain C residue 798 ASP Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 269 optimal weight: 20.0000 chunk 220 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 323 optimal weight: 8.9990 chunk 349 optimal weight: 5.9990 chunk 288 optimal weight: 4.9990 chunk 321 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29172 Z= 0.263 Angle : 0.635 6.944 39580 Z= 0.324 Chirality : 0.042 0.155 4524 Planarity : 0.004 0.048 4984 Dihedral : 5.432 59.194 3848 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.89 % Allowed : 12.56 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3548 helix: -0.42 (0.13), residues: 1484 sheet: -1.69 (0.24), residues: 412 loop : -0.46 (0.17), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 246 HIS 0.004 0.001 HIS C 451 PHE 0.021 0.002 PHE D 164 TYR 0.018 0.002 TYR C 318 ARG 0.010 0.001 ARG B 632 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 305 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.6506 (mpp) cc_final: 0.6038 (mpp) REVERT: B 213 ARG cc_start: 0.8496 (mtt180) cc_final: 0.8187 (mmt-90) REVERT: B 252 PHE cc_start: 0.9159 (t80) cc_final: 0.8713 (t80) REVERT: B 913 THR cc_start: 0.8439 (p) cc_final: 0.8227 (t) REVERT: A 21 MET cc_start: 0.6512 (mpp) cc_final: 0.6044 (mpp) REVERT: A 213 ARG cc_start: 0.8489 (mtt180) cc_final: 0.8203 (mmt-90) REVERT: A 252 PHE cc_start: 0.9162 (t80) cc_final: 0.8717 (t80) REVERT: A 285 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7518 (mmm) REVERT: A 827 ILE cc_start: 0.9386 (tp) cc_final: 0.9185 (tp) REVERT: A 913 THR cc_start: 0.8432 (p) cc_final: 0.8220 (t) REVERT: C 21 MET cc_start: 0.6518 (mpp) cc_final: 0.6041 (mpp) REVERT: C 213 ARG cc_start: 0.8518 (mtt180) cc_final: 0.8250 (mmt-90) REVERT: C 252 PHE cc_start: 0.9103 (t80) cc_final: 0.8433 (t80) REVERT: C 285 MET cc_start: 0.7882 (mmm) cc_final: 0.7662 (mmm) REVERT: C 303 PHE cc_start: 0.8419 (t80) cc_final: 0.7226 (t80) REVERT: D 21 MET cc_start: 0.6483 (mpp) cc_final: 0.6037 (mpp) REVERT: D 213 ARG cc_start: 0.8573 (mtt180) cc_final: 0.8250 (mmt-90) REVERT: D 252 PHE cc_start: 0.9096 (t80) cc_final: 0.8463 (t80) REVERT: D 285 MET cc_start: 0.7883 (mmm) cc_final: 0.7664 (mmm) REVERT: D 303 PHE cc_start: 0.8421 (t80) cc_final: 0.7252 (t80) outliers start: 91 outliers final: 47 residues processed: 357 average time/residue: 0.3815 time to fit residues: 238.2394 Evaluate side-chains 317 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 269 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 913 THR Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 0.0670 chunk 243 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 217 optimal weight: 0.7980 chunk 325 optimal weight: 4.9990 chunk 344 optimal weight: 10.0000 chunk 169 optimal weight: 8.9990 chunk 308 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29172 Z= 0.213 Angle : 0.600 9.466 39580 Z= 0.302 Chirality : 0.041 0.231 4524 Planarity : 0.004 0.044 4984 Dihedral : 5.218 55.539 3848 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.86 % Allowed : 13.42 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.15), residues: 3548 helix: -0.11 (0.13), residues: 1480 sheet: -1.72 (0.24), residues: 420 loop : -0.40 (0.17), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 246 HIS 0.003 0.001 HIS C 350 PHE 0.017 0.001 PHE A 164 TYR 0.012 0.001 TYR D 279 ARG 0.003 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 280 time to evaluate : 3.483 Fit side-chains REVERT: B 21 MET cc_start: 0.6407 (mpp) cc_final: 0.5952 (mpp) REVERT: B 154 MET cc_start: 0.8293 (mpp) cc_final: 0.7816 (mpp) REVERT: B 252 PHE cc_start: 0.9102 (t80) cc_final: 0.8320 (t80) REVERT: B 282 MET cc_start: 0.8329 (tpp) cc_final: 0.8105 (tpp) REVERT: B 303 PHE cc_start: 0.8378 (t80) cc_final: 0.7427 (t80) REVERT: B 460 MET cc_start: 0.8417 (mmm) cc_final: 0.8150 (mmm) REVERT: B 907 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: B 913 THR cc_start: 0.8404 (p) cc_final: 0.8178 (t) REVERT: A 21 MET cc_start: 0.6416 (mpp) cc_final: 0.5958 (mpp) REVERT: A 104 MET cc_start: 0.4603 (mmm) cc_final: 0.4244 (mmm) REVERT: A 154 MET cc_start: 0.8282 (mpp) cc_final: 0.7818 (mpp) REVERT: A 252 PHE cc_start: 0.9097 (t80) cc_final: 0.8339 (t80) REVERT: A 282 MET cc_start: 0.8337 (tpp) cc_final: 0.8103 (tpp) REVERT: A 285 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7528 (mmm) REVERT: A 303 PHE cc_start: 0.8371 (t80) cc_final: 0.7448 (t80) REVERT: A 913 THR cc_start: 0.8405 (p) cc_final: 0.8192 (t) REVERT: C 21 MET cc_start: 0.6417 (mpp) cc_final: 0.5953 (mpp) REVERT: C 154 MET cc_start: 0.8298 (mpp) cc_final: 0.7825 (mpp) REVERT: C 252 PHE cc_start: 0.9078 (t80) cc_final: 0.8251 (t80) REVERT: C 303 PHE cc_start: 0.8339 (t80) cc_final: 0.7140 (t80) REVERT: D 21 MET cc_start: 0.6425 (mpp) cc_final: 0.5954 (mpp) REVERT: D 154 MET cc_start: 0.8293 (mpp) cc_final: 0.7823 (mpp) REVERT: D 252 PHE cc_start: 0.9068 (t80) cc_final: 0.8313 (t80) REVERT: D 303 PHE cc_start: 0.8391 (t80) cc_final: 0.7245 (t80) REVERT: D 907 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7979 (tt0) outliers start: 90 outliers final: 49 residues processed: 345 average time/residue: 0.3315 time to fit residues: 199.4331 Evaluate side-chains 306 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 254 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 820 CYS Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 907 GLN Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 820 CYS Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 820 CYS Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 907 GLN Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 7.9990 chunk 195 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 293 optimal weight: 0.0970 chunk 237 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 175 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN A 151 GLN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 ASN C 907 GLN D 151 GLN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29172 Z= 0.162 Angle : 0.596 8.693 39580 Z= 0.293 Chirality : 0.043 0.255 4524 Planarity : 0.004 0.043 4984 Dihedral : 4.976 49.934 3848 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.28 % Allowed : 14.15 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3548 helix: -0.01 (0.13), residues: 1480 sheet: -1.60 (0.25), residues: 420 loop : -0.39 (0.17), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 246 HIS 0.003 0.001 HIS B 771 PHE 0.020 0.001 PHE B 164 TYR 0.011 0.001 TYR C 279 ARG 0.007 0.000 ARG A1018 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 305 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.6446 (mpp) cc_final: 0.5928 (mpp) REVERT: B 154 MET cc_start: 0.8367 (mpp) cc_final: 0.7869 (mpp) REVERT: B 252 PHE cc_start: 0.9072 (t80) cc_final: 0.8181 (t80) REVERT: B 303 PHE cc_start: 0.8229 (t80) cc_final: 0.7236 (t80) REVERT: B 972 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7770 (ppp80) REVERT: A 21 MET cc_start: 0.6455 (mpp) cc_final: 0.5933 (mpp) REVERT: A 154 MET cc_start: 0.8373 (mpp) cc_final: 0.7875 (mpp) REVERT: A 252 PHE cc_start: 0.9078 (t80) cc_final: 0.8439 (t80) REVERT: A 282 MET cc_start: 0.8287 (tpp) cc_final: 0.8067 (tpp) REVERT: A 285 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7540 (mmm) REVERT: A 830 MET cc_start: 0.7990 (mmm) cc_final: 0.7773 (mmm) REVERT: A 913 THR cc_start: 0.8361 (p) cc_final: 0.8133 (t) REVERT: C 21 MET cc_start: 0.6459 (mpp) cc_final: 0.5937 (mpp) REVERT: C 154 MET cc_start: 0.8370 (mpp) cc_final: 0.7871 (mpp) REVERT: C 252 PHE cc_start: 0.9002 (t80) cc_final: 0.8181 (t80) REVERT: C 303 PHE cc_start: 0.8252 (t80) cc_final: 0.7153 (t80) REVERT: C 907 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: D 21 MET cc_start: 0.6458 (mpp) cc_final: 0.5929 (mpp) REVERT: D 154 MET cc_start: 0.8368 (mpp) cc_final: 0.7870 (mpp) REVERT: D 252 PHE cc_start: 0.9002 (t80) cc_final: 0.8474 (t80) REVERT: D 972 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7784 (ppp80) outliers start: 72 outliers final: 38 residues processed: 357 average time/residue: 0.3227 time to fit residues: 200.7193 Evaluate side-chains 316 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 274 time to evaluate : 3.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 800 CYS Chi-restraints excluded: chain B residue 820 CYS Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain C residue 820 CYS Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 800 CYS Chi-restraints excluded: chain D residue 820 CYS Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 972 ARG Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 7.9990 chunk 309 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 chunk 285 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 28 optimal weight: 0.0030 chunk 113 optimal weight: 0.6980 chunk 180 optimal weight: 30.0000 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29172 Z= 0.164 Angle : 0.588 9.111 39580 Z= 0.289 Chirality : 0.041 0.189 4524 Planarity : 0.004 0.043 4984 Dihedral : 4.801 46.291 3848 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.79 % Allowed : 14.44 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3548 helix: 0.09 (0.13), residues: 1484 sheet: -1.45 (0.26), residues: 420 loop : -0.38 (0.17), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.002 0.001 HIS B 771 PHE 0.020 0.001 PHE B 164 TYR 0.011 0.001 TYR D 279 ARG 0.007 0.000 ARG D1018 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 272 time to evaluate : 3.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.6446 (mpp) cc_final: 0.5876 (mpp) REVERT: B 104 MET cc_start: 0.5471 (mmm) cc_final: 0.4758 (mmm) REVERT: B 154 MET cc_start: 0.8385 (mpp) cc_final: 0.7885 (mpp) REVERT: B 252 PHE cc_start: 0.9091 (t80) cc_final: 0.8379 (t80) REVERT: B 830 MET cc_start: 0.8089 (mmm) cc_final: 0.7808 (tpp) REVERT: B 972 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7846 (ppp80) REVERT: A 21 MET cc_start: 0.6442 (mpp) cc_final: 0.5867 (mpp) REVERT: A 104 MET cc_start: 0.5277 (mmm) cc_final: 0.5060 (mmm) REVERT: A 154 MET cc_start: 0.8394 (mpp) cc_final: 0.7887 (mpp) REVERT: A 252 PHE cc_start: 0.9092 (t80) cc_final: 0.8387 (t80) REVERT: A 285 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7539 (mmm) REVERT: A 827 ILE cc_start: 0.9334 (tt) cc_final: 0.9118 (tp) REVERT: A 830 MET cc_start: 0.8063 (mmm) cc_final: 0.7739 (mmm) REVERT: A 913 THR cc_start: 0.8407 (p) cc_final: 0.8184 (t) REVERT: A 972 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7861 (ppp80) REVERT: C 21 MET cc_start: 0.6445 (mpp) cc_final: 0.5885 (mpp) REVERT: C 104 MET cc_start: 0.5448 (mmm) cc_final: 0.4729 (mmm) REVERT: C 154 MET cc_start: 0.8388 (mpp) cc_final: 0.7897 (mpp) REVERT: C 252 PHE cc_start: 0.8985 (t80) cc_final: 0.8108 (t80) REVERT: C 303 PHE cc_start: 0.8300 (t80) cc_final: 0.7268 (t80) REVERT: C 897 ASP cc_start: 0.7682 (p0) cc_final: 0.7474 (p0) REVERT: C 972 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7864 (ppp80) REVERT: D 21 MET cc_start: 0.6446 (mpp) cc_final: 0.5886 (mpp) REVERT: D 104 MET cc_start: 0.5459 (mmm) cc_final: 0.4738 (mmm) REVERT: D 154 MET cc_start: 0.8381 (mpp) cc_final: 0.7891 (mpp) REVERT: D 252 PHE cc_start: 0.8985 (t80) cc_final: 0.8405 (t80) REVERT: D 907 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: D 972 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7850 (ppp80) outliers start: 88 outliers final: 48 residues processed: 333 average time/residue: 0.3343 time to fit residues: 194.0012 Evaluate side-chains 308 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 254 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 820 CYS Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 820 CYS Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 820 CYS Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 907 GLN Chi-restraints excluded: chain D residue 972 ARG Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 chunk 251 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 289 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 343 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 158 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 GLN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29172 Z= 0.162 Angle : 0.597 9.693 39580 Z= 0.292 Chirality : 0.043 0.237 4524 Planarity : 0.004 0.043 4984 Dihedral : 4.695 43.193 3848 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.16 % Allowed : 15.29 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3548 helix: 0.07 (0.13), residues: 1512 sheet: -1.32 (0.27), residues: 420 loop : -0.42 (0.17), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 246 HIS 0.002 0.001 HIS B 771 PHE 0.024 0.001 PHE A 307 TYR 0.010 0.001 TYR B 279 ARG 0.006 0.000 ARG D1018 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 261 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.6495 (mpp) cc_final: 0.5987 (mpp) REVERT: B 154 MET cc_start: 0.8387 (mpp) cc_final: 0.7879 (mpp) REVERT: B 252 PHE cc_start: 0.9080 (t80) cc_final: 0.8045 (t80) REVERT: B 303 PHE cc_start: 0.8286 (t80) cc_final: 0.7181 (t80) REVERT: B 972 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7786 (ppp80) REVERT: A 21 MET cc_start: 0.6494 (mpp) cc_final: 0.5985 (mpp) REVERT: A 154 MET cc_start: 0.8401 (mpp) cc_final: 0.7871 (mpp) REVERT: A 252 PHE cc_start: 0.9094 (t80) cc_final: 0.8143 (t80) REVERT: A 285 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7618 (mmm) REVERT: A 303 PHE cc_start: 0.8289 (t80) cc_final: 0.7226 (t80) REVERT: A 827 ILE cc_start: 0.9308 (tt) cc_final: 0.9077 (tp) REVERT: A 913 THR cc_start: 0.8408 (p) cc_final: 0.8157 (t) REVERT: A 972 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7810 (ppp80) REVERT: C 21 MET cc_start: 0.6516 (mpp) cc_final: 0.6003 (mpp) REVERT: C 154 MET cc_start: 0.8404 (mpp) cc_final: 0.7892 (mpp) REVERT: C 252 PHE cc_start: 0.8980 (t80) cc_final: 0.8099 (t80) REVERT: C 303 PHE cc_start: 0.8256 (t80) cc_final: 0.7166 (t80) REVERT: C 897 ASP cc_start: 0.7743 (p0) cc_final: 0.7518 (p0) REVERT: C 907 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: C 972 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7809 (ppp80) REVERT: D 21 MET cc_start: 0.6513 (mpp) cc_final: 0.5997 (mpp) REVERT: D 154 MET cc_start: 0.8393 (mpp) cc_final: 0.7886 (mpp) REVERT: D 252 PHE cc_start: 0.8965 (t80) cc_final: 0.8084 (t80) REVERT: D 303 PHE cc_start: 0.8268 (t80) cc_final: 0.7173 (t80) REVERT: D 907 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: D 972 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7790 (ppp80) outliers start: 68 outliers final: 50 residues processed: 310 average time/residue: 0.3307 time to fit residues: 175.3223 Evaluate side-chains 317 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 260 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 820 CYS Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 820 CYS Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 820 CYS Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 907 GLN Chi-restraints excluded: chain D residue 972 ARG Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 204 optimal weight: 0.0770 chunk 103 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 233 optimal weight: 20.0000 chunk 169 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 269 optimal weight: 0.0050 overall best weight: 0.9754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 GLN D 258 ASN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29172 Z= 0.159 Angle : 0.615 11.849 39580 Z= 0.297 Chirality : 0.042 0.234 4524 Planarity : 0.003 0.042 4984 Dihedral : 4.605 39.915 3848 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.22 % Allowed : 15.70 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3548 helix: 0.05 (0.13), residues: 1512 sheet: -1.29 (0.27), residues: 420 loop : -0.41 (0.17), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 246 HIS 0.002 0.001 HIS A 771 PHE 0.020 0.001 PHE C 164 TYR 0.009 0.001 TYR A 279 ARG 0.006 0.000 ARG D1018 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 269 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.6476 (mpp) cc_final: 0.5941 (mpp) REVERT: B 104 MET cc_start: 0.5275 (mmm) cc_final: 0.4514 (mmm) REVERT: B 154 MET cc_start: 0.8395 (mpp) cc_final: 0.7901 (mpp) REVERT: B 252 PHE cc_start: 0.9058 (t80) cc_final: 0.8066 (t80) REVERT: B 303 PHE cc_start: 0.8298 (t80) cc_final: 0.7183 (t80) REVERT: B 830 MET cc_start: 0.7897 (tpp) cc_final: 0.7550 (tpp) REVERT: A 21 MET cc_start: 0.6470 (mpp) cc_final: 0.5942 (mpp) REVERT: A 104 MET cc_start: 0.5500 (mmm) cc_final: 0.4784 (mmm) REVERT: A 154 MET cc_start: 0.8403 (mpp) cc_final: 0.7901 (mpp) REVERT: A 252 PHE cc_start: 0.9082 (t80) cc_final: 0.8129 (t80) REVERT: A 303 PHE cc_start: 0.8310 (t80) cc_final: 0.7187 (t80) REVERT: A 913 THR cc_start: 0.8428 (p) cc_final: 0.8172 (t) REVERT: C 21 MET cc_start: 0.6500 (mpp) cc_final: 0.5951 (mpp) REVERT: C 104 MET cc_start: 0.5247 (mmm) cc_final: 0.4458 (mmm) REVERT: C 154 MET cc_start: 0.8397 (mpp) cc_final: 0.7904 (mpp) REVERT: C 252 PHE cc_start: 0.8975 (t80) cc_final: 0.8084 (t80) REVERT: C 303 PHE cc_start: 0.8316 (t80) cc_final: 0.7262 (t80) REVERT: C 830 MET cc_start: 0.8075 (tpp) cc_final: 0.7530 (mmm) REVERT: C 897 ASP cc_start: 0.7778 (p0) cc_final: 0.7565 (p0) REVERT: D 21 MET cc_start: 0.6490 (mpp) cc_final: 0.5949 (mpp) REVERT: D 104 MET cc_start: 0.5270 (mmm) cc_final: 0.4482 (mmm) REVERT: D 154 MET cc_start: 0.8397 (mpp) cc_final: 0.7922 (mpp) REVERT: D 252 PHE cc_start: 0.8958 (t80) cc_final: 0.8049 (t80) REVERT: D 303 PHE cc_start: 0.8328 (t80) cc_final: 0.7251 (t80) REVERT: D 827 ILE cc_start: 0.9264 (tt) cc_final: 0.9054 (tp) REVERT: D 830 MET cc_start: 0.8081 (tpp) cc_final: 0.7519 (mmm) REVERT: D 907 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: D 972 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7798 (ppp80) outliers start: 70 outliers final: 57 residues processed: 317 average time/residue: 0.3275 time to fit residues: 178.8912 Evaluate side-chains 306 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 247 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 820 CYS Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 820 CYS Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 820 CYS Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 907 GLN Chi-restraints excluded: chain D residue 972 ARG Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 5.9990 chunk 328 optimal weight: 0.9990 chunk 299 optimal weight: 9.9990 chunk 319 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 251 optimal weight: 0.0270 chunk 98 optimal weight: 9.9990 chunk 288 optimal weight: 10.0000 chunk 302 optimal weight: 0.0070 chunk 318 optimal weight: 9.9990 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 GLN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN D 616 HIS D 907 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29172 Z= 0.186 Angle : 0.642 10.870 39580 Z= 0.310 Chirality : 0.043 0.227 4524 Planarity : 0.004 0.043 4984 Dihedral : 4.563 37.303 3848 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.19 % Allowed : 16.09 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 3548 helix: 0.00 (0.13), residues: 1540 sheet: -1.20 (0.27), residues: 416 loop : -0.43 (0.17), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 246 HIS 0.002 0.001 HIS B 771 PHE 0.025 0.001 PHE D 307 TYR 0.008 0.001 TYR C 318 ARG 0.006 0.000 ARG D1018 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 252 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.6478 (mpp) cc_final: 0.5935 (mpp) REVERT: B 104 MET cc_start: 0.5545 (mmm) cc_final: 0.4890 (mmm) REVERT: B 154 MET cc_start: 0.8396 (mpp) cc_final: 0.7902 (mpp) REVERT: B 162 LEU cc_start: 0.9368 (tt) cc_final: 0.9162 (pp) REVERT: B 252 PHE cc_start: 0.9065 (t80) cc_final: 0.8069 (t80) REVERT: B 303 PHE cc_start: 0.8302 (t80) cc_final: 0.7167 (t80) REVERT: B 907 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: A 21 MET cc_start: 0.6478 (mpp) cc_final: 0.5922 (mpp) REVERT: A 104 MET cc_start: 0.5393 (mmm) cc_final: 0.4697 (mmm) REVERT: A 154 MET cc_start: 0.8407 (mpp) cc_final: 0.7895 (mpp) REVERT: A 252 PHE cc_start: 0.9051 (t80) cc_final: 0.8073 (t80) REVERT: A 303 PHE cc_start: 0.8311 (t80) cc_final: 0.7192 (t80) REVERT: A 830 MET cc_start: 0.8046 (tpp) cc_final: 0.7819 (tpp) REVERT: A 913 THR cc_start: 0.8473 (p) cc_final: 0.8218 (t) REVERT: C 21 MET cc_start: 0.6495 (mpp) cc_final: 0.5940 (mpp) REVERT: C 104 MET cc_start: 0.5748 (mmm) cc_final: 0.5034 (mmm) REVERT: C 154 MET cc_start: 0.8404 (mpp) cc_final: 0.7902 (mpp) REVERT: C 213 ARG cc_start: 0.8422 (mtt180) cc_final: 0.8089 (mmt-90) REVERT: C 252 PHE cc_start: 0.8983 (t80) cc_final: 0.8064 (t80) REVERT: C 303 PHE cc_start: 0.8345 (t80) cc_final: 0.7229 (t80) REVERT: C 385 LEU cc_start: 0.8618 (mt) cc_final: 0.8308 (tt) REVERT: D 21 MET cc_start: 0.6499 (mpp) cc_final: 0.5938 (mpp) REVERT: D 104 MET cc_start: 0.5752 (mmm) cc_final: 0.5034 (mmm) REVERT: D 154 MET cc_start: 0.8400 (mpp) cc_final: 0.7903 (mpp) REVERT: D 213 ARG cc_start: 0.8413 (mtt180) cc_final: 0.8070 (mmt-90) REVERT: D 252 PHE cc_start: 0.8977 (t80) cc_final: 0.8374 (t80) REVERT: D 385 LEU cc_start: 0.8606 (mt) cc_final: 0.8304 (tt) REVERT: D 907 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7806 (tt0) outliers start: 69 outliers final: 60 residues processed: 304 average time/residue: 0.3463 time to fit residues: 182.4572 Evaluate side-chains 310 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 248 time to evaluate : 3.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 820 CYS Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 907 GLN Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 820 CYS Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 820 CYS Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 907 GLN Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 160 optimal weight: 0.0050 chunk 235 optimal weight: 0.2980 chunk 354 optimal weight: 0.8980 chunk 326 optimal weight: 6.9990 chunk 282 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 218 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN B 358 ASN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 GLN A 258 ASN A 358 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN C 258 ASN C 358 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29172 Z= 0.156 Angle : 0.663 10.914 39580 Z= 0.314 Chirality : 0.043 0.231 4524 Planarity : 0.004 0.043 4984 Dihedral : 4.486 33.815 3848 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.94 % Allowed : 16.47 % Favored : 81.60 % 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: -0.60 (0.15), residues: 3548 helix: 0.02 (0.13), residues: 1540 sheet: -1.06 (0.27), residues: 408 loop : -0.47 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 246 HIS 0.002 0.001 HIS B 771 PHE 0.020 0.001 PHE B 194 TYR 0.009 0.001 TYR A 318 ARG 0.005 0.000 ARG D1018 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 254 time to evaluate : 2.622 Fit side-chains revert: symmetry clash REVERT: B 21 MET cc_start: 0.6419 (mpp) cc_final: 0.5865 (mpp) REVERT: B 104 MET cc_start: 0.5769 (mmm) cc_final: 0.5099 (mmm) REVERT: B 154 MET cc_start: 0.8381 (mpp) cc_final: 0.7899 (mpp) REVERT: B 162 LEU cc_start: 0.9330 (tt) cc_final: 0.9072 (pp) REVERT: B 252 PHE cc_start: 0.9054 (t80) cc_final: 0.8351 (t80) REVERT: B 907 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: A 21 MET cc_start: 0.6410 (mpp) cc_final: 0.5850 (mpp) REVERT: A 104 MET cc_start: 0.5530 (mmm) cc_final: 0.4949 (mmm) REVERT: A 154 MET cc_start: 0.8392 (mpp) cc_final: 0.7908 (mpp) REVERT: A 252 PHE cc_start: 0.9044 (t80) cc_final: 0.8065 (t80) REVERT: A 303 PHE cc_start: 0.8289 (t80) cc_final: 0.7186 (t80) REVERT: A 830 MET cc_start: 0.8069 (tpp) cc_final: 0.7467 (mmm) REVERT: A 913 THR cc_start: 0.8458 (p) cc_final: 0.8222 (t) REVERT: C 21 MET cc_start: 0.6427 (mpp) cc_final: 0.5874 (mpp) REVERT: C 104 MET cc_start: 0.5746 (mmm) cc_final: 0.5037 (mmm) REVERT: C 154 MET cc_start: 0.8395 (mpp) cc_final: 0.7917 (mpp) REVERT: C 213 ARG cc_start: 0.8408 (mtt180) cc_final: 0.7946 (mmt-90) REVERT: C 252 PHE cc_start: 0.8950 (t80) cc_final: 0.8056 (t80) REVERT: C 303 PHE cc_start: 0.8280 (t80) cc_final: 0.7199 (t80) REVERT: C 385 LEU cc_start: 0.8589 (mt) cc_final: 0.8321 (tt) REVERT: D 21 MET cc_start: 0.6424 (mpp) cc_final: 0.5858 (mpp) REVERT: D 104 MET cc_start: 0.5743 (mmm) cc_final: 0.5041 (mmm) REVERT: D 154 MET cc_start: 0.8393 (mpp) cc_final: 0.7914 (mpp) REVERT: D 213 ARG cc_start: 0.8393 (mtt180) cc_final: 0.8057 (mmt-90) REVERT: D 252 PHE cc_start: 0.8951 (t80) cc_final: 0.8036 (t80) REVERT: D 303 PHE cc_start: 0.8250 (t80) cc_final: 0.7129 (t80) REVERT: D 385 LEU cc_start: 0.8584 (mt) cc_final: 0.8313 (tt) REVERT: D 907 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7680 (tt0) outliers start: 61 outliers final: 53 residues processed: 302 average time/residue: 0.3324 time to fit residues: 174.2272 Evaluate side-chains 299 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 244 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 820 CYS Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 907 GLN Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 820 CYS Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 820 CYS Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 907 GLN Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 7.9990 chunk 300 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 260 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 282 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.0010 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 GLN A 358 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.060479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.045891 restraints weight = 143744.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.047355 restraints weight = 82426.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.048241 restraints weight = 54959.441| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29172 Z= 0.165 Angle : 0.670 17.340 39580 Z= 0.316 Chirality : 0.044 0.230 4524 Planarity : 0.003 0.043 4984 Dihedral : 4.447 31.600 3848 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.84 % Allowed : 17.16 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 3548 helix: 0.12 (0.13), residues: 1512 sheet: -0.99 (0.27), residues: 408 loop : -0.37 (0.17), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 246 HIS 0.002 0.001 HIS B 771 PHE 0.020 0.001 PHE C 164 TYR 0.008 0.001 TYR C 318 ARG 0.004 0.000 ARG D1018 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4976.60 seconds wall clock time: 92 minutes 4.17 seconds (5524.17 seconds total)