Starting phenix.real_space_refine on Wed Mar 20 22:42:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkk_34853/03_2024/8hkk_34853.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkk_34853/03_2024/8hkk_34853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkk_34853/03_2024/8hkk_34853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkk_34853/03_2024/8hkk_34853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkk_34853/03_2024/8hkk_34853.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkk_34853/03_2024/8hkk_34853.pdb" } resolution = 2.84 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= 0.044 sd= 0.156 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: 7 Type Number sf(0) Gaussians K 18 8.98 5 Zn 4 6.06 5 S 212 5.16 5 Na 1 4.78 5 C 18576 2.51 5 N 4768 2.21 5 O 5108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A ASP 843": "OD1" <-> "OD2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A ASP 878": "OD1" <-> "OD2" Residue "A TYR 938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 946": "OE1" <-> "OE2" Residue "A GLU 951": "OE1" <-> "OE2" Residue "A PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1014": "OE1" <-> "OE2" Residue "A ASP 1016": "OD1" <-> "OD2" Residue "A GLU 1044": "OE1" <-> "OE2" Residue "A GLU 1145": "OE1" <-> "OE2" Residue "A GLU 1148": "OE1" <-> "OE2" Residue "B PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B GLU 601": "OE1" <-> "OE2" Residue "B TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "B GLU 830": "OE1" <-> "OE2" Residue "B ASP 843": "OD1" <-> "OD2" Residue "B ASP 878": "OD1" <-> "OD2" Residue "B ASP 894": "OD1" <-> "OD2" Residue "B TYR 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 976": "OD1" <-> "OD2" Residue "B TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1014": "OE1" <-> "OE2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1148": "OE1" <-> "OE2" Residue "B ASP 1187": "OD1" <-> "OD2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 348": "OE1" <-> "OE2" Residue "C ASP 388": "OD1" <-> "OD2" Residue "C ASP 413": "OD1" <-> "OD2" Residue "C ASP 448": "OD1" <-> "OD2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C GLU 509": "OE1" <-> "OE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C GLU 830": "OE1" <-> "OE2" Residue "C ASP 843": "OD1" <-> "OD2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C ASP 878": "OD1" <-> "OD2" Residue "C ASP 894": "OD1" <-> "OD2" Residue "C TYR 938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 951": "OE1" <-> "OE2" Residue "C PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1014": "OE1" <-> "OE2" Residue "C ASP 1016": "OD1" <-> "OD2" Residue "C TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1148": "OE1" <-> "OE2" Residue "C ASP 1187": "OD1" <-> "OD2" Residue "D PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D GLU 509": "OE1" <-> "OE2" Residue "D GLU 544": "OE1" <-> "OE2" Residue "D GLU 576": "OE1" <-> "OE2" Residue "D GLU 601": "OE1" <-> "OE2" Residue "D ASP 602": "OD1" <-> "OD2" Residue "D ASP 843": "OD1" <-> "OD2" Residue "D ASP 878": "OD1" <-> "OD2" Residue "D ASP 894": "OD1" <-> "OD2" Residue "D TYR 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 946": "OE1" <-> "OE2" Residue "D PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1014": "OE1" <-> "OE2" Residue "D ASP 1016": "OD1" <-> "OD2" Residue "D TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1148": "OE1" <-> "OE2" Residue "D ASP 1187": "OD1" <-> "OD2" 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: 28687 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7166 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 7166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7166 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 7166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7166 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 7166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7166 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' K': 6, ' NA': 1, ' ZN': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' ZN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' ZN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' ZN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4448 SG CYS A 777 94.859 62.372 128.271 1.00 77.48 S ATOM 4454 SG CYS A 778 98.691 61.972 128.072 1.00 86.07 S ATOM 4508 SG CYS A 785 97.156 65.349 129.088 1.00116.80 S ATOM 11614 SG CYS B 777 85.146 94.663 128.336 1.00 79.33 S ATOM 11620 SG CYS B 778 85.637 98.482 128.141 1.00 90.83 S ATOM 11674 SG CYS B 785 82.198 97.031 129.102 1.00112.95 S ATOM 18780 SG CYS C 777 53.019 84.899 128.309 1.00 77.01 S ATOM 18786 SG CYS C 778 49.203 85.387 128.159 1.00 84.04 S ATOM 18840 SG CYS C 785 50.660 81.951 129.111 1.00117.77 S ATOM 25946 SG CYS D 777 62.637 52.726 128.313 1.00 74.25 S ATOM 25952 SG CYS D 778 62.212 48.895 128.101 1.00 84.06 S ATOM 26006 SG CYS D 785 65.618 50.419 129.067 1.00105.77 S Time building chain proxies: 15.67, per 1000 atoms: 0.55 Number of scatterers: 28687 At special positions: 0 Unit cell: (148.72, 148.72, 142.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 K 18 19.00 S 212 16.00 Na 1 11.00 O 5108 8.00 N 4768 7.00 C 18576 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: 10.58 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 785 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 777 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 778 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 777 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 785 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 778 " pdb=" ZN C1301 " pdb="ZN ZN C1301 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 777 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 778 " pdb=" ZN D1301 " pdb="ZN ZN D1301 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 785 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 777 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 778 " Number of angles added : 12 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 20 sheets defined 53.3% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 110 through 136 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.633A pdb=" N LEU A 141 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 173 through 198 removed outlier: 3.606A pdb=" N ALA A 178 " --> pdb=" O MET A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 226 through 227 No H-bonds generated for 'chain 'A' and resid 226 through 227' Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.565A pdb=" N LEU A 231 " --> pdb=" O TRP A 228 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN A 233 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 256 removed outlier: 4.084A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 293 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 324 through 357 Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 395 through 400 removed outlier: 6.716A pdb=" N ARG A 398 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 removed outlier: 3.550A pdb=" N ILE A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 493 through 500 removed outlier: 4.686A pdb=" N PHE A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS A 499 " --> pdb=" O ASN A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 removed outlier: 3.533A pdb=" N CYS A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 547 through 557 Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.580A pdb=" N PHE A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.545A pdb=" N TYR A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 822 Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 843 through 851 Processing helix chain 'A' and resid 865 through 873 Processing helix chain 'A' and resid 893 through 897 Processing helix chain 'A' and resid 898 through 912 Processing helix chain 'A' and resid 923 through 930 removed outlier: 4.228A pdb=" N ARG A 928 " --> pdb=" O SER A 925 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 930 " --> pdb=" O MET A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 952 removed outlier: 3.895A pdb=" N SER A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 960 removed outlier: 3.964A pdb=" N PHE A 960 " --> pdb=" O ALA A 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 960' Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 972 through 982 removed outlier: 3.825A pdb=" N ASP A 976 " --> pdb=" O ILE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 996 Processing helix chain 'A' and resid 1013 through 1017 Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1129 through 1143 Processing helix chain 'A' and resid 1144 through 1161 Processing helix chain 'B' and resid 111 through 137 Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.636A pdb=" N LEU B 141 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 173 through 198 removed outlier: 3.515A pdb=" N ALA B 178 " --> pdb=" O MET B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 Proline residue: B 221 - end of helix removed outlier: 3.762A pdb=" N ILE B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Proline residue: B 230 - end of helix No H-bonds generated for 'chain 'B' and resid 227 through 232' Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 240 through 256 removed outlier: 3.889A pdb=" N LEU B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 293 Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 324 through 357 Proline residue: B 343 - end of helix removed outlier: 3.538A pdb=" N GLU B 355 " --> pdb=" O TYR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 394 Processing helix chain 'B' and resid 395 through 400 removed outlier: 6.728A pdb=" N ARG B 398 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 400 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 422 removed outlier: 3.513A pdb=" N VAL B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 463 through 482 Processing helix chain 'B' and resid 493 through 500 removed outlier: 4.669A pdb=" N PHE B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B 499 " --> pdb=" O ASN B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 removed outlier: 3.525A pdb=" N CYS B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'B' and resid 547 through 557 Processing helix chain 'B' and resid 572 through 576 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.594A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 797 removed outlier: 3.524A pdb=" N TYR B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 822 Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 843 through 851 Processing helix chain 'B' and resid 865 through 873 Processing helix chain 'B' and resid 893 through 897 Processing helix chain 'B' and resid 898 through 912 Processing helix chain 'B' and resid 923 through 930 removed outlier: 4.217A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B 930 " --> pdb=" O MET B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 952 removed outlier: 3.949A pdb=" N SER B 943 " --> pdb=" O SER B 939 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 960 removed outlier: 3.856A pdb=" N PHE B 960 " --> pdb=" O ALA B 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 957 through 960' Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 972 through 982 removed outlier: 3.751A pdb=" N ASP B 976 " --> pdb=" O ILE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 997 Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1021 through 1033 Processing helix chain 'B' and resid 1129 through 1143 Processing helix chain 'B' and resid 1144 through 1161 Processing helix chain 'C' and resid 111 through 137 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.663A pdb=" N LEU C 141 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 173 through 198 removed outlier: 3.594A pdb=" N ALA C 178 " --> pdb=" O MET C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 Proline residue: C 221 - end of helix Processing helix chain 'C' and resid 229 through 233 removed outlier: 4.348A pdb=" N ASN C 233 " --> pdb=" O PRO C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 240 through 254 removed outlier: 4.000A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 293 removed outlier: 4.448A pdb=" N GLN C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 324 through 357 Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 382 through 394 Processing helix chain 'C' and resid 413 through 422 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 463 through 482 Processing helix chain 'C' and resid 493 through 500 removed outlier: 4.681A pdb=" N PHE C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS C 499 " --> pdb=" O ASN C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 removed outlier: 3.544A pdb=" N CYS C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'C' and resid 547 through 557 Processing helix chain 'C' and resid 572 through 576 Processing helix chain 'C' and resid 579 through 592 Processing helix chain 'C' and resid 633 through 644 removed outlier: 3.592A pdb=" N PHE C 637 " --> pdb=" O SER C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 797 removed outlier: 3.543A pdb=" N TYR C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 822 Proline residue: C 820 - end of helix Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 865 through 873 Processing helix chain 'C' and resid 893 through 897 Processing helix chain 'C' and resid 898 through 912 Processing helix chain 'C' and resid 923 through 930 removed outlier: 4.228A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C 930 " --> pdb=" O MET C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 952 removed outlier: 3.903A pdb=" N SER C 943 " --> pdb=" O SER C 939 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 960 removed outlier: 3.855A pdb=" N PHE C 960 " --> pdb=" O ALA C 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 957 through 960' Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 972 through 982 removed outlier: 3.664A pdb=" N ASP C 976 " --> pdb=" O ILE C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 997 Processing helix chain 'C' and resid 1013 through 1017 Processing helix chain 'C' and resid 1021 through 1033 Processing helix chain 'C' and resid 1129 through 1143 Processing helix chain 'C' and resid 1144 through 1161 Processing helix chain 'D' and resid 111 through 136 Processing helix chain 'D' and resid 138 through 142 removed outlier: 3.596A pdb=" N LEU D 141 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 173 through 198 removed outlier: 3.538A pdb=" N ALA D 178 " --> pdb=" O MET D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 225 Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 226 through 227 No H-bonds generated for 'chain 'D' and resid 226 through 227' Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 240 through 256 removed outlier: 4.059A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 293 removed outlier: 4.481A pdb=" N GLN D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 324 through 357 Proline residue: D 343 - end of helix removed outlier: 3.846A pdb=" N GLU D 355 " --> pdb=" O TYR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 394 Processing helix chain 'D' and resid 395 through 400 removed outlier: 6.717A pdb=" N ARG D 398 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 400 " --> pdb=" O PRO D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 422 removed outlier: 3.510A pdb=" N VAL D 419 " --> pdb=" O GLN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 463 through 482 Processing helix chain 'D' and resid 493 through 500 removed outlier: 4.673A pdb=" N PHE D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS D 499 " --> pdb=" O ASN D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 removed outlier: 3.519A pdb=" N CYS D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 534 Processing helix chain 'D' and resid 547 through 557 Processing helix chain 'D' and resid 572 through 576 Processing helix chain 'D' and resid 579 through 592 Processing helix chain 'D' and resid 633 through 644 removed outlier: 3.593A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 797 removed outlier: 3.543A pdb=" N TYR D 796 " --> pdb=" O ASP D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 822 Proline residue: D 820 - end of helix Processing helix chain 'D' and resid 843 through 851 Processing helix chain 'D' and resid 865 through 873 Processing helix chain 'D' and resid 893 through 897 Processing helix chain 'D' and resid 898 through 912 Processing helix chain 'D' and resid 923 through 930 removed outlier: 4.231A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET D 930 " --> pdb=" O MET D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 952 removed outlier: 3.951A pdb=" N SER D 943 " --> pdb=" O SER D 939 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 957 through 960 removed outlier: 4.036A pdb=" N PHE D 960 " --> pdb=" O ALA D 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 957 through 960' Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 972 through 982 removed outlier: 3.652A pdb=" N ASP D 976 " --> pdb=" O ILE D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 997 Processing helix chain 'D' and resid 1013 through 1017 Processing helix chain 'D' and resid 1021 through 1033 Processing helix chain 'D' and resid 1129 through 1143 Processing helix chain 'D' and resid 1144 through 1161 Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 432 removed outlier: 6.198A pdb=" N VAL A 404 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU A 432 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE A 406 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N PHE A 454 " --> pdb=" O HIS A 373 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A 375 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS A 453 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLN A 490 " --> pdb=" O CYS A 453 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE A 455 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.522A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 750 through 752 Processing sheet with id=AA4, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.103A pdb=" N ILE A 834 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N MET A 859 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 836 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU A 802 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 879 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 916 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 920 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 3.964A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A1039 " --> pdb=" O TYR A1197 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A1199 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 429 through 432 removed outlier: 6.288A pdb=" N VAL B 404 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU B 432 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE B 406 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 453 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLN B 490 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE B 455 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.527A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 750 through 752 Processing sheet with id=AA9, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.065A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU B 802 " --> pdb=" O ALA B 877 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 879 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER B 916 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 920 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 3.933A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY B1039 " --> pdb=" O TYR B1197 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE B1199 " --> pdb=" O PRO B1037 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 429 through 432 removed outlier: 6.272A pdb=" N VAL C 404 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU C 432 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE C 406 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N PHE C 454 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C 375 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS C 453 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLN C 490 " --> pdb=" O CYS C 453 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE C 455 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.520A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 750 through 752 Processing sheet with id=AB5, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.100A pdb=" N ILE C 834 " --> pdb=" O TYR C 857 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N MET C 859 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU C 836 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU C 802 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 879 " --> pdb=" O LEU C 802 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER C 916 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 920 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 3.962A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY C1039 " --> pdb=" O TYR C1197 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C1199 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 429 through 432 removed outlier: 6.148A pdb=" N VAL D 404 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU D 432 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE D 406 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N PHE D 454 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL D 375 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU D 456 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N CYS D 377 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS D 453 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLN D 490 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE D 455 " --> pdb=" O GLN D 490 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.560A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 750 through 752 Processing sheet with id=AC1, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.073A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU D 802 " --> pdb=" O ALA D 877 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN D 879 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 920 " --> pdb=" O VAL D 882 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 3.954A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY D1039 " --> pdb=" O TYR D1197 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE D1199 " --> pdb=" O PRO D1037 " (cutoff:3.500A) 1393 hydrogen bonds defined for protein. 3903 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: 10.28 Time building geometry restraints manager: 11.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 1.03: 3 1.03 - 1.40: 11880 1.40 - 1.77: 17130 1.77 - 2.13: 313 2.13 - 2.50: 2 Bond restraints: 29328 Sorted by residual: bond pdb=" CG PRO D 237 " pdb=" CD PRO D 237 " ideal model delta sigma weight residual 1.503 0.662 0.841 3.40e-02 8.65e+02 6.12e+02 bond pdb=" CB PRO C 237 " pdb=" CG PRO C 237 " ideal model delta sigma weight residual 1.492 2.502 -1.010 5.00e-02 4.00e+02 4.08e+02 bond pdb=" CB PRO B 237 " pdb=" CG PRO B 237 " ideal model delta sigma weight residual 1.492 2.493 -1.001 5.00e-02 4.00e+02 4.01e+02 bond pdb=" CG PRO B 237 " pdb=" CD PRO B 237 " ideal model delta sigma weight residual 1.503 0.978 0.525 3.40e-02 8.65e+02 2.39e+02 bond pdb=" CG PRO C 237 " pdb=" CD PRO C 237 " ideal model delta sigma weight residual 1.503 0.991 0.512 3.40e-02 8.65e+02 2.26e+02 ... (remaining 29323 not shown) Histogram of bond angle deviations from ideal: 0.01 - 34.11: 2 34.11 - 68.21: 0 68.21 - 102.31: 161 102.31 - 136.41: 39628 136.41 - 170.51: 5 Bond angle restraints: 39796 Sorted by residual: angle pdb=" CB PRO C 237 " pdb=" CG PRO C 237 " pdb=" CD PRO C 237 " ideal model delta sigma weight residual 106.10 0.01 106.09 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CB PRO B 237 " pdb=" CG PRO B 237 " pdb=" CD PRO B 237 " ideal model delta sigma weight residual 106.10 2.52 103.58 3.20e+00 9.77e-02 1.05e+03 angle pdb=" N GLY C 147 " pdb=" CA GLY C 147 " pdb=" C GLY C 147 " ideal model delta sigma weight residual 113.18 169.32 -56.14 2.37e+00 1.78e-01 5.61e+02 angle pdb=" C TRP A 146 " pdb=" CA TRP A 146 " pdb=" CB TRP A 146 " ideal model delta sigma weight residual 112.06 76.20 35.86 1.57e+00 4.06e-01 5.22e+02 angle pdb=" C GLY C 147 " pdb=" N CYS C 148 " pdb=" CA CYS C 148 " ideal model delta sigma weight residual 121.80 170.51 -48.71 2.44e+00 1.68e-01 3.99e+02 ... (remaining 39791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.80: 16557 27.80 - 55.60: 922 55.60 - 83.40: 97 83.40 - 111.20: 11 111.20 - 138.99: 1 Dihedral angle restraints: 17588 sinusoidal: 6976 harmonic: 10612 Sorted by residual: dihedral pdb=" C TRP A 146 " pdb=" N TRP A 146 " pdb=" CA TRP A 146 " pdb=" CB TRP A 146 " ideal model delta harmonic sigma weight residual -122.60 -90.31 -32.29 0 2.50e+00 1.60e-01 1.67e+02 dihedral pdb=" N PRO D 149 " pdb=" C PRO D 149 " pdb=" CA PRO D 149 " pdb=" CB PRO D 149 " ideal model delta harmonic sigma weight residual 115.10 136.11 -21.01 0 2.50e+00 1.60e-01 7.06e+01 dihedral pdb=" C PRO D 149 " pdb=" N PRO D 149 " pdb=" CA PRO D 149 " pdb=" CB PRO D 149 " ideal model delta harmonic sigma weight residual -120.70 -140.75 20.05 0 2.50e+00 1.60e-01 6.43e+01 ... (remaining 17585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 4533 0.224 - 0.449: 10 0.449 - 0.673: 2 0.673 - 0.898: 2 0.898 - 1.122: 1 Chirality restraints: 4548 Sorted by residual: chirality pdb=" CA PRO D 149 " pdb=" N PRO D 149 " pdb=" C PRO D 149 " pdb=" CB PRO D 149 " both_signs ideal model delta sigma weight residual False 2.72 1.60 1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" CA PRO B 149 " pdb=" N PRO B 149 " pdb=" C PRO B 149 " pdb=" CB PRO B 149 " both_signs ideal model delta sigma weight residual False 2.72 1.92 0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CA CYS C 148 " pdb=" N CYS C 148 " pdb=" C CYS C 148 " pdb=" CB CYS C 148 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.21e+01 ... (remaining 4545 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 228 " 0.106 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO A 229 " -0.262 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 147 " -0.030 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C GLY C 147 " 0.099 2.00e-02 2.50e+03 pdb=" O GLY C 147 " -0.034 2.00e-02 2.50e+03 pdb=" N CYS C 148 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 148 " -0.093 5.00e-02 4.00e+02 1.39e-01 3.11e+01 pdb=" N PRO B 149 " 0.241 5.00e-02 4.00e+02 pdb=" CA PRO B 149 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO B 149 " -0.073 5.00e-02 4.00e+02 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.40: 113 2.40 - 3.08: 19327 3.08 - 3.77: 51748 3.77 - 4.45: 84905 4.45 - 5.14: 133006 Nonbonded interactions: 289099 Sorted by model distance: nonbonded pdb=" CE MET B 267 " pdb=" CD2 LEU B 349 " model vdw 1.710 3.880 nonbonded pdb=" O TRP A 146 " pdb=" CG TRP A 146 " model vdw 1.802 3.260 nonbonded pdb=" O TRP A 146 " pdb=" CB TRP A 146 " model vdw 1.866 2.752 nonbonded pdb=" CD1 PHE B 235 " pdb=" NE2 HIS B 291 " model vdw 1.914 3.420 nonbonded pdb=" OD1 ASP C 782 " pdb=" CG MET C 859 " model vdw 1.970 3.440 ... (remaining 289094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 110 through 1205 or resid 1301 or resid 1303 through 1305) \ ) selection = (chain 'B' and (resid 110 through 1205 or resid 1301 or resid 1303 through 1305) \ ) selection = (chain 'C' and (resid 110 through 1205 or resid 1301 or resid 1303 through 1305) \ ) selection = (chain 'D' and (resid 110 through 1205 or resid 1301 or resid 1303 through 1305) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.770 Check model and map are aligned: 0.460 Set scattering table: 0.250 Process input model: 79.740 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.160 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.010 29328 Z= 0.756 Angle : 1.187 106.087 39796 Z= 0.548 Chirality : 0.051 1.122 4548 Planarity : 0.008 0.152 4992 Dihedral : 16.136 138.994 10700 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.10 % Favored : 97.79 % Rotamer: Outliers : 0.92 % Allowed : 20.87 % Favored : 78.21 % Cbeta Deviations : 0.23 % 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: -0.41 (0.13), residues: 3532 helix: -0.12 (0.12), residues: 1704 sheet: -0.27 (0.25), residues: 348 loop : -0.24 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 177 HIS 0.014 0.001 HIS C1159 PHE 0.043 0.001 PHE D 235 TYR 0.023 0.001 TYR A 317 ARG 0.008 0.000 ARG A 398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 517 time to evaluate : 3.370 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: A 228 TRP cc_start: 0.6715 (m100) cc_final: 0.5643 (m-10) REVERT: A 292 LEU cc_start: 0.8823 (tp) cc_final: 0.8578 (tt) REVERT: A 385 LEU cc_start: 0.8933 (tt) cc_final: 0.8718 (tp) REVERT: A 582 TYR cc_start: 0.8236 (t80) cc_final: 0.7888 (t80) REVERT: A 859 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8150 (ttt) REVERT: B 124 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8317 (pp) REVERT: C 174 MET cc_start: 0.6820 (ptp) cc_final: 0.6500 (pmm) REVERT: C 182 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8250 (pp) REVERT: C 234 LEU cc_start: 0.8720 (tm) cc_final: 0.8481 (tt) REVERT: C 252 MET cc_start: 0.6833 (ttt) cc_final: 0.6614 (tmt) REVERT: C 293 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7646 (mt-10) REVERT: D 174 MET cc_start: 0.6994 (tpp) cc_final: 0.5872 (mpm) REVERT: D 237 PRO cc_start: 0.8556 (Cg_exo) cc_final: 0.8055 (Cg_endo) REVERT: D 243 TRP cc_start: 0.6892 (m-10) cc_final: 0.6571 (m-90) REVERT: D 293 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7776 (mt-10) REVERT: D 385 LEU cc_start: 0.8938 (tt) cc_final: 0.8710 (tp) REVERT: D 908 MET cc_start: 0.8386 (mmt) cc_final: 0.7897 (mmt) REVERT: D 944 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7919 (mmtm) outliers start: 29 outliers final: 13 residues processed: 535 average time/residue: 1.3391 time to fit residues: 838.8327 Evaluate side-chains 471 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 455 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 1045 SER Chi-restraints excluded: chain D residue 1176 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 149 optimal weight: 0.0570 chunk 92 optimal weight: 20.0000 chunk 182 optimal weight: 40.0000 chunk 144 optimal weight: 5.9990 chunk 279 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 chunk 207 optimal weight: 0.0570 chunk 323 optimal weight: 7.9990 overall best weight: 2.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 470 GLN A 490 GLN A 505 HIS A 535 HIS A 632 ASN A 816 ASN A 845 HIS A 865 ASN A 904 ASN A1159 HIS A1174 GLN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 270 GLN B 291 HIS B 470 GLN B 490 GLN B 505 HIS B 535 HIS B 632 ASN B 816 ASN B 845 HIS B 865 ASN ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 HIS C 218 ASN C 298 ASN C 415 GLN C 470 GLN C 490 GLN C 505 HIS C 535 HIS C 632 ASN C 816 ASN C 904 ASN C1159 HIS D 156 ASN D 180 GLN D 218 ASN D 298 ASN D 490 GLN D 505 HIS D 535 HIS D 632 ASN D 816 ASN ** D 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.181 29328 Z= 0.394 Angle : 0.668 14.730 39796 Z= 0.332 Chirality : 0.045 0.297 4548 Planarity : 0.007 0.153 4992 Dihedral : 5.045 55.735 3926 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.83 % Favored : 97.06 % Rotamer: Outliers : 4.74 % Allowed : 20.26 % Favored : 75.00 % 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: 0.18 (0.14), residues: 3532 helix: 0.56 (0.12), residues: 1708 sheet: -0.58 (0.25), residues: 356 loop : -0.03 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 177 HIS 0.011 0.002 HIS C1159 PHE 0.023 0.002 PHE B 120 TYR 0.025 0.002 TYR A 351 ARG 0.012 0.001 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 473 time to evaluate : 3.140 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: A 177 TRP cc_start: 0.6532 (t60) cc_final: 0.5991 (t60) REVERT: A 228 TRP cc_start: 0.6821 (m100) cc_final: 0.5695 (m-10) REVERT: A 241 ASN cc_start: 0.8265 (t0) cc_final: 0.7858 (t0) REVERT: A 252 MET cc_start: 0.6396 (tmt) cc_final: 0.5647 (mpt) REVERT: A 267 MET cc_start: 0.7329 (tmm) cc_final: 0.6338 (pmt) REVERT: A 323 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8164 (mmtm) REVERT: A 770 LEU cc_start: 0.8278 (mt) cc_final: 0.8048 (mt) REVERT: A 959 MET cc_start: 0.8776 (ttp) cc_final: 0.8552 (ttm) REVERT: B 372 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7909 (mmtp) REVERT: B 976 ASP cc_start: 0.8275 (m-30) cc_final: 0.8030 (m-30) REVERT: C 174 MET cc_start: 0.6985 (ptp) cc_final: 0.6556 (pmm) REVERT: C 177 TRP cc_start: 0.7537 (t60) cc_final: 0.6953 (t60) REVERT: C 182 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8357 (pp) REVERT: C 188 PHE cc_start: 0.7640 (t80) cc_final: 0.6964 (t80) REVERT: C 200 LYS cc_start: 0.6153 (OUTLIER) cc_final: 0.5909 (mptt) REVERT: C 241 ASN cc_start: 0.7652 (t0) cc_final: 0.7446 (t0) REVERT: C 252 MET cc_start: 0.6864 (ttt) cc_final: 0.6382 (tmt) REVERT: C 354 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7442 (ppp) REVERT: D 182 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7988 (tp) REVERT: D 200 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6777 (tppt) REVERT: D 204 TRP cc_start: 0.6090 (OUTLIER) cc_final: 0.5482 (t60) REVERT: D 235 PHE cc_start: 0.8197 (t80) cc_final: 0.7978 (t80) REVERT: D 250 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8404 (tm-30) REVERT: D 293 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7699 (mt-10) REVERT: D 944 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7899 (mmtm) REVERT: D 974 MET cc_start: 0.8284 (ppp) cc_final: 0.7953 (tmm) outliers start: 149 outliers final: 61 residues processed: 551 average time/residue: 1.2725 time to fit residues: 827.8910 Evaluate side-chains 523 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 454 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 PRO Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 149 PRO Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 840 ASN Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 269 optimal weight: 6.9990 chunk 220 optimal weight: 0.8980 chunk 89 optimal weight: 40.0000 chunk 323 optimal weight: 0.0030 chunk 349 optimal weight: 8.9990 chunk 288 optimal weight: 8.9990 chunk 321 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 259 optimal weight: 0.4980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 ASN A 845 HIS A 865 ASN A1159 HIS B 241 ASN B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 632 ASN B 845 HIS B 904 ASN B1159 HIS B1174 GLN C 632 ASN C 865 ASN C1159 HIS D 156 ASN D 298 ASN D 632 ASN D 904 ASN D1159 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 29328 Z= 0.205 Angle : 0.566 11.436 39796 Z= 0.280 Chirality : 0.042 0.289 4548 Planarity : 0.005 0.145 4992 Dihedral : 4.454 46.238 3908 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.35 % Favored : 97.54 % Rotamer: Outliers : 4.33 % Allowed : 21.09 % Favored : 74.59 % 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: 0.68 (0.14), residues: 3532 helix: 1.03 (0.13), residues: 1680 sheet: -0.53 (0.26), residues: 356 loop : 0.21 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 177 HIS 0.010 0.001 HIS C1159 PHE 0.028 0.002 PHE B 307 TYR 0.017 0.001 TYR C 553 ARG 0.003 0.000 ARG D 968 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 466 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TRP cc_start: 0.6565 (t60) cc_final: 0.6133 (t60) REVERT: A 228 TRP cc_start: 0.6671 (m100) cc_final: 0.5654 (m-10) REVERT: A 241 ASN cc_start: 0.8160 (t0) cc_final: 0.7622 (t0) REVERT: A 252 MET cc_start: 0.6360 (tmt) cc_final: 0.5727 (mpt) REVERT: A 267 MET cc_start: 0.7157 (tmm) cc_final: 0.6199 (pmt) REVERT: A 334 MET cc_start: 0.6391 (tmm) cc_final: 0.6075 (tmm) REVERT: A 770 LEU cc_start: 0.8283 (mt) cc_final: 0.8059 (mt) REVERT: A 829 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8190 (ptmm) REVERT: A 940 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6975 (mt) REVERT: B 200 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6354 (mptt) REVERT: B 334 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6548 (tmm) REVERT: B 347 GLU cc_start: 0.7723 (pp20) cc_final: 0.7389 (mm-30) REVERT: B 372 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7672 (mttt) REVERT: B 867 ASP cc_start: 0.7801 (m-30) cc_final: 0.7413 (m-30) REVERT: B 976 ASP cc_start: 0.8151 (m-30) cc_final: 0.7904 (m-30) REVERT: C 174 MET cc_start: 0.7041 (ptp) cc_final: 0.6578 (pmm) REVERT: C 177 TRP cc_start: 0.7597 (t60) cc_final: 0.6963 (t60) REVERT: C 182 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8276 (pp) REVERT: C 200 LYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5860 (mptt) REVERT: C 293 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7596 (mt-10) REVERT: C 354 MET cc_start: 0.8004 (mtm) cc_final: 0.7445 (ppp) REVERT: D 182 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7998 (tp) REVERT: D 200 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6692 (tppt) REVERT: D 204 TRP cc_start: 0.6155 (OUTLIER) cc_final: 0.5536 (t60) REVERT: D 235 PHE cc_start: 0.8216 (t80) cc_final: 0.7968 (t80) REVERT: D 250 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8550 (tm-30) REVERT: D 293 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7663 (mt-10) REVERT: D 782 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: D 867 ASP cc_start: 0.7673 (m-30) cc_final: 0.7414 (m-30) REVERT: D 944 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7916 (mmtm) outliers start: 136 outliers final: 56 residues processed: 531 average time/residue: 1.3331 time to fit residues: 831.9975 Evaluate side-chains 518 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 450 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 566 MET Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 975 LEU Chi-restraints excluded: chain D residue 1021 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 20.0000 chunk 243 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 325 optimal weight: 5.9990 chunk 344 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 308 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 845 HIS A1159 HIS B 241 ASN B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 632 ASN B 845 HIS B1159 HIS ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN C 632 ASN C 865 ASN C1159 HIS D 298 ASN D 470 GLN D 490 GLN D 632 ASN D1159 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 29328 Z= 0.323 Angle : 0.602 10.584 39796 Z= 0.295 Chirality : 0.043 0.276 4548 Planarity : 0.005 0.140 4992 Dihedral : 4.526 48.578 3908 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.83 % Favored : 97.06 % Rotamer: Outliers : 5.25 % Allowed : 20.67 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 3532 helix: 1.05 (0.12), residues: 1708 sheet: -0.93 (0.25), residues: 400 loop : 0.25 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 177 HIS 0.010 0.002 HIS C 844 PHE 0.028 0.002 PHE B 307 TYR 0.018 0.002 TYR B 403 ARG 0.005 0.000 ARG D 961 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 458 time to evaluate : 3.159 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: A 177 TRP cc_start: 0.6546 (t60) cc_final: 0.6133 (t60) REVERT: A 228 TRP cc_start: 0.6740 (m100) cc_final: 0.5686 (m-10) REVERT: A 241 ASN cc_start: 0.8183 (t0) cc_final: 0.7727 (t0) REVERT: A 267 MET cc_start: 0.7214 (tmm) cc_final: 0.6356 (pmt) REVERT: A 334 MET cc_start: 0.6475 (tmm) cc_final: 0.6174 (tmm) REVERT: A 355 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: A 372 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7914 (mttm) REVERT: A 770 LEU cc_start: 0.8316 (mt) cc_final: 0.8093 (mt) REVERT: A 829 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8201 (ptmm) REVERT: A 859 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8052 (ttm) REVERT: A 974 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7866 (tmm) REVERT: B 193 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6210 (mt) REVERT: B 200 LYS cc_start: 0.6504 (OUTLIER) cc_final: 0.6267 (mptt) REVERT: B 204 TRP cc_start: 0.6124 (OUTLIER) cc_final: 0.5467 (t60) REVERT: B 334 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6488 (tmm) REVERT: B 372 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7775 (mttt) REVERT: B 867 ASP cc_start: 0.7752 (m-30) cc_final: 0.7401 (m-30) REVERT: B 976 ASP cc_start: 0.8300 (m-30) cc_final: 0.8077 (m-30) REVERT: B 1140 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7598 (tp) REVERT: C 174 MET cc_start: 0.7061 (ptp) cc_final: 0.6535 (pmm) REVERT: C 177 TRP cc_start: 0.7664 (t60) cc_final: 0.7031 (t60) REVERT: C 182 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8283 (pp) REVERT: C 200 LYS cc_start: 0.6036 (OUTLIER) cc_final: 0.5780 (mptt) REVERT: C 354 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7452 (ppp) REVERT: C 566 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.6741 (tmt) REVERT: D 182 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.8031 (tp) REVERT: D 193 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6733 (mt) REVERT: D 200 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6723 (tppt) REVERT: D 204 TRP cc_start: 0.6166 (OUTLIER) cc_final: 0.5548 (t60) REVERT: D 241 ASN cc_start: 0.7747 (t0) cc_final: 0.7521 (t0) REVERT: D 293 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7679 (mt-10) REVERT: D 426 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8548 (m) REVERT: D 566 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.6562 (tmt) REVERT: D 782 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7536 (m-30) REVERT: D 944 LYS cc_start: 0.8306 (mtmm) cc_final: 0.7915 (mmtm) REVERT: D 974 MET cc_start: 0.8320 (ppp) cc_final: 0.7990 (tmm) REVERT: D 1137 ARG cc_start: 0.7346 (ttp-170) cc_final: 0.7094 (ttp-170) outliers start: 165 outliers final: 75 residues processed: 549 average time/residue: 1.2470 time to fit residues: 811.1537 Evaluate side-chains 544 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 447 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 566 MET Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR 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: 4.9990 chunk 4 optimal weight: 20.0000 chunk 256 optimal weight: 4.9990 chunk 141 optimal weight: 0.1980 chunk 293 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 175 optimal weight: 1.9990 chunk 308 optimal weight: 0.0670 chunk 86 optimal weight: 0.0770 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 496 ASN A 632 ASN A 845 HIS A 931 GLN A1159 HIS B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 496 ASN B 632 ASN B 845 HIS B1159 HIS C 180 GLN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 ASN C 845 HIS C1159 HIS C1174 GLN D 298 ASN D 632 ASN D1159 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 29328 Z= 0.187 Angle : 0.562 11.169 39796 Z= 0.274 Chirality : 0.041 0.268 4548 Planarity : 0.005 0.136 4992 Dihedral : 4.352 49.300 3908 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.55 % Favored : 97.34 % Rotamer: Outliers : 4.61 % Allowed : 21.37 % Favored : 74.01 % 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: 1.00 (0.14), residues: 3532 helix: 1.35 (0.13), residues: 1660 sheet: -0.53 (0.26), residues: 356 loop : 0.35 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 177 HIS 0.009 0.001 HIS C 844 PHE 0.029 0.001 PHE B 307 TYR 0.019 0.001 TYR D 938 ARG 0.004 0.000 ARG D 417 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 462 time to evaluate : 3.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TRP cc_start: 0.6581 (t60) cc_final: 0.6125 (t60) REVERT: A 228 TRP cc_start: 0.6694 (m100) cc_final: 0.5681 (m-10) REVERT: A 241 ASN cc_start: 0.8150 (t0) cc_final: 0.7500 (t0) REVERT: A 252 MET cc_start: 0.6369 (tmt) cc_final: 0.5551 (mmt) REVERT: A 267 MET cc_start: 0.6921 (tmm) cc_final: 0.6237 (pmt) REVERT: A 334 MET cc_start: 0.6370 (tmm) cc_final: 0.6041 (tmm) REVERT: A 372 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7813 (mttm) REVERT: A 576 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6391 (mm-30) REVERT: A 585 PHE cc_start: 0.7820 (t80) cc_final: 0.7604 (t80) REVERT: A 770 LEU cc_start: 0.8309 (mt) cc_final: 0.8093 (mt) REVERT: A 829 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8189 (ptmm) REVERT: A 859 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7990 (ttm) REVERT: A 969 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8860 (p) REVERT: B 204 TRP cc_start: 0.6118 (OUTLIER) cc_final: 0.5460 (t60) REVERT: B 334 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6548 (tmm) REVERT: B 347 GLU cc_start: 0.7745 (pp20) cc_final: 0.7359 (mm-30) REVERT: B 372 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7657 (mttt) REVERT: B 566 MET cc_start: 0.8078 (tmt) cc_final: 0.7769 (tmt) REVERT: B 867 ASP cc_start: 0.7725 (m-30) cc_final: 0.7428 (m-30) REVERT: B 976 ASP cc_start: 0.8178 (m-30) cc_final: 0.7931 (m-30) REVERT: B 1140 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7606 (tp) REVERT: C 182 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8380 (pp) REVERT: C 200 LYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5783 (mptt) REVERT: C 293 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7443 (mt-10) REVERT: C 354 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7369 (ppp) REVERT: C 566 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7162 (tmt) REVERT: D 182 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8008 (tp) REVERT: D 200 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6742 (tppt) REVERT: D 204 TRP cc_start: 0.6037 (OUTLIER) cc_final: 0.5393 (t60) REVERT: D 241 ASN cc_start: 0.7699 (t0) cc_final: 0.7425 (t0) REVERT: D 250 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8667 (tm-30) REVERT: D 281 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9038 (tt) REVERT: D 293 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7680 (mt-10) REVERT: D 426 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8533 (m) REVERT: D 566 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7365 (tmt) REVERT: D 576 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6727 (mm-30) REVERT: D 782 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7503 (m-30) REVERT: D 944 LYS cc_start: 0.8306 (mtmm) cc_final: 0.7920 (mmtm) REVERT: D 1137 ARG cc_start: 0.7272 (ttp-170) cc_final: 0.7051 (ttp-170) outliers start: 145 outliers final: 75 residues processed: 540 average time/residue: 1.3111 time to fit residues: 837.3929 Evaluate side-chains 540 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 446 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 566 MET Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 975 LEU Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1021 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 3.9990 chunk 309 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 202 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 chunk 285 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 603 ASN A 632 ASN A 845 HIS A1159 HIS B 241 ASN B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 632 ASN B 845 HIS B1159 HIS ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 ASN C 845 HIS C1159 HIS D 298 ASN D 490 GLN D 632 ASN D1159 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 29328 Z= 0.254 Angle : 0.598 11.536 39796 Z= 0.288 Chirality : 0.042 0.260 4548 Planarity : 0.005 0.133 4992 Dihedral : 4.367 52.129 3906 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.94 % Favored : 96.94 % Rotamer: Outliers : 4.61 % Allowed : 21.76 % Favored : 73.63 % 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: 0.96 (0.14), residues: 3532 helix: 1.38 (0.13), residues: 1660 sheet: -0.82 (0.25), residues: 400 loop : 0.37 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 177 HIS 0.011 0.001 HIS B 844 PHE 0.028 0.002 PHE A 307 TYR 0.019 0.002 TYR B 582 ARG 0.005 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 452 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TRP cc_start: 0.6565 (t60) cc_final: 0.6146 (t60) REVERT: A 193 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5429 (mt) REVERT: A 228 TRP cc_start: 0.6727 (m100) cc_final: 0.5695 (m-10) REVERT: A 241 ASN cc_start: 0.8157 (t0) cc_final: 0.7493 (t0) REVERT: A 267 MET cc_start: 0.6926 (tmm) cc_final: 0.6362 (pmt) REVERT: A 334 MET cc_start: 0.6475 (tmm) cc_final: 0.6099 (tmm) REVERT: A 355 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: A 372 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7871 (mttm) REVERT: A 585 PHE cc_start: 0.7904 (t80) cc_final: 0.7594 (t80) REVERT: A 770 LEU cc_start: 0.8330 (mt) cc_final: 0.8118 (mt) REVERT: A 829 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8205 (ptmm) REVERT: B 193 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6824 (pp) REVERT: B 204 TRP cc_start: 0.6179 (OUTLIER) cc_final: 0.5507 (t60) REVERT: B 334 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6690 (tmm) REVERT: B 372 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7702 (mttt) REVERT: B 867 ASP cc_start: 0.7704 (m-30) cc_final: 0.7379 (m-30) REVERT: B 976 ASP cc_start: 0.8227 (m-30) cc_final: 0.7980 (m-30) REVERT: C 200 LYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5820 (mptt) REVERT: C 354 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7385 (ppp) REVERT: C 566 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7588 (tmt) REVERT: C 782 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: C 1189 ARG cc_start: 0.7947 (mmm160) cc_final: 0.7707 (mmm-85) REVERT: D 182 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8024 (tp) REVERT: D 193 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6777 (mt) REVERT: D 200 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6719 (tppt) REVERT: D 204 TRP cc_start: 0.6048 (OUTLIER) cc_final: 0.5358 (t60) REVERT: D 241 ASN cc_start: 0.7882 (t0) cc_final: 0.7514 (t0) REVERT: D 250 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8674 (tm-30) REVERT: D 293 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7681 (mt-10) REVERT: D 426 SER cc_start: 0.8919 (OUTLIER) cc_final: 0.8542 (m) REVERT: D 566 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7466 (tmt) REVERT: D 782 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7515 (m-30) REVERT: D 944 LYS cc_start: 0.8318 (mtmm) cc_final: 0.7914 (mmtm) REVERT: D 974 MET cc_start: 0.8309 (ppp) cc_final: 0.7949 (tmm) REVERT: D 1137 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.7063 (ttp-170) outliers start: 145 outliers final: 80 residues processed: 527 average time/residue: 1.2946 time to fit residues: 804.3465 Evaluate side-chains 548 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 449 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1138 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 566 MET Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 196 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 289 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 343 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 603 ASN A 632 ASN A 845 HIS A1159 HIS B 241 ASN B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 632 ASN B 845 HIS B1159 HIS C 241 ASN C 632 ASN C 845 HIS C 931 GLN C1159 HIS D 298 ASN D 632 ASN D 879 ASN D1159 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 29328 Z= 0.321 Angle : 0.617 11.818 39796 Z= 0.298 Chirality : 0.043 0.258 4548 Planarity : 0.005 0.130 4992 Dihedral : 4.386 26.334 3904 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 4.80 % Allowed : 21.79 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3532 helix: 1.36 (0.13), residues: 1660 sheet: -0.95 (0.25), residues: 400 loop : 0.36 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 177 HIS 0.011 0.002 HIS B1159 PHE 0.035 0.002 PHE C 307 TYR 0.017 0.002 TYR D 938 ARG 0.014 0.001 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 447 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TRP cc_start: 0.6580 (t60) cc_final: 0.6168 (t60) REVERT: A 193 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5418 (mt) REVERT: A 228 TRP cc_start: 0.6797 (m100) cc_final: 0.5711 (m-10) REVERT: A 241 ASN cc_start: 0.8203 (t0) cc_final: 0.7524 (t0) REVERT: A 252 MET cc_start: 0.6194 (tmt) cc_final: 0.5286 (mmt) REVERT: A 267 MET cc_start: 0.6583 (tmm) cc_final: 0.6182 (pmt) REVERT: A 334 MET cc_start: 0.6574 (tmm) cc_final: 0.6129 (tmm) REVERT: A 355 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: A 585 PHE cc_start: 0.7984 (t80) cc_final: 0.7724 (t80) REVERT: A 829 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8192 (ptmm) REVERT: A 876 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7079 (p90) REVERT: B 192 MET cc_start: 0.7518 (mtp) cc_final: 0.7264 (mtp) REVERT: B 193 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6544 (pp) REVERT: B 204 TRP cc_start: 0.6182 (OUTLIER) cc_final: 0.5508 (t60) REVERT: B 334 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6769 (tmm) REVERT: B 372 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7720 (mttt) REVERT: B 413 ASP cc_start: 0.6838 (t0) cc_final: 0.6591 (t0) REVERT: B 867 ASP cc_start: 0.7685 (m-30) cc_final: 0.7407 (m-30) REVERT: B 876 TYR cc_start: 0.7836 (p90) cc_final: 0.7042 (p90) REVERT: B 976 ASP cc_start: 0.8290 (m-30) cc_final: 0.8072 (m-30) REVERT: C 168 LEU cc_start: 0.8551 (tm) cc_final: 0.7708 (mt) REVERT: C 200 LYS cc_start: 0.6108 (OUTLIER) cc_final: 0.5810 (mptt) REVERT: C 354 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7384 (ppp) REVERT: C 566 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7589 (tmt) REVERT: C 1194 ASP cc_start: 0.7879 (m-30) cc_final: 0.7291 (m-30) REVERT: D 182 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8052 (tp) REVERT: D 200 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6675 (tppt) REVERT: D 204 TRP cc_start: 0.6021 (OUTLIER) cc_final: 0.5432 (t60) REVERT: D 241 ASN cc_start: 0.7923 (t0) cc_final: 0.7483 (t0) REVERT: D 250 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8675 (tm-30) REVERT: D 293 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7664 (mt-10) REVERT: D 426 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8548 (m) REVERT: D 782 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: D 944 LYS cc_start: 0.8324 (mtmm) cc_final: 0.7905 (mmtm) REVERT: D 950 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7437 (ttp80) REVERT: D 974 MET cc_start: 0.8366 (ppp) cc_final: 0.8000 (tmm) REVERT: D 1137 ARG cc_start: 0.7316 (ttp-170) cc_final: 0.7066 (ttp-170) outliers start: 151 outliers final: 83 residues processed: 535 average time/residue: 1.2549 time to fit residues: 796.0378 Evaluate side-chains 548 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 447 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1138 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 950 ARG Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Chi-restraints excluded: chain D residue 1176 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 103 optimal weight: 30.0000 chunk 67 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 chunk 233 optimal weight: 0.3980 chunk 169 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 269 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A 632 ASN A 845 HIS A 879 ASN A1159 HIS B 241 ASN B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 632 ASN B 845 HIS B1159 HIS C 490 GLN C 632 ASN C 845 HIS C1159 HIS D 298 ASN D 490 GLN D 496 ASN D 632 ASN D1159 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 29328 Z= 0.210 Angle : 0.601 12.272 39796 Z= 0.288 Chirality : 0.041 0.252 4548 Planarity : 0.005 0.128 4992 Dihedral : 4.272 26.193 3904 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.86 % Favored : 97.03 % Rotamer: Outliers : 4.20 % Allowed : 22.81 % Favored : 73.00 % 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: 1.06 (0.14), residues: 3532 helix: 1.49 (0.13), residues: 1660 sheet: -0.87 (0.26), residues: 400 loop : 0.43 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 177 HIS 0.010 0.001 HIS B 844 PHE 0.031 0.002 PHE C 307 TYR 0.016 0.001 TYR B 403 ARG 0.009 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 456 time to evaluate : 3.431 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: A 177 TRP cc_start: 0.6605 (t60) cc_final: 0.6211 (t60) REVERT: A 193 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5385 (mt) REVERT: A 228 TRP cc_start: 0.6791 (m100) cc_final: 0.5721 (m-10) REVERT: A 241 ASN cc_start: 0.8111 (t0) cc_final: 0.7398 (t0) REVERT: A 252 MET cc_start: 0.6223 (tmt) cc_final: 0.5352 (mmt) REVERT: A 267 MET cc_start: 0.6529 (tmm) cc_final: 0.6131 (pmt) REVERT: A 334 MET cc_start: 0.6598 (tmm) cc_final: 0.6144 (tmm) REVERT: A 355 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: A 585 PHE cc_start: 0.7942 (t80) cc_final: 0.7677 (t80) REVERT: A 829 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8177 (ptmm) REVERT: A 1011 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8092 (tptt) REVERT: B 192 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7236 (mtp) REVERT: B 193 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6575 (pp) REVERT: B 334 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6743 (tmm) REVERT: B 372 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7680 (mttt) REVERT: B 413 ASP cc_start: 0.6785 (t0) cc_final: 0.6546 (t0) REVERT: B 867 ASP cc_start: 0.7690 (m-30) cc_final: 0.7417 (m-30) REVERT: B 876 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.6997 (p90) REVERT: B 976 ASP cc_start: 0.8222 (m-30) cc_final: 0.7972 (m-30) REVERT: C 168 LEU cc_start: 0.8529 (tm) cc_final: 0.7682 (mt) REVERT: C 200 LYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5800 (mptt) REVERT: C 234 LEU cc_start: 0.8737 (tm) cc_final: 0.8377 (tp) REVERT: C 354 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7413 (ppp) REVERT: C 566 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.6980 (tmt) REVERT: C 950 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7432 (ttp80) REVERT: C 1014 GLU cc_start: 0.7768 (tp30) cc_final: 0.7512 (mm-30) REVERT: C 1194 ASP cc_start: 0.7863 (m-30) cc_final: 0.7285 (m-30) REVERT: D 182 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8030 (tp) REVERT: D 193 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6424 (mt) REVERT: D 200 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6735 (tppt) REVERT: D 204 TRP cc_start: 0.6022 (OUTLIER) cc_final: 0.5340 (t60) REVERT: D 241 ASN cc_start: 0.7917 (t0) cc_final: 0.7483 (t0) REVERT: D 250 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8715 (tm-30) REVERT: D 293 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7644 (mt-10) REVERT: D 426 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8594 (m) REVERT: D 566 MET cc_start: 0.8042 (tmt) cc_final: 0.7620 (tmt) REVERT: D 585 PHE cc_start: 0.7978 (t80) cc_final: 0.7684 (t80) REVERT: D 782 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7559 (m-30) REVERT: D 944 LYS cc_start: 0.8300 (mtmm) cc_final: 0.7889 (mmtm) REVERT: D 950 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7403 (ttp80) REVERT: D 1137 ARG cc_start: 0.7296 (ttp-170) cc_final: 0.7053 (ttp-170) outliers start: 132 outliers final: 75 residues processed: 528 average time/residue: 1.3130 time to fit residues: 816.0063 Evaluate side-chains 540 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 445 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 950 ARG Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1138 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 950 ARG Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 6.9990 chunk 328 optimal weight: 0.6980 chunk 299 optimal weight: 0.7980 chunk 319 optimal weight: 0.2980 chunk 192 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 288 optimal weight: 5.9990 chunk 302 optimal weight: 2.9990 chunk 318 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A 632 ASN A 845 HIS A1159 HIS B 241 ASN B 270 GLN B 291 HIS B 298 ASN B 632 ASN B 845 HIS B1159 HIS C 241 ASN C 632 ASN C 845 HIS C 865 ASN C1159 HIS D 298 ASN D 632 ASN D 865 ASN D 931 GLN D1159 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 29328 Z= 0.186 Angle : 0.593 12.868 39796 Z= 0.283 Chirality : 0.041 0.245 4548 Planarity : 0.005 0.127 4992 Dihedral : 4.137 25.742 3904 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.66 % Favored : 97.23 % Rotamer: Outliers : 3.69 % Allowed : 23.35 % Favored : 72.96 % 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: 1.28 (0.14), residues: 3532 helix: 1.66 (0.13), residues: 1636 sheet: -0.70 (0.26), residues: 396 loop : 0.55 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 325 HIS 0.010 0.001 HIS D1159 PHE 0.034 0.001 PHE C 307 TYR 0.024 0.001 TYR C 582 ARG 0.006 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 460 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.9108 (mm) cc_final: 0.8907 (tp) REVERT: A 177 TRP cc_start: 0.6580 (t60) cc_final: 0.6183 (t60) REVERT: A 193 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5381 (mt) REVERT: A 228 TRP cc_start: 0.6783 (m100) cc_final: 0.5725 (m-10) REVERT: A 241 ASN cc_start: 0.8062 (t0) cc_final: 0.7368 (t0) REVERT: A 252 MET cc_start: 0.6139 (tmt) cc_final: 0.5271 (mmt) REVERT: A 267 MET cc_start: 0.6458 (tmm) cc_final: 0.6101 (pmt) REVERT: A 334 MET cc_start: 0.6593 (tmm) cc_final: 0.6169 (tmm) REVERT: A 355 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: A 576 GLU cc_start: 0.6224 (mm-30) cc_final: 0.5688 (mp0) REVERT: A 1011 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8128 (mmtt) REVERT: A 1137 ARG cc_start: 0.7431 (ttp-170) cc_final: 0.7230 (ttp-170) REVERT: B 193 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6508 (pp) REVERT: B 334 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6731 (tmm) REVERT: B 372 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7635 (mttt) REVERT: B 413 ASP cc_start: 0.6785 (t0) cc_final: 0.6570 (t0) REVERT: B 566 MET cc_start: 0.8082 (ttp) cc_final: 0.6653 (tmt) REVERT: B 782 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: B 867 ASP cc_start: 0.7667 (m-30) cc_final: 0.7373 (m-30) REVERT: B 876 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.6884 (p90) REVERT: B 1016 ASP cc_start: 0.7194 (m-30) cc_final: 0.6970 (m-30) REVERT: C 168 LEU cc_start: 0.8373 (tm) cc_final: 0.7516 (mt) REVERT: C 169 TRP cc_start: 0.7830 (m100) cc_final: 0.7129 (m-10) REVERT: C 200 LYS cc_start: 0.6147 (OUTLIER) cc_final: 0.5859 (tppt) REVERT: C 234 LEU cc_start: 0.8736 (tm) cc_final: 0.8352 (tp) REVERT: C 354 MET cc_start: 0.7919 (mtm) cc_final: 0.7384 (ppp) REVERT: C 566 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7584 (tmt) REVERT: C 950 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7365 (ttp80) REVERT: C 1014 GLU cc_start: 0.7757 (tp30) cc_final: 0.7514 (mm-30) REVERT: D 182 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.8024 (tp) REVERT: D 193 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6407 (mt) REVERT: D 200 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6740 (tppt) REVERT: D 204 TRP cc_start: 0.6022 (OUTLIER) cc_final: 0.5334 (t60) REVERT: D 235 PHE cc_start: 0.8259 (t80) cc_final: 0.8050 (t80) REVERT: D 241 ASN cc_start: 0.7843 (t0) cc_final: 0.7401 (t0) REVERT: D 250 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8744 (tm-30) REVERT: D 293 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7657 (mt-10) REVERT: D 426 SER cc_start: 0.8920 (OUTLIER) cc_final: 0.8594 (m) REVERT: D 566 MET cc_start: 0.7886 (tmt) cc_final: 0.7437 (tmt) REVERT: D 747 VAL cc_start: 0.6774 (OUTLIER) cc_final: 0.6388 (m) REVERT: D 782 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: D 944 LYS cc_start: 0.8241 (mtmm) cc_final: 0.7885 (mmtm) REVERT: D 950 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7404 (ttp80) REVERT: D 1137 ARG cc_start: 0.7287 (ttp-170) cc_final: 0.7048 (ttp-170) outliers start: 116 outliers final: 63 residues processed: 525 average time/residue: 1.3244 time to fit residues: 819.8464 Evaluate side-chains 533 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 452 time to evaluate : 3.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 950 ARG Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 950 ARG Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 0.8980 chunk 338 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 235 optimal weight: 8.9990 chunk 354 optimal weight: 0.9980 chunk 326 optimal weight: 1.9990 chunk 282 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 218 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 603 ASN A 632 ASN A 845 HIS A1159 HIS B 241 ASN B 270 GLN B 291 HIS B 298 ASN B 632 ASN B 845 HIS C 632 ASN C 845 HIS C 865 ASN C1159 HIS D 298 ASN D 632 ASN D 845 HIS D 865 ASN D1159 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 29328 Z= 0.217 Angle : 0.608 12.876 39796 Z= 0.292 Chirality : 0.042 0.245 4548 Planarity : 0.005 0.124 4992 Dihedral : 4.147 25.158 3904 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 3.18 % Allowed : 24.11 % Favored : 72.71 % 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: 1.22 (0.14), residues: 3532 helix: 1.61 (0.13), residues: 1656 sheet: -0.75 (0.26), residues: 400 loop : 0.51 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 177 HIS 0.011 0.001 HIS C 844 PHE 0.044 0.002 PHE D 188 TYR 0.023 0.001 TYR B 582 ARG 0.012 0.000 ARG C 948 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 454 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.9099 (mm) cc_final: 0.8869 (tp) REVERT: A 176 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7800 (tm) REVERT: A 177 TRP cc_start: 0.6545 (t60) cc_final: 0.6130 (t60) REVERT: A 228 TRP cc_start: 0.6755 (m100) cc_final: 0.5689 (m-10) REVERT: A 241 ASN cc_start: 0.8079 (t0) cc_final: 0.7379 (t0) REVERT: A 252 MET cc_start: 0.6134 (tmt) cc_final: 0.5275 (mmt) REVERT: A 267 MET cc_start: 0.6328 (tmm) cc_final: 0.5972 (pmt) REVERT: A 305 PHE cc_start: 0.8653 (t80) cc_final: 0.8441 (t80) REVERT: A 334 MET cc_start: 0.6617 (tmm) cc_final: 0.6184 (tmm) REVERT: A 355 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: A 576 GLU cc_start: 0.6186 (mm-30) cc_final: 0.5717 (mp0) REVERT: A 876 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.6888 (p90) REVERT: A 1011 LYS cc_start: 0.8483 (mtpt) cc_final: 0.8151 (mmtt) REVERT: B 193 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6552 (pp) REVERT: B 372 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7670 (mttt) REVERT: B 413 ASP cc_start: 0.6843 (t0) cc_final: 0.6607 (t0) REVERT: B 566 MET cc_start: 0.8167 (ttp) cc_final: 0.7838 (ppp) REVERT: B 585 PHE cc_start: 0.7938 (t80) cc_final: 0.7642 (t80) REVERT: B 867 ASP cc_start: 0.7665 (m-30) cc_final: 0.7402 (m-30) REVERT: B 876 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.6919 (p90) REVERT: B 1016 ASP cc_start: 0.7220 (m-30) cc_final: 0.6997 (m-30) REVERT: C 168 LEU cc_start: 0.8344 (tm) cc_final: 0.7545 (mt) REVERT: C 169 TRP cc_start: 0.7846 (m100) cc_final: 0.6963 (m-10) REVERT: C 188 PHE cc_start: 0.7448 (t80) cc_final: 0.7248 (t80) REVERT: C 200 LYS cc_start: 0.6192 (OUTLIER) cc_final: 0.5901 (tppt) REVERT: C 234 LEU cc_start: 0.8734 (tm) cc_final: 0.8365 (tp) REVERT: C 354 MET cc_start: 0.7912 (mtm) cc_final: 0.7390 (ppp) REVERT: C 566 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7563 (tmt) REVERT: C 892 GLU cc_start: 0.6830 (pp20) cc_final: 0.6140 (pp20) REVERT: C 947 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7815 (tppt) REVERT: C 950 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7347 (ttp80) REVERT: C 1014 GLU cc_start: 0.7763 (tp30) cc_final: 0.7451 (mm-30) REVERT: D 182 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.8037 (tp) REVERT: D 193 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6406 (mt) REVERT: D 200 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6757 (tppt) REVERT: D 204 TRP cc_start: 0.5967 (OUTLIER) cc_final: 0.5283 (t60) REVERT: D 235 PHE cc_start: 0.8235 (t80) cc_final: 0.8032 (t80) REVERT: D 241 ASN cc_start: 0.7952 (t0) cc_final: 0.7489 (t0) REVERT: D 250 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8743 (tm-30) REVERT: D 293 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7597 (mt-10) REVERT: D 426 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8594 (m) REVERT: D 566 MET cc_start: 0.7891 (tmt) cc_final: 0.7375 (tmt) REVERT: D 747 VAL cc_start: 0.6797 (OUTLIER) cc_final: 0.6420 (m) REVERT: D 782 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: D 944 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7884 (mmtm) REVERT: D 950 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7400 (ttp80) REVERT: D 1137 ARG cc_start: 0.7302 (ttp-170) cc_final: 0.7056 (ttp-170) outliers start: 100 outliers final: 64 residues processed: 514 average time/residue: 1.3484 time to fit residues: 817.2553 Evaluate side-chains 530 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 449 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 950 ARG Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 950 ARG Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.7980 chunk 300 optimal weight: 3.9990 chunk 86 optimal weight: 0.0870 chunk 260 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 chunk 282 optimal weight: 10.0000 chunk 118 optimal weight: 0.4980 chunk 290 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 603 ASN A 632 ASN A 845 HIS A1159 HIS B 241 ASN B 270 GLN B 291 HIS B 298 ASN B 632 ASN B 845 HIS C 291 HIS C 632 ASN C 845 HIS C 879 ASN C1159 HIS D 156 ASN D 298 ASN D 632 ASN D 845 HIS D 865 ASN D1159 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.132006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.098261 restraints weight = 53333.603| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.43 r_work: 0.3146 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 29328 Z= 0.191 Angle : 0.608 12.827 39796 Z= 0.290 Chirality : 0.041 0.242 4548 Planarity : 0.005 0.122 4992 Dihedral : 4.102 25.171 3903 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.55 % Favored : 97.34 % Rotamer: Outliers : 3.05 % Allowed : 24.11 % Favored : 72.84 % 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: 1.33 (0.14), residues: 3532 helix: 1.73 (0.13), residues: 1632 sheet: -0.84 (0.25), residues: 424 loop : 0.62 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 177 HIS 0.018 0.001 HIS C 291 PHE 0.042 0.001 PHE A 188 TYR 0.023 0.001 TYR B 582 ARG 0.005 0.000 ARG C 948 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11828.47 seconds wall clock time: 209 minutes 5.94 seconds (12545.94 seconds total)