Starting phenix.real_space_refine on Mon Feb 19 19:56:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e79_27938/02_2024/8e79_27938.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e79_27938/02_2024/8e79_27938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e79_27938/02_2024/8e79_27938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e79_27938/02_2024/8e79_27938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e79_27938/02_2024/8e79_27938.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e79_27938/02_2024/8e79_27938.pdb" } resolution = 3.71 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= 0.002 sd= 0.092 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 Zn 2 6.06 5 P 107 5.49 5 Mg 1 5.21 5 S 93 5.16 5 C 15730 2.51 5 N 4538 2.21 5 O 5155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 12": "OD1" <-> "OD2" Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ASP 59": "OD1" <-> "OD2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 109": "OD1" <-> "OD2" Residue "C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C ASP 441": "OD1" <-> "OD2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "C TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 521": "OD1" <-> "OD2" Residue "C ASP 549": "OD1" <-> "OD2" Residue "C ASP 551": "OD1" <-> "OD2" Residue "C PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 640": "OD1" <-> "OD2" Residue "C GLU 651": "OE1" <-> "OE2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "C TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 697": "OE1" <-> "OE2" Residue "C TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 768": "OE1" <-> "OE2" Residue "C GLU 795": "OE1" <-> "OE2" Residue "C GLU 843": "OE1" <-> "OE2" Residue "C GLU 902": "OE1" <-> "OE2" Residue "C ASP 903": "OD1" <-> "OD2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1038": "OD1" <-> "OD2" Residue "C TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "D ASP 339": "OD1" <-> "OD2" Residue "D PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 488": "OE1" <-> "OE2" Residue "D GLU 493": "OE1" <-> "OE2" Residue "D GLU 518": "OE1" <-> "OE2" Residue "D ASP 535": "OD1" <-> "OD2" Residue "D ASP 580": "OD1" <-> "OD2" Residue "D TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 598": "OE1" <-> "OE2" Residue "D GLU 647": "OE1" <-> "OE2" Residue "D TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 747": "OD1" <-> "OD2" Residue "D GLU 780": "OE1" <-> "OE2" Residue "D GLU 791": "OE1" <-> "OE2" Residue "D TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 795": "OD1" <-> "OD2" Residue "D TYR 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 946": "OD1" <-> "OD2" Residue "D GLU 948": "OE1" <-> "OE2" Residue "D GLU 993": "OE1" <-> "OE2" Residue "D TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1120": "OE1" <-> "OE2" Residue "D GLU 1174": "OE1" <-> "OE2" Residue "D GLU 1185": "OE1" <-> "OE2" Residue "D GLU 1187": "OE1" <-> "OE2" Residue "D GLU 1277": "OE1" <-> "OE2" Residue "E TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "N TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 19": "OE1" <-> "OE2" Residue "N GLU 28": "OE1" <-> "OE2" Residue "N PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 105": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25626 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1769 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 221} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 8459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8459 Classifications: {'peptide': 1091} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1029} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 9913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9913 Classifications: {'peptide': 1269} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1208} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 645 Classifications: {'peptide': 82} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 75} Chain: "N" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 898 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 106} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 690 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain breaks: 1 Chain: "P" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 764 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "R" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 761 Classifications: {'RNA': 36} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 3, 'rna3p': 32} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12458 SG CYS D 60 107.550 86.659 111.146 1.00124.43 S ATOM 12476 SG CYS D 62 108.212 88.169 113.859 1.00126.44 S ATOM 12585 SG CYS D 75 108.552 84.616 115.158 1.00123.04 S ATOM 12611 SG CYS D 78 106.395 85.410 114.803 1.00121.69 S ATOM 19026 SG CYS D 891 79.841 26.414 87.583 1.00 83.34 S ATOM 19593 SG CYS D 968 78.806 30.593 89.158 1.00 81.92 S ATOM 19635 SG CYS D 975 79.391 29.783 86.621 1.00 77.68 S ATOM 19653 SG CYS D 978 77.274 28.499 86.291 1.00 80.68 S Time building chain proxies: 14.74, per 1000 atoms: 0.58 Number of scatterers: 25626 At special positions: 0 Unit cell: (128.75, 131.84, 196.73, 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 2 29.99 S 93 16.00 P 107 15.00 Mg 1 11.99 O 5155 8.00 N 4538 7.00 C 15730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.63 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " Number of angles added : 12 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 42 sheets defined 39.4% alpha, 16.3% beta 43 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 9.59 Creating SS restraints... Processing helix chain 'A' and resid 31 through 43 Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.564A pdb=" N ILE A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.517A pdb=" N ALA A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.270A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'B' and resid 34 through 45 Processing helix chain 'B' and resid 72 through 82 removed outlier: 4.185A pdb=" N SER B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 203 through 224 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.030A pdb=" N TRP C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.536A pdb=" N GLU C 76 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.890A pdb=" N VAL C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 removed outlier: 3.500A pdb=" N ARG C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.650A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 404 removed outlier: 3.591A pdb=" N LEU C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 420 through 433 removed outlier: 3.528A pdb=" N VAL C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.532A pdb=" N GLY C 448 " --> pdb=" O ASN C 444 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 468 removed outlier: 4.308A pdb=" N ALA C 468 " --> pdb=" O ARG C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 4.137A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.542A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 610 removed outlier: 3.716A pdb=" N MET C 607 " --> pdb=" O ASN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 639 removed outlier: 3.726A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 removed outlier: 3.523A pdb=" N GLU C 744 " --> pdb=" O ARG C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 921 through 926 removed outlier: 3.817A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.529A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 removed outlier: 3.675A pdb=" N ASP C1039 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1072 Processing helix chain 'C' and resid 1073 through 1080 Processing helix chain 'C' and resid 1082 through 1090 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.174A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.788A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C1131 " --> pdb=" O GLU C1127 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 142 through 187 removed outlier: 3.706A pdb=" N ASN D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.561A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.672A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.566A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 4.217A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 305 removed outlier: 3.934A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D 299 " --> pdb=" O ARG D 295 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.548A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 361 removed outlier: 3.630A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 401 through 411 removed outlier: 3.550A pdb=" N LEU D 406 " --> pdb=" O SER D 403 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS D 407 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLY D 408 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS D 409 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN D 410 " --> pdb=" O LYS D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.799A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.452A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 554 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 614 through 623 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 725 removed outlier: 3.629A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.615A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.808A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.078A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR D 872 " --> pdb=" O ALA D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 975 through 980 removed outlier: 3.791A pdb=" N TYR D 979 " --> pdb=" O CYS D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1003 removed outlier: 3.538A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1126 Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.569A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.389A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 3.995A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1227 Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1248 through 1254 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.963A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 removed outlier: 3.572A pdb=" N LEU E 43 " --> pdb=" O PRO E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 71 removed outlier: 3.512A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.530A pdb=" N ILE E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 34 Processing helix chain 'N' and resid 76 through 86 removed outlier: 3.727A pdb=" N VAL N 86 " --> pdb=" O LEU N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 117 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 3.648A pdb=" N LEU A 14 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 100 removed outlier: 7.470A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 100 removed outlier: 3.833A pdb=" N GLY A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 168 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 11 removed outlier: 3.599A pdb=" N PHE B 21 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 11 removed outlier: 3.599A pdb=" N PHE B 21 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS B 191 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL B 178 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 3.694A pdb=" N SER B 53 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 4.011A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.498A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.789A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.440A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 191 Processing sheet with id=AB8, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.243A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC3, first strand: chain 'C' and resid 558 through 562 removed outlier: 3.535A pdb=" N VAL C 559 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 571 " --> pdb=" O VAL C 559 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.505A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.908A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'C' and resid 895 through 899 removed outlier: 7.045A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 748 through 756 removed outlier: 3.945A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.671A pdb=" N GLU C 768 " --> pdb=" O VAL C 806 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 806 " --> pdb=" O GLU C 768 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.214A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1067 through 1068 removed outlier: 3.806A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.874A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 10 " --> pdb=" O ASP D1243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 35 removed outlier: 3.763A pdb=" N LYS D 40 " --> pdb=" O ASN D 35 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.266A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.573A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 328 through 330 Processing sheet with id=AD9, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE1, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.763A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1075 through 1081 removed outlier: 3.733A pdb=" N VAL D1075 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS D1079 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR D1062 " --> pdb=" O LYS D1079 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.668A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1271 through 1274 removed outlier: 3.615A pdb=" N THR E 107 " --> pdb=" O ALA D1271 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU E 105 " --> pdb=" O GLN D1273 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 9 through 13 removed outlier: 3.519A pdb=" N LEU N 70 " --> pdb=" O MET N 43 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 47 through 52 971 hydrogen bonds defined for protein. 2691 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 12.86 Time building geometry restraints manager: 12.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8034 1.33 - 1.45: 3804 1.45 - 1.57: 14075 1.57 - 1.69: 210 1.69 - 1.81: 165 Bond restraints: 26288 Sorted by residual: bond pdb=" N GLY D -1 " pdb=" CA GLY D -1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.16e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.69e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.61e+00 bond pdb=" CA GLY D1027 " pdb=" C GLY D1027 " ideal model delta sigma weight residual 1.518 1.499 0.019 1.24e-02 6.50e+03 2.29e+00 bond pdb=" N GLY D1027 " pdb=" CA GLY D1027 " ideal model delta sigma weight residual 1.445 1.457 -0.012 8.30e-03 1.45e+04 2.25e+00 ... (remaining 26283 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.27: 953 105.27 - 112.45: 13784 112.45 - 119.63: 9009 119.63 - 126.81: 11769 126.81 - 133.99: 567 Bond angle restraints: 36082 Sorted by residual: angle pdb=" C LEU D 579 " pdb=" CA LEU D 579 " pdb=" CB LEU D 579 " ideal model delta sigma weight residual 117.23 111.01 6.22 1.36e+00 5.41e-01 2.09e+01 angle pdb=" N VAL C 742 " pdb=" CA VAL C 742 " pdb=" C VAL C 742 " ideal model delta sigma weight residual 112.12 108.34 3.78 8.40e-01 1.42e+00 2.03e+01 angle pdb=" C HIS A 124 " pdb=" N ILE A 125 " pdb=" CA ILE A 125 " ideal model delta sigma weight residual 122.97 118.65 4.32 9.80e-01 1.04e+00 1.94e+01 angle pdb=" N SER B 4 " pdb=" CA SER B 4 " pdb=" CB SER B 4 " ideal model delta sigma weight residual 114.17 110.22 3.95 1.14e+00 7.69e-01 1.20e+01 angle pdb=" C GLU D 147 " pdb=" N LEU D 148 " pdb=" CA LEU D 148 " ideal model delta sigma weight residual 120.44 125.15 -4.71 1.36e+00 5.41e-01 1.20e+01 ... (remaining 36077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 15306 35.30 - 70.60: 586 70.60 - 105.89: 29 105.89 - 141.19: 1 141.19 - 176.49: 5 Dihedral angle restraints: 15927 sinusoidal: 7302 harmonic: 8625 Sorted by residual: dihedral pdb=" CA GLU B 24 " pdb=" C GLU B 24 " pdb=" N PRO B 25 " pdb=" CA PRO B 25 " ideal model delta harmonic sigma weight residual -180.00 -136.07 -43.93 0 5.00e+00 4.00e-02 7.72e+01 dihedral pdb=" O4' C R 19 " pdb=" C1' C R 19 " pdb=" N1 C R 19 " pdb=" C2 C R 19 " ideal model delta sinusoidal sigma weight residual -128.00 -23.91 -104.09 1 1.70e+01 3.46e-03 4.13e+01 dihedral pdb=" CA GLN C1062 " pdb=" C GLN C1062 " pdb=" N PHE C1063 " pdb=" CA PHE C1063 " ideal model delta harmonic sigma weight residual 180.00 148.96 31.04 0 5.00e+00 4.00e-02 3.85e+01 ... (remaining 15924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2973 0.040 - 0.079: 826 0.079 - 0.118: 284 0.118 - 0.158: 50 0.158 - 0.197: 1 Chirality restraints: 4134 Sorted by residual: chirality pdb=" C1' G R 29 " pdb=" O4' G R 29 " pdb=" C2' G R 29 " pdb=" N9 G R 29 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA ILE C 594 " pdb=" N ILE C 594 " pdb=" C ILE C 594 " pdb=" CB ILE C 594 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE C 801 " pdb=" N ILE C 801 " pdb=" C ILE C 801 " pdb=" CB ILE C 801 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 4131 not shown) Planarity restraints: 4364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 24 " 0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO B 25 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 144 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" C ARG D 144 " -0.036 2.00e-02 2.50e+03 pdb=" O ARG D 144 " 0.013 2.00e-02 2.50e+03 pdb=" N HIS D 145 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C R 19 " 0.023 2.00e-02 2.50e+03 1.35e-02 4.13e+00 pdb=" N1 C R 19 " -0.033 2.00e-02 2.50e+03 pdb=" C2 C R 19 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C R 19 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C R 19 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C R 19 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C R 19 " 0.004 2.00e-02 2.50e+03 pdb=" C5 C R 19 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C R 19 " -0.001 2.00e-02 2.50e+03 ... (remaining 4361 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 84 2.38 - 3.01: 15468 3.01 - 3.64: 36156 3.64 - 4.27: 53668 4.27 - 4.90: 90761 Nonbonded interactions: 196137 Sorted by model distance: nonbonded pdb=" O3' U R 42 " pdb="MG MG D2002 " model vdw 1.756 2.170 nonbonded pdb=" OG1 THR D 970 " pdb=" O GLY D 973 " model vdw 1.915 2.440 nonbonded pdb=" O GLY D 257 " pdb=" OG SER D 260 " model vdw 2.000 2.440 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.010 2.170 nonbonded pdb=" O THR B 41 " pdb=" OG SER B 45 " model vdw 2.053 2.440 ... (remaining 196132 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 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 226)) \ selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 7.150 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 86.720 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 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 : 0.004 0.040 26288 Z= 0.262 Angle : 0.623 6.221 36082 Z= 0.369 Chirality : 0.042 0.197 4134 Planarity : 0.004 0.083 4364 Dihedral : 16.497 176.492 10383 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.67 % Favored : 93.16 % Rotamer: Outliers : 0.91 % Allowed : 9.57 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.04 % 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: -1.08 (0.15), residues: 2999 helix: 0.91 (0.16), residues: 1044 sheet: -0.88 (0.27), residues: 372 loop : -1.88 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 778 HIS 0.005 0.001 HIS A 61 PHE 0.013 0.001 PHE N 64 TYR 0.014 0.001 TYR C 344 ARG 0.004 0.000 ARG D 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 345 time to evaluate : 3.010 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 12 ASP cc_start: 0.7972 (m-30) cc_final: 0.7050 (p0) REVERT: A 17 ASN cc_start: 0.8152 (p0) cc_final: 0.7807 (p0) REVERT: A 221 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7338 (tp) REVERT: B 191 LYS cc_start: 0.8990 (ttmt) cc_final: 0.8710 (ttpp) REVERT: C 219 ARG cc_start: 0.8615 (ttp-110) cc_final: 0.8329 (ptp90) REVERT: C 262 LEU cc_start: 0.8562 (mt) cc_final: 0.8361 (mp) REVERT: C 396 MET cc_start: 0.8412 (ttp) cc_final: 0.8159 (ttp) REVERT: C 645 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7498 (mt-10) REVERT: C 661 MET cc_start: 0.8923 (tmm) cc_final: 0.8713 (tmm) REVERT: C 904 MET cc_start: 0.8942 (mmt) cc_final: 0.8354 (mmt) REVERT: D 177 LEU cc_start: -0.2278 (OUTLIER) cc_final: -0.2939 (mt) REVERT: D 248 TYR cc_start: 0.8712 (m-80) cc_final: 0.8439 (m-80) REVERT: D 278 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7731 (ptp-170) REVERT: D 443 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7647 (mp) REVERT: D 450 GLU cc_start: 0.8118 (tp30) cc_final: 0.7794 (tp30) REVERT: D 480 ARG cc_start: 0.7663 (mpt180) cc_final: 0.7314 (mpt180) REVERT: D 488 GLU cc_start: 0.7999 (tp30) cc_final: 0.7449 (tp30) REVERT: D 869 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7449 (t70) REVERT: D 1097 ARG cc_start: 0.3243 (OUTLIER) cc_final: 0.3029 (ptm-80) REVERT: D 1279 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7502 (ttm-80) REVERT: N 10 TYR cc_start: 0.8514 (m-80) cc_final: 0.8311 (m-10) REVERT: N 113 ASN cc_start: 0.7948 (m-40) cc_final: 0.7725 (m-40) outliers start: 23 outliers final: 10 residues processed: 360 average time/residue: 0.4133 time to fit residues: 228.1048 Evaluate side-chains 302 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 287 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 29 HIS Chi-restraints excluded: chain N residue 41 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 50.0000 chunk 233 optimal weight: 0.5980 chunk 129 optimal weight: 0.4980 chunk 79 optimal weight: 0.0060 chunk 157 optimal weight: 6.9990 chunk 124 optimal weight: 0.1980 chunk 241 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 279 optimal weight: 6.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN B 124 HIS C 935 HIS ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 882 GLN N 29 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26288 Z= 0.167 Angle : 0.573 8.195 36082 Z= 0.303 Chirality : 0.042 0.199 4134 Planarity : 0.004 0.070 4364 Dihedral : 17.146 178.852 4679 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.00 % Favored : 94.83 % Rotamer: Outliers : 2.14 % Allowed : 11.35 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.57 (0.15), residues: 2999 helix: 1.39 (0.16), residues: 1060 sheet: -0.69 (0.26), residues: 390 loop : -1.63 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 938 HIS 0.003 0.001 HIS C 599 PHE 0.023 0.001 PHE N 64 TYR 0.017 0.001 TYR D 251 ARG 0.014 0.000 ARG N 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 340 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7975 (m-30) cc_final: 0.7078 (p0) REVERT: A 89 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7030 (mp0) REVERT: A 198 THR cc_start: 0.9334 (p) cc_final: 0.9019 (t) REVERT: B 17 ASN cc_start: 0.8895 (p0) cc_final: 0.8496 (p0) REVERT: B 224 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8083 (tm-30) REVERT: C 76 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7984 (pp20) REVERT: C 121 GLU cc_start: 0.8560 (tp30) cc_final: 0.8015 (tp30) REVERT: C 172 GLU cc_start: 0.7852 (tt0) cc_final: 0.7634 (tt0) REVERT: C 197 LYS cc_start: 0.8382 (mttt) cc_final: 0.7633 (mtmm) REVERT: C 219 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8240 (ptp90) REVERT: C 252 PHE cc_start: 0.7548 (m-80) cc_final: 0.7224 (m-10) REVERT: C 396 MET cc_start: 0.8433 (ttp) cc_final: 0.8168 (ttp) REVERT: C 551 ASP cc_start: 0.8247 (m-30) cc_final: 0.7413 (t0) REVERT: C 645 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7489 (mt-10) REVERT: C 652 GLU cc_start: 0.7906 (pt0) cc_final: 0.7685 (pt0) REVERT: C 661 MET cc_start: 0.8752 (tmm) cc_final: 0.8508 (tmm) REVERT: C 672 MET cc_start: 0.9179 (mmm) cc_final: 0.8894 (mmt) REVERT: C 797 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.7632 (ptp-110) REVERT: C 1072 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: C 1087 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: D 155 MET cc_start: 0.7795 (ttp) cc_final: 0.6818 (ppp) REVERT: D 177 LEU cc_start: -0.2685 (OUTLIER) cc_final: -0.3274 (mt) REVERT: D 223 TRP cc_start: 0.8259 (t-100) cc_final: 0.8028 (t-100) REVERT: D 242 ARG cc_start: 0.8484 (tpp-160) cc_final: 0.8109 (mmt180) REVERT: D 278 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7729 (ptp-170) REVERT: D 339 ASP cc_start: 0.7983 (m-30) cc_final: 0.7132 (m-30) REVERT: D 350 ARG cc_start: 0.8383 (tpp-160) cc_final: 0.8008 (mmt180) REVERT: D 450 GLU cc_start: 0.7982 (tp30) cc_final: 0.7486 (tp30) REVERT: D 488 GLU cc_start: 0.8275 (tp30) cc_final: 0.7721 (tp30) REVERT: D 535 ASP cc_start: 0.7830 (p0) cc_final: 0.7616 (p0) REVERT: D 776 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7905 (mm-30) REVERT: D 854 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.6921 (t-90) REVERT: D 1097 ARG cc_start: 0.3502 (OUTLIER) cc_final: 0.3169 (ptm-80) REVERT: D 1279 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.7303 (ttm-80) REVERT: N 90 MET cc_start: 0.7698 (mtp) cc_final: 0.7482 (mtp) outliers start: 54 outliers final: 27 residues processed: 375 average time/residue: 0.3999 time to fit residues: 230.2612 Evaluate side-chains 337 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 304 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 41 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 280 optimal weight: 0.0770 chunk 302 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 277 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 505 HIS D 959 GLN N 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26288 Z= 0.238 Angle : 0.563 8.107 36082 Z= 0.298 Chirality : 0.042 0.163 4134 Planarity : 0.004 0.072 4364 Dihedral : 16.968 178.433 4664 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.77 % Favored : 94.13 % Rotamer: Outliers : 3.72 % Allowed : 12.46 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.44 (0.15), residues: 2999 helix: 1.47 (0.16), residues: 1056 sheet: -0.63 (0.26), residues: 406 loop : -1.51 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 938 HIS 0.004 0.001 HIS D 544 PHE 0.018 0.001 PHE D 131 TYR 0.018 0.001 TYR D 65 ARG 0.015 0.000 ARG N 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 329 time to evaluate : 3.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8083 (m-30) cc_final: 0.7100 (p0) REVERT: A 89 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7001 (mp0) REVERT: A 198 THR cc_start: 0.9359 (p) cc_final: 0.9037 (t) REVERT: B 224 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8066 (tm-30) REVERT: C 76 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7877 (pp20) REVERT: C 197 LYS cc_start: 0.8543 (mttt) cc_final: 0.7781 (mtmm) REVERT: C 219 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.8264 (ptp90) REVERT: C 396 MET cc_start: 0.8400 (ttp) cc_final: 0.8044 (ttp) REVERT: C 528 ILE cc_start: 0.8953 (mm) cc_final: 0.8744 (mm) REVERT: C 551 ASP cc_start: 0.8330 (m-30) cc_final: 0.7400 (t0) REVERT: C 645 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7629 (mt-10) REVERT: C 652 GLU cc_start: 0.7998 (pt0) cc_final: 0.7768 (pt0) REVERT: C 797 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7705 (ptp-110) REVERT: C 1051 MET cc_start: 0.7253 (ttt) cc_final: 0.7016 (ttm) REVERT: C 1072 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: C 1094 ASP cc_start: 0.9034 (p0) cc_final: 0.8751 (p0) REVERT: D 69 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7940 (ptt90) REVERT: D 177 LEU cc_start: -0.2985 (OUTLIER) cc_final: -0.3580 (mt) REVERT: D 350 ARG cc_start: 0.8464 (tpp-160) cc_final: 0.8028 (mmt180) REVERT: D 450 GLU cc_start: 0.8044 (tp30) cc_final: 0.7519 (tp30) REVERT: D 475 MET cc_start: 0.8817 (mmm) cc_final: 0.8343 (mmm) REVERT: D 854 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7037 (t-90) REVERT: D 882 GLN cc_start: 0.8134 (tt0) cc_final: 0.7342 (pt0) REVERT: D 991 ILE cc_start: 0.8794 (mp) cc_final: 0.8526 (mm) REVERT: D 1097 ARG cc_start: 0.3726 (OUTLIER) cc_final: 0.3217 (ptm-80) outliers start: 94 outliers final: 51 residues processed: 390 average time/residue: 0.4187 time to fit residues: 256.0479 Evaluate side-chains 352 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 295 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 29 HIS Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 41 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 chunk 297 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26288 Z= 0.187 Angle : 0.540 9.926 36082 Z= 0.284 Chirality : 0.041 0.164 4134 Planarity : 0.004 0.069 4364 Dihedral : 16.919 178.373 4664 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.57 % Favored : 94.33 % Rotamer: Outliers : 3.04 % Allowed : 14.55 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.27 (0.16), residues: 2999 helix: 1.56 (0.17), residues: 1063 sheet: -0.42 (0.27), residues: 386 loop : -1.42 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 938 HIS 0.019 0.001 HIS N 29 PHE 0.014 0.001 PHE N 64 TYR 0.017 0.001 TYR D 241 ARG 0.007 0.000 ARG C 925 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 312 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8103 (m-30) cc_final: 0.7116 (p0) REVERT: A 17 ASN cc_start: 0.8378 (p0) cc_final: 0.7756 (p0) REVERT: A 89 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7043 (mp0) REVERT: A 198 THR cc_start: 0.9330 (p) cc_final: 0.8914 (t) REVERT: B 224 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7998 (tm-30) REVERT: C 76 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7965 (pp20) REVERT: C 197 LYS cc_start: 0.8563 (mttt) cc_final: 0.7887 (mtmm) REVERT: C 219 ARG cc_start: 0.8535 (ttp-110) cc_final: 0.8334 (ptp90) REVERT: C 396 MET cc_start: 0.8335 (ttp) cc_final: 0.7989 (ttp) REVERT: C 551 ASP cc_start: 0.8339 (m-30) cc_final: 0.7397 (t0) REVERT: C 645 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7656 (mt-10) REVERT: C 652 GLU cc_start: 0.7995 (pt0) cc_final: 0.7756 (pt0) REVERT: C 672 MET cc_start: 0.9149 (mmm) cc_final: 0.8801 (mmt) REVERT: C 1072 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: C 1094 ASP cc_start: 0.9026 (p0) cc_final: 0.8690 (p0) REVERT: D 155 MET cc_start: 0.7460 (ttp) cc_final: 0.6771 (ppp) REVERT: D 177 LEU cc_start: -0.2945 (OUTLIER) cc_final: -0.3508 (mt) REVERT: D 242 ARG cc_start: 0.8604 (tpp-160) cc_final: 0.8259 (mmt180) REVERT: D 251 TYR cc_start: 0.7907 (m-80) cc_final: 0.7013 (m-80) REVERT: D 256 MET cc_start: 0.7806 (tmm) cc_final: 0.7515 (tmm) REVERT: D 294 LYS cc_start: 0.8525 (mttm) cc_final: 0.8161 (mttt) REVERT: D 339 ASP cc_start: 0.7940 (m-30) cc_final: 0.7077 (m-30) REVERT: D 450 GLU cc_start: 0.8082 (tp30) cc_final: 0.7581 (tp30) REVERT: D 475 MET cc_start: 0.8797 (mmm) cc_final: 0.8374 (mmm) REVERT: D 854 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7237 (t-90) REVERT: D 882 GLN cc_start: 0.8071 (tt0) cc_final: 0.7280 (pt0) REVERT: D 991 ILE cc_start: 0.8828 (mp) cc_final: 0.8573 (mm) REVERT: D 1097 ARG cc_start: 0.3563 (OUTLIER) cc_final: 0.3292 (ptm-80) REVERT: N 35 MET cc_start: 0.7004 (mtm) cc_final: 0.6551 (mmp) REVERT: N 114 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7586 (ttp80) outliers start: 77 outliers final: 52 residues processed: 362 average time/residue: 0.3970 time to fit residues: 222.9042 Evaluate side-chains 360 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 303 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 41 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 0.3980 chunk 168 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 254 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN B 124 HIS C 935 HIS N 29 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26288 Z= 0.263 Angle : 0.566 13.017 36082 Z= 0.298 Chirality : 0.042 0.159 4134 Planarity : 0.004 0.070 4364 Dihedral : 16.925 178.464 4664 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.00 % Favored : 93.90 % Rotamer: Outliers : 3.56 % Allowed : 15.26 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.27 (0.16), residues: 2999 helix: 1.50 (0.16), residues: 1060 sheet: -0.47 (0.27), residues: 390 loop : -1.35 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 938 HIS 0.006 0.001 HIS D 505 PHE 0.016 0.001 PHE C 254 TYR 0.017 0.001 TYR D 241 ARG 0.008 0.000 ARG C 925 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 312 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8095 (m-30) cc_final: 0.7093 (p0) REVERT: A 17 ASN cc_start: 0.8404 (p0) cc_final: 0.7730 (p0) REVERT: A 89 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7033 (mp0) REVERT: A 198 THR cc_start: 0.9330 (p) cc_final: 0.8909 (t) REVERT: B 224 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7994 (tm-30) REVERT: C 197 LYS cc_start: 0.8549 (mttt) cc_final: 0.7838 (mtmm) REVERT: C 551 ASP cc_start: 0.8391 (m-30) cc_final: 0.7479 (t0) REVERT: C 645 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7681 (mt-10) REVERT: C 1072 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: C 1094 ASP cc_start: 0.9037 (p0) cc_final: 0.8667 (p0) REVERT: D 69 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7971 (ptt90) REVERT: D 83 THR cc_start: 0.8685 (t) cc_final: 0.8208 (p) REVERT: D 117 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9053 (tp) REVERT: D 177 LEU cc_start: -0.2778 (OUTLIER) cc_final: -0.3448 (mt) REVERT: D 242 ARG cc_start: 0.8681 (tpp-160) cc_final: 0.8332 (mmt180) REVERT: D 251 TYR cc_start: 0.7733 (m-80) cc_final: 0.7492 (m-80) REVERT: D 256 MET cc_start: 0.7786 (tmm) cc_final: 0.7455 (tmm) REVERT: D 450 GLU cc_start: 0.8178 (tp30) cc_final: 0.7696 (tp30) REVERT: D 854 HIS cc_start: 0.8105 (OUTLIER) cc_final: 0.7222 (t-90) REVERT: D 882 GLN cc_start: 0.8136 (tt0) cc_final: 0.7318 (pt0) REVERT: D 991 ILE cc_start: 0.8910 (mp) cc_final: 0.8628 (mm) REVERT: N 35 MET cc_start: 0.7200 (mtm) cc_final: 0.6826 (mmp) outliers start: 90 outliers final: 67 residues processed: 371 average time/residue: 0.4135 time to fit residues: 240.3887 Evaluate side-chains 367 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 295 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 41 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 0.8980 chunk 268 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 174 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 247 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS D 494 HIS N 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26288 Z= 0.270 Angle : 0.574 13.548 36082 Z= 0.302 Chirality : 0.042 0.161 4134 Planarity : 0.004 0.071 4364 Dihedral : 16.921 177.186 4661 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.14 % Favored : 93.76 % Rotamer: Outliers : 3.99 % Allowed : 15.18 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2999 helix: 1.47 (0.16), residues: 1068 sheet: -0.45 (0.27), residues: 385 loop : -1.32 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 938 HIS 0.006 0.001 HIS D 505 PHE 0.019 0.002 PHE N 64 TYR 0.018 0.001 TYR D 134 ARG 0.017 0.000 ARG N 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 309 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8075 (m-30) cc_final: 0.7070 (p0) REVERT: A 17 ASN cc_start: 0.8401 (p0) cc_final: 0.7780 (p0) REVERT: A 89 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7048 (mp0) REVERT: A 198 THR cc_start: 0.9309 (p) cc_final: 0.9108 (p) REVERT: B 224 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8015 (tm-30) REVERT: C 239 LYS cc_start: 0.8320 (mttp) cc_final: 0.8071 (mttt) REVERT: C 551 ASP cc_start: 0.8388 (m-30) cc_final: 0.7478 (t0) REVERT: C 645 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7771 (mt-10) REVERT: C 797 ARG cc_start: 0.8084 (ttp-110) cc_final: 0.7581 (mtm-85) REVERT: C 1049 TYR cc_start: 0.8543 (m-80) cc_final: 0.8211 (m-80) REVERT: C 1072 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: C 1094 ASP cc_start: 0.9077 (p0) cc_final: 0.8640 (p0) REVERT: D 22 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8019 (tm-30) REVERT: D 69 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7944 (ptt90) REVERT: D 81 GLU cc_start: 0.7876 (tt0) cc_final: 0.6619 (tm-30) REVERT: D 117 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9095 (tp) REVERT: D 177 LEU cc_start: -0.2565 (OUTLIER) cc_final: -0.3315 (mt) REVERT: D 226 PHE cc_start: 0.8320 (t80) cc_final: 0.8027 (t80) REVERT: D 242 ARG cc_start: 0.8680 (tpp-160) cc_final: 0.8332 (mmt180) REVERT: D 256 MET cc_start: 0.7947 (tmm) cc_final: 0.7741 (tmm) REVERT: D 339 ASP cc_start: 0.7952 (m-30) cc_final: 0.7177 (m-30) REVERT: D 450 GLU cc_start: 0.8238 (tp30) cc_final: 0.7783 (tp30) REVERT: D 475 MET cc_start: 0.8812 (mmm) cc_final: 0.8446 (mmm) REVERT: D 854 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7264 (t-90) REVERT: D 882 GLN cc_start: 0.8218 (tt0) cc_final: 0.7446 (pt0) REVERT: N 35 MET cc_start: 0.7267 (mtm) cc_final: 0.6856 (mmp) REVERT: N 41 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7958 (tp30) outliers start: 101 outliers final: 70 residues processed: 379 average time/residue: 0.3796 time to fit residues: 223.8997 Evaluate side-chains 373 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 297 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 29 HIS Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 250 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 296 optimal weight: 0.9980 chunk 185 optimal weight: 0.5980 chunk 180 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 ASN E 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26288 Z= 0.173 Angle : 0.541 14.695 36082 Z= 0.283 Chirality : 0.041 0.162 4134 Planarity : 0.004 0.066 4364 Dihedral : 16.846 177.484 4657 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.36 % Rotamer: Outliers : 3.40 % Allowed : 16.01 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.07 (0.16), residues: 2999 helix: 1.67 (0.17), residues: 1063 sheet: -0.22 (0.27), residues: 390 loop : -1.28 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 938 HIS 0.031 0.001 HIS N 29 PHE 0.012 0.001 PHE C 254 TYR 0.014 0.001 TYR C 344 ARG 0.009 0.000 ARG C 925 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 317 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8085 (m-30) cc_final: 0.7074 (p0) REVERT: A 17 ASN cc_start: 0.8403 (p0) cc_final: 0.7768 (p0) REVERT: A 89 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7135 (mp0) REVERT: A 198 THR cc_start: 0.9264 (p) cc_final: 0.8885 (t) REVERT: B 224 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7970 (tm-30) REVERT: C 76 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7903 (pp20) REVERT: C 197 LYS cc_start: 0.8581 (mttt) cc_final: 0.7893 (mtmm) REVERT: C 239 LYS cc_start: 0.8383 (mttp) cc_final: 0.8102 (mttt) REVERT: C 282 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8163 (ttm-80) REVERT: C 528 ILE cc_start: 0.8930 (mp) cc_final: 0.8703 (mm) REVERT: C 551 ASP cc_start: 0.8388 (m-30) cc_final: 0.7529 (t0) REVERT: C 645 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7798 (mt-10) REVERT: C 672 MET cc_start: 0.9117 (mmm) cc_final: 0.8739 (mmt) REVERT: C 713 MET cc_start: 0.8490 (mmt) cc_final: 0.8022 (mmm) REVERT: C 797 ARG cc_start: 0.8076 (ttp-110) cc_final: 0.7626 (mtm-85) REVERT: C 918 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.8007 (m-40) REVERT: C 1072 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: D 22 GLN cc_start: 0.8316 (tm-30) cc_final: 0.8011 (tm-30) REVERT: D 117 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9055 (tp) REVERT: D 177 LEU cc_start: -0.2561 (OUTLIER) cc_final: -0.3306 (mt) REVERT: D 226 PHE cc_start: 0.8332 (t80) cc_final: 0.8034 (t80) REVERT: D 242 ARG cc_start: 0.8636 (tpp-160) cc_final: 0.8385 (mmt180) REVERT: D 251 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: D 256 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7659 (tmm) REVERT: D 350 ARG cc_start: 0.8375 (tpp-160) cc_final: 0.8064 (tpp-160) REVERT: D 389 ARG cc_start: 0.8099 (mtp-110) cc_final: 0.7693 (mtm110) REVERT: D 450 GLU cc_start: 0.8224 (tp30) cc_final: 0.7765 (tp30) REVERT: D 475 MET cc_start: 0.8774 (mmm) cc_final: 0.8478 (mmm) REVERT: D 854 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7223 (t-90) REVERT: D 882 GLN cc_start: 0.8093 (tt0) cc_final: 0.7300 (pt0) REVERT: D 991 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8525 (mm) REVERT: N 35 MET cc_start: 0.7312 (mtm) cc_final: 0.6827 (mmp) REVERT: N 41 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7934 (tp30) REVERT: N 47 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7416 (tm-30) outliers start: 86 outliers final: 65 residues processed: 371 average time/residue: 0.3930 time to fit residues: 227.9224 Evaluate side-chains 378 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 303 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 918 ASN Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 29 HIS Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 202 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 540 GLN N 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26288 Z= 0.253 Angle : 0.567 14.652 36082 Z= 0.298 Chirality : 0.042 0.159 4134 Planarity : 0.004 0.073 4364 Dihedral : 16.856 177.473 4657 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.00 % Favored : 93.93 % Rotamer: Outliers : 3.64 % Allowed : 16.33 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2999 helix: 1.61 (0.16), residues: 1064 sheet: -0.37 (0.27), residues: 392 loop : -1.25 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 223 HIS 0.006 0.001 HIS N 29 PHE 0.019 0.001 PHE D 252 TYR 0.015 0.001 TYR D 134 ARG 0.009 0.000 ARG C 925 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 304 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8113 (m-30) cc_final: 0.7059 (p0) REVERT: A 17 ASN cc_start: 0.8410 (p0) cc_final: 0.7803 (p0) REVERT: A 89 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7077 (mp0) REVERT: A 198 THR cc_start: 0.9287 (p) cc_final: 0.9078 (p) REVERT: B 224 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7995 (tm-30) REVERT: C 76 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7991 (pp20) REVERT: C 197 LYS cc_start: 0.8567 (mttt) cc_final: 0.7866 (mtmm) REVERT: C 239 LYS cc_start: 0.8383 (mttp) cc_final: 0.8097 (mttt) REVERT: C 271 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7208 (p0) REVERT: C 282 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.8185 (ttm-80) REVERT: C 415 GLN cc_start: 0.9201 (tt0) cc_final: 0.8849 (tt0) REVERT: C 433 THR cc_start: 0.8788 (m) cc_final: 0.8082 (p) REVERT: C 458 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8698 (pp) REVERT: C 551 ASP cc_start: 0.8375 (m-30) cc_final: 0.7467 (t0) REVERT: C 645 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7822 (mt-10) REVERT: C 661 MET cc_start: 0.8700 (tmm) cc_final: 0.8362 (tmm) REVERT: C 672 MET cc_start: 0.9126 (mmm) cc_final: 0.8744 (mmt) REVERT: C 797 ARG cc_start: 0.8096 (ttp-110) cc_final: 0.7671 (mtm-85) REVERT: C 918 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7992 (m-40) REVERT: C 1072 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: C 1094 ASP cc_start: 0.9208 (p0) cc_final: 0.8983 (p0) REVERT: C 1103 TYR cc_start: 0.7789 (t80) cc_final: 0.7506 (t80) REVERT: D 1 MET cc_start: 0.6471 (mtm) cc_final: 0.5968 (mpp) REVERT: D 22 GLN cc_start: 0.8337 (tm-30) cc_final: 0.8035 (tm-30) REVERT: D 117 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9108 (tp) REVERT: D 177 LEU cc_start: -0.2425 (OUTLIER) cc_final: -0.3394 (mt) REVERT: D 226 PHE cc_start: 0.8319 (t80) cc_final: 0.8006 (t80) REVERT: D 242 ARG cc_start: 0.8665 (tpp-160) cc_final: 0.8421 (mmt180) REVERT: D 251 TYR cc_start: 0.8090 (m-80) cc_final: 0.7631 (m-80) REVERT: D 256 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7707 (tmm) REVERT: D 294 LYS cc_start: 0.8492 (mttm) cc_final: 0.8242 (tttt) REVERT: D 350 ARG cc_start: 0.8375 (tpp-160) cc_final: 0.8148 (tpp-160) REVERT: D 389 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7695 (mtm110) REVERT: D 450 GLU cc_start: 0.8247 (tp30) cc_final: 0.7787 (tp30) REVERT: D 475 MET cc_start: 0.8794 (mmm) cc_final: 0.8475 (mmm) REVERT: D 854 HIS cc_start: 0.8106 (OUTLIER) cc_final: 0.7217 (t-90) REVERT: D 882 GLN cc_start: 0.8179 (tt0) cc_final: 0.7384 (pt0) REVERT: N 35 MET cc_start: 0.7332 (mtm) cc_final: 0.6847 (mmp) REVERT: N 41 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7954 (tp30) REVERT: N 47 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7353 (tm-30) outliers start: 92 outliers final: 69 residues processed: 363 average time/residue: 0.3780 time to fit residues: 215.3340 Evaluate side-chains 377 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 298 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 918 ASN Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 29 HIS Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 7.9990 chunk 284 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 276 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 249 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 275 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS N 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26288 Z= 0.273 Angle : 0.579 14.904 36082 Z= 0.302 Chirality : 0.042 0.167 4134 Planarity : 0.004 0.069 4364 Dihedral : 16.865 177.359 4657 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.00 % Favored : 93.96 % Rotamer: Outliers : 3.48 % Allowed : 16.53 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.13 (0.16), residues: 2999 helix: 1.58 (0.16), residues: 1062 sheet: -0.40 (0.27), residues: 392 loop : -1.24 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 223 HIS 0.008 0.001 HIS N 29 PHE 0.015 0.001 PHE C 906 TYR 0.016 0.001 TYR D 134 ARG 0.010 0.000 ARG C 925 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 303 time to evaluate : 2.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8122 (m-30) cc_final: 0.7063 (p0) REVERT: A 17 ASN cc_start: 0.8399 (p0) cc_final: 0.7778 (p0) REVERT: A 89 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7084 (mp0) REVERT: A 198 THR cc_start: 0.9273 (p) cc_final: 0.9056 (p) REVERT: B 224 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7996 (tm-30) REVERT: C 76 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7997 (pp20) REVERT: C 197 LYS cc_start: 0.8564 (mttt) cc_final: 0.7859 (mtmm) REVERT: C 239 LYS cc_start: 0.8408 (mttp) cc_final: 0.8132 (mttt) REVERT: C 282 ARG cc_start: 0.8486 (ttm-80) cc_final: 0.8202 (ttm-80) REVERT: C 415 GLN cc_start: 0.9209 (tt0) cc_final: 0.8859 (tt0) REVERT: C 433 THR cc_start: 0.8799 (m) cc_final: 0.8113 (p) REVERT: C 458 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8697 (pp) REVERT: C 551 ASP cc_start: 0.8356 (m-30) cc_final: 0.7432 (t0) REVERT: C 645 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7838 (mt-10) REVERT: C 661 MET cc_start: 0.8687 (tmm) cc_final: 0.8332 (tmm) REVERT: C 672 MET cc_start: 0.9121 (mmm) cc_final: 0.8733 (mmt) REVERT: C 797 ARG cc_start: 0.8094 (ttp-110) cc_final: 0.7674 (mtm-85) REVERT: C 918 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.8008 (m-40) REVERT: C 1072 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: C 1103 TYR cc_start: 0.7840 (t80) cc_final: 0.7577 (t80) REVERT: D 1 MET cc_start: 0.6350 (mtm) cc_final: 0.5932 (mpp) REVERT: D 22 GLN cc_start: 0.8325 (tm-30) cc_final: 0.8012 (tm-30) REVERT: D 117 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9110 (tp) REVERT: D 177 LEU cc_start: -0.2310 (OUTLIER) cc_final: -0.3409 (mt) REVERT: D 226 PHE cc_start: 0.8312 (t80) cc_final: 0.8003 (t80) REVERT: D 242 ARG cc_start: 0.8687 (tpp-160) cc_final: 0.8418 (mmt180) REVERT: D 251 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: D 256 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7707 (tmm) REVERT: D 294 LYS cc_start: 0.8510 (mttm) cc_final: 0.8271 (tttt) REVERT: D 389 ARG cc_start: 0.8122 (mtp-110) cc_final: 0.7740 (mtm110) REVERT: D 450 GLU cc_start: 0.8273 (tp30) cc_final: 0.7813 (tp30) REVERT: D 475 MET cc_start: 0.8785 (mmm) cc_final: 0.8463 (mmm) REVERT: D 854 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7274 (t-90) REVERT: D 882 GLN cc_start: 0.8195 (tt0) cc_final: 0.7393 (pt0) REVERT: D 1097 ARG cc_start: 0.4262 (pmt100) cc_final: 0.3623 (ptm-80) REVERT: D 1112 MET cc_start: 0.7953 (mmm) cc_final: 0.7414 (mmm) REVERT: N 35 MET cc_start: 0.7328 (mtm) cc_final: 0.6880 (mmp) REVERT: N 41 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7945 (tp30) REVERT: N 47 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7379 (tm-30) outliers start: 88 outliers final: 72 residues processed: 361 average time/residue: 0.3755 time to fit residues: 212.3420 Evaluate side-chains 381 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 299 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 918 ASN Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 29 HIS Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 9.9990 chunk 292 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 203 optimal weight: 0.6980 chunk 306 optimal weight: 40.0000 chunk 282 optimal weight: 0.9990 chunk 244 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 149 optimal weight: 0.4980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1139 GLN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26288 Z= 0.157 Angle : 0.541 15.020 36082 Z= 0.281 Chirality : 0.041 0.192 4134 Planarity : 0.004 0.066 4364 Dihedral : 16.752 177.489 4657 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.76 % Rotamer: Outliers : 2.77 % Allowed : 17.52 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 0.06 (0.16), residues: 2999 helix: 1.75 (0.17), residues: 1068 sheet: -0.20 (0.27), residues: 387 loop : -1.16 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 938 HIS 0.034 0.001 HIS N 29 PHE 0.020 0.001 PHE D 252 TYR 0.015 0.001 TYR N 68 ARG 0.009 0.000 ARG C 925 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 318 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8129 (m-30) cc_final: 0.7084 (p0) REVERT: A 17 ASN cc_start: 0.8340 (p0) cc_final: 0.7765 (p0) REVERT: A 89 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7153 (mp0) REVERT: A 123 MET cc_start: 0.8744 (ptp) cc_final: 0.8518 (ptp) REVERT: A 198 THR cc_start: 0.9208 (p) cc_final: 0.9001 (p) REVERT: B 224 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7947 (tm-30) REVERT: C 76 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7998 (pp20) REVERT: C 197 LYS cc_start: 0.8567 (mttt) cc_final: 0.7902 (mtmm) REVERT: C 215 ASP cc_start: 0.7675 (p0) cc_final: 0.7441 (p0) REVERT: C 231 ARG cc_start: 0.7239 (mtp-110) cc_final: 0.7026 (mtp180) REVERT: C 239 LYS cc_start: 0.8387 (mttp) cc_final: 0.8085 (mttt) REVERT: C 271 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7233 (p0) REVERT: C 282 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.8184 (ttm-80) REVERT: C 433 THR cc_start: 0.8720 (m) cc_final: 0.8051 (p) REVERT: C 458 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8701 (pp) REVERT: C 551 ASP cc_start: 0.8364 (m-30) cc_final: 0.7488 (t0) REVERT: C 645 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7840 (mt-10) REVERT: C 661 MET cc_start: 0.8701 (tmm) cc_final: 0.8345 (tmm) REVERT: C 713 MET cc_start: 0.8560 (mmt) cc_final: 0.8171 (mmm) REVERT: C 797 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7568 (mtm-85) REVERT: C 918 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8059 (m-40) REVERT: C 1051 MET cc_start: 0.7460 (mmm) cc_final: 0.7198 (mtp) REVERT: C 1072 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: C 1103 TYR cc_start: 0.7724 (t80) cc_final: 0.7458 (t80) REVERT: D 22 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7995 (tm-30) REVERT: D 117 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9074 (tp) REVERT: D 177 LEU cc_start: -0.2394 (OUTLIER) cc_final: -0.3355 (mt) REVERT: D 226 PHE cc_start: 0.8281 (t80) cc_final: 0.7994 (t80) REVERT: D 242 ARG cc_start: 0.8665 (tpp-160) cc_final: 0.8416 (mmt180) REVERT: D 251 TYR cc_start: 0.7888 (m-80) cc_final: 0.7588 (m-80) REVERT: D 256 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7701 (tmm) REVERT: D 389 ARG cc_start: 0.8106 (mtp-110) cc_final: 0.7733 (mtm110) REVERT: D 450 GLU cc_start: 0.8175 (tp30) cc_final: 0.7733 (tp30) REVERT: D 475 MET cc_start: 0.8711 (mmm) cc_final: 0.8399 (mmm) REVERT: D 854 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.7308 (t-90) REVERT: D 882 GLN cc_start: 0.7999 (tt0) cc_final: 0.7303 (pt0) REVERT: D 981 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8080 (ttp80) REVERT: D 1097 ARG cc_start: 0.4251 (pmt100) cc_final: 0.3739 (ptm-80) REVERT: D 1112 MET cc_start: 0.7890 (mmm) cc_final: 0.7393 (mmm) REVERT: N 35 MET cc_start: 0.7381 (mtm) cc_final: 0.6931 (mmp) REVERT: N 41 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: N 47 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7248 (tm-30) outliers start: 70 outliers final: 53 residues processed: 366 average time/residue: 0.3966 time to fit residues: 226.9768 Evaluate side-chains 367 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 304 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 918 ASN Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 3.9990 chunk 260 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS C 386 GLN C 388 GLN ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1139 GLN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.157500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.112931 restraints weight = 32909.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.111443 restraints weight = 51115.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112909 restraints weight = 48991.207| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 26288 Z= 0.518 Angle : 0.723 15.074 36082 Z= 0.377 Chirality : 0.047 0.176 4134 Planarity : 0.005 0.072 4364 Dihedral : 16.939 177.181 4657 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.64 % Favored : 92.30 % Rotamer: Outliers : 3.20 % Allowed : 17.44 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.51 (0.15), residues: 2999 helix: 1.16 (0.16), residues: 1067 sheet: -0.64 (0.26), residues: 403 loop : -1.37 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 63 HIS 0.010 0.001 HIS D 505 PHE 0.032 0.002 PHE C 906 TYR 0.030 0.002 TYR C 344 ARG 0.012 0.001 ARG C 925 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5224.82 seconds wall clock time: 96 minutes 26.39 seconds (5786.39 seconds total)