Starting phenix.real_space_refine on Fri Mar 22 11:44:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gl8_40194/03_2024/8gl8_40194_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gl8_40194/03_2024/8gl8_40194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gl8_40194/03_2024/8gl8_40194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gl8_40194/03_2024/8gl8_40194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gl8_40194/03_2024/8gl8_40194_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gl8_40194/03_2024/8gl8_40194_updated.pdb" } resolution = 2.2 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= 0.014 sd= 1.271 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 79 5.16 5 C 20366 2.51 5 N 5395 2.21 5 O 7439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 900": "OE1" <-> "OE2" Residue "A GLU 1130": "OE1" <-> "OE2" Residue "A ASP 1148": "OD1" <-> "OD2" Residue "A GLU 1176": "OE1" <-> "OE2" Residue "A TYR 1191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1202": "OD1" <-> "OD2" Residue "A GLU 1555": "OE1" <-> "OE2" Residue "A GLU 1559": "OE1" <-> "OE2" Residue "A GLU 1592": "OE1" <-> "OE2" Residue "A ASP 1645": "OD1" <-> "OD2" Residue "A ASP 1809": "OD1" <-> "OD2" Residue "A TYR 1844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2039": "OE1" <-> "OE2" Residue "A ASP 2048": "OD1" <-> "OD2" Residue "A GLU 2053": "OE1" <-> "OE2" Residue "A GLU 2081": "OE1" <-> "OE2" Residue "A GLU 2125": "OE1" <-> "OE2" Residue "A GLU 2258": "OE1" <-> "OE2" Residue "A TYR 2298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2320": "OD1" <-> "OD2" Residue "A GLU 2333": "OE1" <-> "OE2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ASP 70": "OD1" <-> "OD2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F ASP 173": "OD1" <-> "OD2" Residue "F PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 243": "OD1" <-> "OD2" Residue "F GLU 289": "OE1" <-> "OE2" Residue "F PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 397": "OD1" <-> "OD2" Residue "G GLU 33": "OE1" <-> "OE2" Residue "G GLU 88": "OE1" <-> "OE2" Residue "G ASP 102": "OD1" <-> "OD2" Residue "G ASP 111": "OD1" <-> "OD2" Residue "G ASP 151": "OD1" <-> "OD2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 187": "OD1" <-> "OD2" Residue "I GLU 382": "OE1" <-> "OE2" Residue "I GLU 387": "OE1" <-> "OE2" Residue "I ASP 407": "OD1" <-> "OD2" Residue "I ASP 602": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33279 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 18190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2290, 18190 Classifications: {'peptide': 2290} Link IDs: {'PCIS': 3, 'PTRANS': 105, 'TRANS': 2181} Chain breaks: 3 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 2861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2861 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Chain: "D" Number of atoms: 748 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'TRANS': 74} Conformer: "B" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'TRANS': 74} bond proxies already assigned to first conformer: 459 Chain: "G" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1435 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "C" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1414 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 169} Chain breaks: 1 Chain: "E" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1251 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 1, 'TRANS': 150} Chain: "I" Number of atoms: 5168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 5168 Classifications: {'peptide': 624} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 605} Chain breaks: 2 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'MAN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 767 Classifications: {'water': 767} Link IDs: {None: 766} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "F" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "I" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N ALYS D1076 " occ=0.57 ... (16 atoms not shown) pdb=" NZ BLYS D1076 " occ=0.43 residue: pdb=" N ALYS D1077 " occ=0.57 ... (16 atoms not shown) pdb=" NZ BLYS D1077 " occ=0.43 residue: pdb=" N AVAL D1078 " occ=0.57 ... (12 atoms not shown) pdb=" CG2BVAL D1078 " occ=0.43 residue: pdb=" N AGLU D1079 " occ=0.57 ... (16 atoms not shown) pdb=" OE2BGLU D1079 " occ=0.43 residue: pdb=" N AASN D1080 " occ=0.57 ... (14 atoms not shown) pdb=" ND2BASN D1080 " occ=0.43 residue: pdb=" N ATHR D1081 " occ=0.57 ... (12 atoms not shown) pdb=" CG2BTHR D1081 " occ=0.43 residue: pdb=" N AGLU D1082 " occ=0.57 ... (16 atoms not shown) pdb=" OE2BGLU D1082 " occ=0.43 residue: pdb=" N APHE D1083 " occ=0.57 ... (20 atoms not shown) pdb=" CZ BPHE D1083 " occ=0.43 residue: pdb=" N AGLN D1084 " occ=0.57 ... (16 atoms not shown) pdb=" NE2BGLN D1084 " occ=0.43 residue: pdb=" N AVAL D1085 " occ=0.57 ... (12 atoms not shown) pdb=" CG2BVAL D1085 " occ=0.43 residue: pdb=" N ASER D1086 " occ=0.57 ... (10 atoms not shown) pdb=" OG BSER D1086 " occ=0.43 residue: pdb=" N AASN D1087 " occ=0.57 ... (14 atoms not shown) pdb=" ND2BASN D1087 " occ=0.43 ... (remaining 6 not shown) Time building chain proxies: 17.27, per 1000 atoms: 0.52 Number of scatterers: 33279 At special positions: 0 Unit cell: (292.032, 280.384, 295.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 79 16.00 O 7439 8.00 N 5395 7.00 C 20366 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 Links applied MAN-SER " MAN I 901 " - " SER I 249 " " MAN I 902 " - " SER I 212 " " MAN I 903 " - " SER I 371 " " MAN I 904 " - " SER I 408 " MAN-THR " MAN I 906 " - " THR I 288 " Time building additional restraints: 12.49 Conformation dependent library (CDL) restraints added in 5.7 seconds 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 33 sheets defined 28.8% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.85 Creating SS restraints... Processing helix chain 'A' and resid 81 through 102 Processing helix chain 'A' and resid 108 through 114 removed outlier: 4.180A pdb=" N LYS A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 306 removed outlier: 4.667A pdb=" N ASP A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 402 through 405 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 518 through 522 removed outlier: 3.551A pdb=" N LEU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 518 through 522' Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 579 through 582 No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 644 through 646 No H-bonds generated for 'chain 'A' and resid 644 through 646' Processing helix chain 'A' and resid 651 through 654 No H-bonds generated for 'chain 'A' and resid 651 through 654' Processing helix chain 'A' and resid 658 through 661 No H-bonds generated for 'chain 'A' and resid 658 through 661' Processing helix chain 'A' and resid 664 through 669 removed outlier: 4.216A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 673 No H-bonds generated for 'chain 'A' and resid 671 through 673' Processing helix chain 'A' and resid 731 through 734 No H-bonds generated for 'chain 'A' and resid 731 through 734' Processing helix chain 'A' and resid 811 through 819 Processing helix chain 'A' and resid 846 through 848 No H-bonds generated for 'chain 'A' and resid 846 through 848' Processing helix chain 'A' and resid 873 through 875 No H-bonds generated for 'chain 'A' and resid 873 through 875' Processing helix chain 'A' and resid 899 through 902 Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.859A pdb=" N SER A 919 " --> pdb=" O VAL A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 943 No H-bonds generated for 'chain 'A' and resid 940 through 943' Processing helix chain 'A' and resid 983 through 985 No H-bonds generated for 'chain 'A' and resid 983 through 985' Processing helix chain 'A' and resid 999 through 1002 No H-bonds generated for 'chain 'A' and resid 999 through 1002' Processing helix chain 'A' and resid 1049 through 1051 No H-bonds generated for 'chain 'A' and resid 1049 through 1051' Processing helix chain 'A' and resid 1082 through 1088 Processing helix chain 'A' and resid 1100 through 1103 No H-bonds generated for 'chain 'A' and resid 1100 through 1103' Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1128 through 1132 Processing helix chain 'A' and resid 1413 through 1416 No H-bonds generated for 'chain 'A' and resid 1413 through 1416' Processing helix chain 'A' and resid 1419 through 1421 No H-bonds generated for 'chain 'A' and resid 1419 through 1421' Processing helix chain 'A' and resid 1427 through 1439 removed outlier: 4.046A pdb=" N SER A1439 " --> pdb=" O ILE A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1457 No H-bonds generated for 'chain 'A' and resid 1455 through 1457' Processing helix chain 'A' and resid 1572 through 1575 Processing helix chain 'A' and resid 1608 through 1613 Processing helix chain 'A' and resid 1618 through 1628 removed outlier: 3.605A pdb=" N ALA A1628 " --> pdb=" O ILE A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1659 No H-bonds generated for 'chain 'A' and resid 1657 through 1659' Processing helix chain 'A' and resid 1831 through 1833 No H-bonds generated for 'chain 'A' and resid 1831 through 1833' Processing helix chain 'A' and resid 1857 through 1860 No H-bonds generated for 'chain 'A' and resid 1857 through 1860' Processing helix chain 'A' and resid 1942 through 1944 No H-bonds generated for 'chain 'A' and resid 1942 through 1944' Processing helix chain 'A' and resid 1977 through 1980 No H-bonds generated for 'chain 'A' and resid 1977 through 1980' Processing helix chain 'A' and resid 1988 through 1994 Processing helix chain 'A' and resid 2072 through 2074 No H-bonds generated for 'chain 'A' and resid 2072 through 2074' Processing helix chain 'A' and resid 2085 through 2105 removed outlier: 3.722A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2135 Processing helix chain 'A' and resid 2148 through 2160 Proline residue: A2153 - end of helix Processing helix chain 'A' and resid 2187 through 2189 No H-bonds generated for 'chain 'A' and resid 2187 through 2189' Processing helix chain 'B' and resid 28 through 41 Processing helix chain 'B' and resid 127 through 135 Proline residue: B 134 - end of helix Processing helix chain 'F' and resid 31 through 34 Processing helix chain 'F' and resid 39 through 43 Processing helix chain 'F' and resid 62 through 67 removed outlier: 3.704A pdb=" N ALA F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 296 Processing helix chain 'F' and resid 300 through 307 removed outlier: 3.761A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 321 removed outlier: 4.170A pdb=" N LYS F 320 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU F 321 " --> pdb=" O GLU F 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 37 Processing helix chain 'G' and resid 40 through 76 Processing helix chain 'G' and resid 83 through 108 Processing helix chain 'G' and resid 113 through 119 Processing helix chain 'G' and resid 123 through 139 Processing helix chain 'G' and resid 159 through 161 No H-bonds generated for 'chain 'G' and resid 159 through 161' Processing helix chain 'G' and resid 164 through 175 Processing helix chain 'G' and resid 182 through 192 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 40 through 77 removed outlier: 3.747A pdb=" N GLU C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 107 Processing helix chain 'C' and resid 115 through 140 Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 164 through 172 Processing helix chain 'C' and resid 203 through 222 removed outlier: 3.764A pdb=" N ILE C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 39 Processing helix chain 'E' and resid 42 through 76 Processing helix chain 'E' and resid 84 through 108 Processing helix chain 'E' and resid 115 through 140 Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 165 through 173 Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 42 through 58 Processing helix chain 'I' and resid 89 through 102 Processing helix chain 'I' and resid 118 through 131 Processing helix chain 'I' and resid 135 through 148 Processing helix chain 'I' and resid 155 through 168 Processing helix chain 'I' and resid 172 through 184 Processing helix chain 'I' and resid 190 through 206 Processing helix chain 'I' and resid 210 through 223 Processing helix chain 'I' and resid 227 through 244 Processing helix chain 'I' and resid 247 through 258 Processing helix chain 'I' and resid 266 through 278 Processing helix chain 'I' and resid 287 through 298 Processing helix chain 'I' and resid 301 through 320 Proline residue: I 305 - end of helix removed outlier: 5.295A pdb=" N ASP I 308 " --> pdb=" O PRO I 305 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR I 312 " --> pdb=" O VAL I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 324 through 336 Processing helix chain 'I' and resid 342 through 358 Processing helix chain 'I' and resid 362 through 375 removed outlier: 3.621A pdb=" N THR I 374 " --> pdb=" O ASP I 370 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS I 375 " --> pdb=" O SER I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 414 removed outlier: 3.600A pdb=" N LEU I 393 " --> pdb=" O ASN I 389 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP I 394 " --> pdb=" O ARG I 390 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASN I 395 " --> pdb=" O LYS I 391 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL I 396 " --> pdb=" O ASN I 392 " (cutoff:3.500A) Processing helix chain 'I' and resid 418 through 442 Processing helix chain 'I' and resid 552 through 564 Processing helix chain 'I' and resid 570 through 592 Processing helix chain 'I' and resid 599 through 609 Processing helix chain 'I' and resid 616 through 630 Processing helix chain 'I' and resid 633 through 645 Processing helix chain 'I' and resid 652 through 656 Processing helix chain 'I' and resid 674 through 679 Processing helix chain 'I' and resid 685 through 696 removed outlier: 4.608A pdb=" N ASN I 695 " --> pdb=" O ASP I 691 " (cutoff:3.500A) Processing helix chain 'I' and resid 701 through 717 Processing helix chain 'I' and resid 720 through 733 Processing helix chain 'I' and resid 738 through 755 removed outlier: 3.592A pdb=" N GLU I 748 " --> pdb=" O ARG I 744 " (cutoff:3.500A) Proline residue: I 752 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 47 through 53 Processing sheet with id= B, first strand: chain 'A' and resid 763 through 767 removed outlier: 6.553A pdb=" N PHE A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE A1640 " --> pdb=" O PRO A1585 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N PHE A1662 " --> pdb=" O GLY A1641 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN A1743 " --> pdb=" O ALA A1677 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR A1679 " --> pdb=" O ARG A1741 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG A1741 " --> pdb=" O TYR A1679 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP A1681 " --> pdb=" O SER A1739 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A1739 " --> pdb=" O ASP A1681 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN A1683 " --> pdb=" O ARG A1737 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG A1737 " --> pdb=" O GLN A1683 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A1685 " --> pdb=" O ILE A1735 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE A1735 " --> pdb=" O ASN A1685 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A1687 " --> pdb=" O THR A1733 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A1733 " --> pdb=" O ALA A1687 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASN A1689 " --> pdb=" O PHE A1731 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE A1731 " --> pdb=" O ASN A1689 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA A1691 " --> pdb=" O ILE A1729 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A1729 " --> pdb=" O ALA A1691 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN A1728 " --> pdb=" O GLY A1771 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE A1789 " --> pdb=" O PRO A1816 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A1847 " --> pdb=" O SER A1881 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN A1951 " --> pdb=" O LYS A2016 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASP A2034 " --> pdb=" O SER A2068 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A2208 " --> pdb=" O THR A2069 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A2287 " --> pdb=" O ALA A2274 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A2322 " --> pdb=" O ASP A2360 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A2348 " --> pdb=" O THR A2334 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL A2336 " --> pdb=" O LEU A2346 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU A2346 " --> pdb=" O VAL A2336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A2351 " --> pdb=" O LYS A2379 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY A 141 " --> pdb=" O PHE A2401 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE A 205 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLN A 246 " --> pdb=" O GLN A 218 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL A 220 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS A 244 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL A 222 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY A 242 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN A 224 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 240 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG A 755 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A 754 " --> pdb=" O ARG A 782 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 145 through 152 Processing sheet with id= D, first strand: chain 'A' and resid 264 through 270 Processing sheet with id= E, first strand: chain 'A' and resid 275 through 282 Processing sheet with id= F, first strand: chain 'A' and resid 291 through 293 removed outlier: 3.855A pdb=" N TYR A 447 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 425 through 428 removed outlier: 5.956A pdb=" N LEU A 503 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU A 347 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 505 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N VAL A 504 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N PHE A 464 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 460 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR A 467 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 465 through 468 Processing sheet with id= I, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= J, first strand: chain 'A' and resid 527 through 529 Processing sheet with id= K, first strand: chain 'A' and resid 717 through 720 Processing sheet with id= L, first strand: chain 'A' and resid 866 through 869 removed outlier: 3.682A pdb=" N ASP A1194 " --> pdb=" O GLN A1215 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS A1217 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE A1192 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1250 through 1254 Processing sheet with id= N, first strand: chain 'A' and resid 987 through 993 Processing sheet with id= O, first strand: chain 'A' and resid 1283 through 1291 Processing sheet with id= P, first strand: chain 'A' and resid 1313 through 1315 Processing sheet with id= Q, first strand: chain 'A' and resid 1342 through 1348 Processing sheet with id= R, first strand: chain 'A' and resid 1423 through 1426 removed outlier: 6.318A pdb=" N LEU A1510 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR A 857 " --> pdb=" O LEU A1510 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 1739 through 1742 Processing sheet with id= T, first strand: chain 'A' and resid 1848 through 1853 Processing sheet with id= U, first strand: chain 'A' and resid 2027 through 2032 removed outlier: 6.163A pdb=" N GLU A2258 " --> pdb=" O LYS A2198 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A2200 " --> pdb=" O ASP A2256 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP A2256 " --> pdb=" O PHE A2200 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU A2202 " --> pdb=" O ARG A2254 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG A2254 " --> pdb=" O LEU A2202 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 2044 through 2047 Processing sheet with id= W, first strand: chain 'A' and resid 2215 through 2217 Processing sheet with id= X, first strand: chain 'A' and resid 2276 through 2278 Processing sheet with id= Y, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= Z, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.330A pdb=" N GLU B 141 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 90 through 98 Processing sheet with id= AB, first strand: chain 'F' and resid 118 through 120 removed outlier: 3.955A pdb=" N ARG F 131 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 1041 through 1045 Processing sheet with id= AD, first strand: chain 'D' and resid 1106 through 1112 removed outlier: 6.393A pdb=" N ASP D1066 " --> pdb=" O LEU D1071 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU D1071 " --> pdb=" O ASP D1066 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 27 through 30 removed outlier: 6.116A pdb=" N PHE G 144 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE G 30 " --> pdb=" O PHE G 144 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE G 146 " --> pdb=" O ILE G 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'C' and resid 27 through 29 removed outlier: 6.230A pdb=" N PHE C 144 " --> pdb=" O GLY C 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'E' and resid 27 through 30 removed outlier: 6.200A pdb=" N PHE E 144 " --> pdb=" O GLY E 28 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE E 30 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE E 146 " --> pdb=" O ILE E 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG 1445 hydrogen bonds defined for protein. 4017 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.60 Time building geometry restraints manager: 13.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10610 1.34 - 1.46: 7273 1.46 - 1.58: 14791 1.58 - 1.70: 4 1.70 - 1.82: 155 Bond restraints: 32833 Sorted by residual: bond pdb=" C1 LMN A2501 " pdb=" O5 LMN A2501 " ideal model delta sigma weight residual 1.403 1.552 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" CCS LMN A2501 " pdb=" OBZ LMN A2501 " ideal model delta sigma weight residual 1.394 1.480 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" CCR LMN A2501 " pdb=" OBY LMN A2501 " ideal model delta sigma weight residual 1.393 1.476 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C4 LMN A2501 " pdb=" O4 LMN A2501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C1 LMN A2501 " pdb=" O1 LMN A2501 " ideal model delta sigma weight residual 1.374 1.305 0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 32828 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.54: 688 106.54 - 113.44: 17385 113.44 - 120.35: 12159 120.35 - 127.25: 13968 127.25 - 134.16: 200 Bond angle restraints: 44400 Sorted by residual: angle pdb=" CA LYS A 79 " pdb=" CB LYS A 79 " pdb=" CG LYS A 79 " ideal model delta sigma weight residual 114.10 122.82 -8.72 2.00e+00 2.50e-01 1.90e+01 angle pdb=" CA LYS I 725 " pdb=" CB LYS I 725 " pdb=" CG LYS I 725 " ideal model delta sigma weight residual 114.10 121.95 -7.85 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CB LYS C 83 " pdb=" CG LYS C 83 " pdb=" CD LYS C 83 " ideal model delta sigma weight residual 111.30 120.28 -8.98 2.30e+00 1.89e-01 1.52e+01 angle pdb=" N PHE A 199 " pdb=" CA PHE A 199 " pdb=" C PHE A 199 " ideal model delta sigma weight residual 110.80 119.04 -8.24 2.13e+00 2.20e-01 1.49e+01 angle pdb=" N VAL A1987 " pdb=" CA VAL A1987 " pdb=" C VAL A1987 " ideal model delta sigma weight residual 113.20 109.70 3.50 9.60e-01 1.09e+00 1.33e+01 ... (remaining 44395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.93: 18358 27.93 - 55.86: 1395 55.86 - 83.80: 196 83.80 - 111.73: 39 111.73 - 139.66: 5 Dihedral angle restraints: 19993 sinusoidal: 8272 harmonic: 11721 Sorted by residual: dihedral pdb=" CA ARG F 121 " pdb=" C ARG F 121 " pdb=" N GLN F 122 " pdb=" CA GLN F 122 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA MET I 260 " pdb=" C MET I 260 " pdb=" N ASN I 261 " pdb=" CA ASN I 261 " ideal model delta harmonic sigma weight residual -180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CAB LMN A2501 " pdb=" CAX LMN A2501 " pdb=" CAZ LMN A2501 " pdb=" CBB LMN A2501 " ideal model delta sinusoidal sigma weight residual -179.97 -40.31 -139.66 1 3.00e+01 1.11e-03 1.88e+01 ... (remaining 19990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3867 0.052 - 0.103: 777 0.103 - 0.155: 171 0.155 - 0.206: 5 0.206 - 0.258: 1 Chirality restraints: 4821 Sorted by residual: chirality pdb=" CA PHE A 199 " pdb=" N PHE A 199 " pdb=" C PHE A 199 " pdb=" CB PHE A 199 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CCQ LMN A2501 " pdb=" CCF LMN A2501 " pdb=" CCH LMN A2501 " pdb=" OCB LMN A2501 " both_signs ideal model delta sigma weight residual False -2.61 -2.42 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CCV LMN A2501 " pdb=" CCR LMN A2501 " pdb=" CCT LMN A2501 " pdb=" OAU LMN A2501 " both_signs ideal model delta sigma weight residual False 2.28 2.47 -0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 4818 not shown) Planarity restraints: 5825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1639 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C PHE A1639 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE A1639 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A1640 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 176 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C SER A 176 " -0.041 2.00e-02 2.50e+03 pdb=" O SER A 176 " 0.016 2.00e-02 2.50e+03 pdb=" N MET A 177 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A2351 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C ASN A2351 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN A2351 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A2352 " -0.012 2.00e-02 2.50e+03 ... (remaining 5822 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 502 2.62 - 3.19: 27794 3.19 - 3.76: 53649 3.76 - 4.33: 78185 4.33 - 4.90: 123569 Nonbonded interactions: 283699 Sorted by model distance: nonbonded pdb=" O LEU I 182 " pdb=" OG1 THR I 186 " model vdw 2.055 2.440 nonbonded pdb=" ND2 ASN A1392 " pdb=" O GLY A1476 " model vdw 2.152 2.520 nonbonded pdb=" OD1 ASP A1165 " pdb=" O HOH A2601 " model vdw 2.153 2.440 nonbonded pdb=" OE1 GLN A 753 " pdb=" OG SER A 794 " model vdw 2.157 2.440 nonbonded pdb=" OD1 ASN A1163 " pdb=" O HOH A2601 " model vdw 2.160 2.440 ... (remaining 283694 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 'C' and resid 24 through 173) selection = (chain 'E' and resid 24 through 173) selection = (chain 'G' and resid 24 through 173) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.820 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: 20.480 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 91.470 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.120 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:10.900 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.003 0.149 32833 Z= 0.222 Angle : 0.569 10.627 44400 Z= 0.300 Chirality : 0.043 0.258 4821 Planarity : 0.003 0.052 5825 Dihedral : 19.298 139.662 12481 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.70 % Allowed : 23.00 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 3969 helix: 1.78 (0.16), residues: 1171 sheet: 0.52 (0.15), residues: 1105 loop : -0.57 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 674 HIS 0.004 0.001 HIS I 271 PHE 0.023 0.001 PHE A1009 TYR 0.015 0.001 TYR I 294 ARG 0.015 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 415 time to evaluate : 3.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: A 2207 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6726 (ttp-110) REVERT: I 674 TRP cc_start: 0.7481 (m-90) cc_final: 0.6976 (m-90) outliers start: 125 outliers final: 110 residues processed: 529 average time/residue: 1.3267 time to fit residues: 852.5790 Evaluate side-chains 520 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 408 time to evaluate : 3.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1665 SER Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1739 SER Chi-restraints excluded: chain A residue 1783 SER Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1856 SER Chi-restraints excluded: chain A residue 1881 SER Chi-restraints excluded: chain A residue 1943 THR Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 1945 ILE Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2011 SER Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2092 SER Chi-restraints excluded: chain A residue 2132 VAL Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2207 ARG Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2319 SER Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 390 SER Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 194 SER Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 340 LYS Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 372 THR Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 438 LYS Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 616 LEU Chi-restraints excluded: chain I residue 631 THR Chi-restraints excluded: chain I residue 639 ILE Chi-restraints excluded: chain I residue 641 SER Chi-restraints excluded: chain I residue 650 SER Chi-restraints excluded: chain I residue 666 SER Chi-restraints excluded: chain I residue 690 ILE Chi-restraints excluded: chain I residue 698 SER Chi-restraints excluded: chain I residue 713 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 6.9990 chunk 299 optimal weight: 0.9980 chunk 166 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 201 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 309 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 358 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN A1247 ASN A1293 GLN A1528 ASN ** A1853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2332 ASN A2350 GLN A2400 ASN F 101 ASN F 385 ASN ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN D1075 ASN D1105 ASN G 48 GLN G 58 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 261 ASN I 679 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.0546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32833 Z= 0.339 Angle : 0.605 7.605 44400 Z= 0.324 Chirality : 0.046 0.250 4821 Planarity : 0.004 0.050 5825 Dihedral : 10.381 104.827 4808 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.10 % Allowed : 20.92 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.13), residues: 3969 helix: 1.56 (0.16), residues: 1179 sheet: 0.58 (0.15), residues: 1105 loop : -0.64 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1580 HIS 0.006 0.001 HIS I 271 PHE 0.025 0.002 PHE A1009 TYR 0.022 0.002 TYR I 294 ARG 0.011 0.001 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 411 time to evaluate : 3.809 Fit side-chains revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.6532 (tm-30) REVERT: A 221 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: A 344 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.7756 (mp) REVERT: A 407 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8091 (mp) REVERT: A 1495 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6749 (m-30) REVERT: A 1680 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: A 2053 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7387 (tm-30) REVERT: B 93 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7490 (tm) REVERT: E 26 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6784 (ttt90) REVERT: I 167 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7592 (tmm) REVERT: I 382 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7796 (tt0) REVERT: I 674 TRP cc_start: 0.7541 (m-90) cc_final: 0.6988 (m-90) outliers start: 174 outliers final: 92 residues processed: 530 average time/residue: 1.4686 time to fit residues: 935.3994 Evaluate side-chains 506 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 403 time to evaluate : 4.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1373 THR Chi-restraints excluded: chain A residue 1495 ASP Chi-restraints excluded: chain A residue 1519 MET Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1739 SER Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1879 SER Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2012 ASN Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2028 LYS Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2092 SER Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2379 LYS Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1067 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 167 MET Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 372 THR Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 639 ILE Chi-restraints excluded: chain I residue 702 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 359 optimal weight: 0.8980 chunk 388 optimal weight: 10.0000 chunk 320 optimal weight: 3.9990 chunk 356 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 288 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN A 982 ASN A1247 ASN A1528 ASN A1880 ASN A2332 ASN A2350 GLN A2400 ASN F 385 ASN ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN D1075 ASN D1105 ASN G 58 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32833 Z= 0.219 Angle : 0.548 9.032 44400 Z= 0.293 Chirality : 0.044 0.446 4821 Planarity : 0.004 0.046 5825 Dihedral : 8.448 89.221 4708 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.50 % Allowed : 21.83 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.13), residues: 3969 helix: 1.64 (0.16), residues: 1170 sheet: 0.52 (0.15), residues: 1110 loop : -0.63 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1580 HIS 0.004 0.001 HIS I 271 PHE 0.024 0.001 PHE A1009 TYR 0.018 0.001 TYR I 294 ARG 0.005 0.000 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 412 time to evaluate : 4.181 Fit side-chains revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6516 (tm-30) REVERT: A 221 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: A 344 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.7727 (mp) REVERT: A 407 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8143 (mp) REVERT: A 554 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7439 (p0) REVERT: A 1189 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7308 (pp20) REVERT: A 1580 TRP cc_start: 0.6907 (OUTLIER) cc_final: 0.3961 (p-90) REVERT: A 1680 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: A 2053 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: B 93 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7449 (tm) REVERT: F 76 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8712 (mm) REVERT: F 171 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5744 (pm20) REVERT: F 293 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.6945 (tptp) REVERT: I 382 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: I 674 TRP cc_start: 0.7583 (m-90) cc_final: 0.6986 (m-90) outliers start: 153 outliers final: 78 residues processed: 518 average time/residue: 1.4560 time to fit residues: 907.0498 Evaluate side-chains 496 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 404 time to evaluate : 3.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1783 SER Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1890 MET Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2011 SER Chi-restraints excluded: chain A residue 2012 ASN Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2198 LYS Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2350 GLN Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2379 LYS Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1067 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 639 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 0.9980 chunk 270 optimal weight: 0.9990 chunk 186 optimal weight: 0.0870 chunk 39 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 360 optimal weight: 2.9990 chunk 381 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 341 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN A 982 ASN A1247 ASN A1528 ASN A1792 ASN A1853 GLN A2332 ASN A2400 ASN F 101 ASN F 385 ASN ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN D1075 ASN D1105 ASN G 58 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 261 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.0562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32833 Z= 0.230 Angle : 0.543 7.755 44400 Z= 0.292 Chirality : 0.044 0.368 4821 Planarity : 0.004 0.046 5825 Dihedral : 7.626 89.180 4686 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.39 % Allowed : 21.72 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.13), residues: 3969 helix: 1.64 (0.16), residues: 1177 sheet: 0.56 (0.15), residues: 1104 loop : -0.63 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1580 HIS 0.004 0.001 HIS I 271 PHE 0.024 0.002 PHE A1009 TYR 0.018 0.001 TYR I 294 ARG 0.005 0.000 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 419 time to evaluate : 4.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6506 (tm-30) REVERT: A 221 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: A 344 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.7735 (mp) REVERT: A 407 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8166 (mp) REVERT: A 554 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7498 (p0) REVERT: A 1189 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7271 (pp20) REVERT: A 1286 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: A 1580 TRP cc_start: 0.6977 (OUTLIER) cc_final: 0.3924 (p-90) REVERT: A 1680 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: A 2053 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: A 2188 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6771 (mmp) REVERT: B 93 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7396 (tm) REVERT: F 171 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.5675 (pm20) REVERT: F 293 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7002 (tptp) REVERT: D 1061 GLU cc_start: 0.7498 (tt0) cc_final: 0.7222 (tt0) REVERT: G 33 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: I 382 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: I 564 GLN cc_start: 0.7940 (tp40) cc_final: 0.7621 (tp-100) REVERT: I 674 TRP cc_start: 0.7601 (m-90) cc_final: 0.7033 (m-90) outliers start: 149 outliers final: 78 residues processed: 518 average time/residue: 1.4395 time to fit residues: 899.0094 Evaluate side-chains 501 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 407 time to evaluate : 4.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1783 SER Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1879 SER Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2011 SER Chi-restraints excluded: chain A residue 2012 ASN Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2028 LYS Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2188 MET Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1067 ILE Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 639 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 325 optimal weight: 4.9990 chunk 263 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 342 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN A 246 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 727 GLN A 982 ASN A1247 ASN A1528 ASN A1792 ASN A1795 ASN A1880 ASN A2332 ASN A2350 GLN A2400 ASN F 385 ASN ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN D1075 ASN D1105 ASN G 58 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 261 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32833 Z= 0.290 Angle : 0.573 7.742 44400 Z= 0.309 Chirality : 0.045 0.311 4821 Planarity : 0.004 0.048 5825 Dihedral : 7.382 84.734 4674 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.02 % Allowed : 21.26 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.13), residues: 3969 helix: 1.57 (0.16), residues: 1177 sheet: 0.59 (0.15), residues: 1096 loop : -0.64 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1580 HIS 0.005 0.001 HIS I 271 PHE 0.024 0.002 PHE A1009 TYR 0.020 0.002 TYR I 294 ARG 0.005 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 414 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7467 (ttm170) REVERT: A 188 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: A 221 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: A 344 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.7737 (mp) REVERT: A 407 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8171 (mp) REVERT: A 1189 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7258 (pp20) REVERT: A 1286 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: A 1580 TRP cc_start: 0.7065 (OUTLIER) cc_final: 0.4035 (p-90) REVERT: A 1680 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: A 1745 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8244 (ptp-110) REVERT: A 2053 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: A 2188 MET cc_start: 0.7074 (mmp) cc_final: 0.6787 (mmp) REVERT: B 93 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7435 (tm) REVERT: F 69 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7536 (mt-10) REVERT: F 76 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8718 (mm) REVERT: F 171 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5710 (pm20) REVERT: F 293 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7012 (tptp) REVERT: D 1061 GLU cc_start: 0.7495 (tt0) cc_final: 0.7261 (tt0) REVERT: G 33 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: I 382 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: I 564 GLN cc_start: 0.7864 (tp40) cc_final: 0.7606 (tp-100) outliers start: 170 outliers final: 93 residues processed: 529 average time/residue: 1.4606 time to fit residues: 929.0230 Evaluate side-chains 512 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 402 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1373 THR Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1745 ARG Chi-restraints excluded: chain A residue 1783 SER Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1879 SER Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2011 SER Chi-restraints excluded: chain A residue 2012 ASN Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2028 LYS Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2198 LYS Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2350 GLN Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2379 LYS Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 390 SER Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 372 THR Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 631 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 0.0980 chunk 343 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 224 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 chunk 382 optimal weight: 1.9990 chunk 317 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN A 246 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN A 752 GLN A 982 ASN A1247 ASN A1528 ASN A1792 ASN A2332 ASN A2400 ASN F 101 ASN F 385 ASN ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN D1075 ASN D1105 ASN G 58 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32833 Z= 0.183 Angle : 0.524 7.721 44400 Z= 0.283 Chirality : 0.043 0.268 4821 Planarity : 0.003 0.047 5825 Dihedral : 7.004 86.366 4672 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.99 % Allowed : 22.43 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.13), residues: 3969 helix: 1.71 (0.16), residues: 1170 sheet: 0.54 (0.15), residues: 1102 loop : -0.61 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1580 HIS 0.003 0.001 HIS I 271 PHE 0.023 0.001 PHE A1009 TYR 0.017 0.001 TYR I 294 ARG 0.006 0.000 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 413 time to evaluate : 3.682 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7482 (ttm170) REVERT: A 188 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6471 (tm-30) REVERT: A 221 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: A 246 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: A 344 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7693 (mp) REVERT: A 407 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8198 (mp) REVERT: A 554 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7428 (p0) REVERT: A 1122 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8745 (mp) REVERT: A 1189 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7217 (pp20) REVERT: A 1286 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: A 1580 TRP cc_start: 0.7005 (OUTLIER) cc_final: 0.3995 (p-90) REVERT: A 1680 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: A 1745 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8235 (ptp-110) REVERT: A 2053 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: A 2188 MET cc_start: 0.7013 (mmp) cc_final: 0.6678 (mmp) REVERT: A 2326 ASP cc_start: 0.7677 (m-30) cc_final: 0.7442 (m-30) REVERT: B 93 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7295 (tm) REVERT: F 69 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7541 (mt-10) REVERT: F 76 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8631 (mm) REVERT: F 171 GLU cc_start: 0.5896 (OUTLIER) cc_final: 0.5635 (pm20) REVERT: F 293 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7016 (tptp) REVERT: D 1061 GLU cc_start: 0.7500 (tt0) cc_final: 0.7275 (tt0) REVERT: G 33 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7151 (mm-30) REVERT: I 382 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: I 564 GLN cc_start: 0.7807 (tp40) cc_final: 0.7592 (tp-100) outliers start: 134 outliers final: 65 residues processed: 511 average time/residue: 1.4641 time to fit residues: 901.1204 Evaluate side-chains 489 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 404 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1745 ARG Chi-restraints excluded: chain A residue 1783 SER Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2011 SER Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 568 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 321 optimal weight: 0.7980 chunk 213 optimal weight: 0.0070 chunk 380 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 232 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 727 GLN A 752 GLN A1247 ASN A1528 ASN A1792 ASN A1880 ASN A2136 ASN A2332 ASN A2400 ASN F 385 ASN ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN D1075 ASN D1105 ASN G 58 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 261 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32833 Z= 0.166 Angle : 0.518 9.742 44400 Z= 0.278 Chirality : 0.043 0.239 4821 Planarity : 0.003 0.046 5825 Dihedral : 6.750 86.591 4665 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.68 % Allowed : 22.77 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.13), residues: 3969 helix: 1.74 (0.16), residues: 1175 sheet: 0.56 (0.15), residues: 1101 loop : -0.59 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1580 HIS 0.004 0.001 HIS A1672 PHE 0.023 0.001 PHE A1009 TYR 0.016 0.001 TYR I 294 ARG 0.007 0.000 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 412 time to evaluate : 3.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7492 (ttm170) REVERT: A 125 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.5954 (pp) REVERT: A 188 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6475 (tm-30) REVERT: A 221 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: A 344 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.7684 (mp) REVERT: A 407 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8233 (mp) REVERT: A 554 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7444 (p0) REVERT: A 1189 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7230 (pp20) REVERT: A 1286 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: A 1580 TRP cc_start: 0.6947 (OUTLIER) cc_final: 0.3923 (p-90) REVERT: A 1680 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.6959 (tm-30) REVERT: A 1745 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8249 (ptp-110) REVERT: A 2053 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: A 2188 MET cc_start: 0.6976 (mmp) cc_final: 0.6667 (mmp) REVERT: A 2326 ASP cc_start: 0.7663 (m-30) cc_final: 0.7416 (m-30) REVERT: B 93 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7218 (tm) REVERT: F 69 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7477 (mt-10) REVERT: F 171 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.5566 (pm20) REVERT: F 293 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7023 (tptp) REVERT: D 1061 GLU cc_start: 0.7514 (tt0) cc_final: 0.7210 (tt0) REVERT: G 33 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7147 (mm-30) REVERT: I 382 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: I 564 GLN cc_start: 0.7735 (tp40) cc_final: 0.7527 (tp-100) outliers start: 123 outliers final: 66 residues processed: 499 average time/residue: 1.4705 time to fit residues: 886.2880 Evaluate side-chains 489 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 405 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1745 ARG Chi-restraints excluded: chain A residue 1783 SER Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 363 THR Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain I residue 568 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 259 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 196 GLN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN A 576 GLN A 613 GLN A 727 GLN A 752 GLN A 982 ASN A1247 ASN A1792 ASN A2136 ASN A2332 ASN A2350 GLN A2400 ASN F 101 ASN F 385 ASN ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN D1075 ASN D1105 ASN G 58 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 261 ASN I 679 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 32833 Z= 0.410 Angle : 0.639 9.662 44400 Z= 0.345 Chirality : 0.048 0.218 4821 Planarity : 0.004 0.053 5825 Dihedral : 7.125 76.696 4659 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.71 % Rotamer: Outliers : 3.88 % Allowed : 22.49 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.13), residues: 3969 helix: 1.48 (0.15), residues: 1182 sheet: 0.59 (0.15), residues: 1106 loop : -0.69 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1580 HIS 0.007 0.002 HIS I 271 PHE 0.025 0.002 PHE A1009 TYR 0.023 0.002 TYR A1303 ARG 0.007 0.001 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 402 time to evaluate : 4.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: A 95 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7467 (ttm170) REVERT: A 188 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6509 (tm-30) REVERT: A 190 ASN cc_start: 0.8363 (m110) cc_final: 0.8076 (m-40) REVERT: A 221 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: A 344 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.7791 (mp) REVERT: A 407 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8075 (mp) REVERT: A 1189 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7313 (pp20) REVERT: A 1580 TRP cc_start: 0.7173 (OUTLIER) cc_final: 0.4229 (p-90) REVERT: A 1680 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: A 1745 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8284 (ptp-110) REVERT: A 2053 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: A 2273 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8356 (ttm170) REVERT: A 2326 ASP cc_start: 0.7660 (m-30) cc_final: 0.7420 (m-30) REVERT: B 93 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7289 (tm) REVERT: F 171 GLU cc_start: 0.6047 (OUTLIER) cc_final: 0.5818 (pm20) REVERT: F 293 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7026 (tptp) REVERT: D 1061 GLU cc_start: 0.7540 (tt0) cc_final: 0.7320 (tt0) REVERT: I 382 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: I 564 GLN cc_start: 0.7812 (tp40) cc_final: 0.7569 (tp-100) outliers start: 130 outliers final: 74 residues processed: 492 average time/residue: 1.5049 time to fit residues: 892.3004 Evaluate side-chains 482 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 392 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1528 ASN Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1745 ARG Chi-restraints excluded: chain A residue 1783 SER Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1879 SER Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2011 SER Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2028 LYS Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2350 GLN Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 390 SER Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 639 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.5980 chunk 364 optimal weight: 0.7980 chunk 332 optimal weight: 0.9980 chunk 354 optimal weight: 0.5980 chunk 213 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 278 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 320 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 chunk 353 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 246 GLN A 374 ASN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 727 GLN A 752 GLN A 982 ASN A1222 GLN A1247 ASN A1528 ASN A1565 ASN A1792 ASN A1880 ASN A2020 ASN A2136 ASN A2332 ASN A2400 ASN F 101 ASN F 385 ASN ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN D1075 ASN D1105 ASN G 58 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 679 GLN I 733 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32833 Z= 0.168 Angle : 0.531 8.933 44400 Z= 0.286 Chirality : 0.043 0.217 4821 Planarity : 0.003 0.046 5825 Dihedral : 6.662 80.441 4659 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.02 % Allowed : 23.60 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.13), residues: 3969 helix: 1.69 (0.16), residues: 1169 sheet: 0.55 (0.15), residues: 1101 loop : -0.62 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1580 HIS 0.003 0.001 HIS A1672 PHE 0.023 0.001 PHE A1009 TYR 0.015 0.001 TYR A2159 ARG 0.008 0.000 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 411 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: A 95 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7485 (ttm170) REVERT: A 125 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.5819 (pp) REVERT: A 188 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.6750 (tm-30) REVERT: A 221 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: A 246 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: A 344 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7666 (mp) REVERT: A 407 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8223 (mp) REVERT: A 554 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7425 (p0) REVERT: A 1189 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7177 (pp20) REVERT: A 1529 MET cc_start: 0.8042 (ttt) cc_final: 0.7755 (ttt) REVERT: A 1580 TRP cc_start: 0.7013 (OUTLIER) cc_final: 0.4022 (p-90) REVERT: A 1680 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: A 1745 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8203 (ptp-110) REVERT: A 2053 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: A 2326 ASP cc_start: 0.7668 (m-30) cc_final: 0.7410 (m-30) REVERT: B 93 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7265 (tm) REVERT: F 76 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8623 (mm) REVERT: F 171 GLU cc_start: 0.5889 (OUTLIER) cc_final: 0.5648 (pm20) REVERT: D 1061 GLU cc_start: 0.7537 (tt0) cc_final: 0.7234 (tt0) REVERT: G 33 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7149 (mm-30) REVERT: E 115 MET cc_start: 0.8153 (mmt) cc_final: 0.7898 (mmt) REVERT: I 382 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7653 (tt0) outliers start: 100 outliers final: 59 residues processed: 481 average time/residue: 1.4783 time to fit residues: 853.0115 Evaluate side-chains 477 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 399 time to evaluate : 3.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1745 ARG Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2011 SER Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 631 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 232 optimal weight: 5.9990 chunk 375 optimal weight: 6.9990 chunk 228 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 260 optimal weight: 0.2980 chunk 393 optimal weight: 0.2980 chunk 362 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 242 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN A 246 GLN A 374 ASN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 613 GLN A 727 GLN A1247 ASN A1528 ASN A1792 ASN A2020 ASN A2136 ASN A2400 ASN B 90 HIS F 101 ASN F 385 ASN ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN D1075 ASN D1105 ASN G 58 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 261 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32833 Z= 0.192 Angle : 0.540 13.332 44400 Z= 0.291 Chirality : 0.043 0.214 4821 Planarity : 0.003 0.046 5825 Dihedral : 6.568 79.538 4659 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.82 % Allowed : 23.85 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.13), residues: 3969 helix: 1.70 (0.16), residues: 1170 sheet: 0.54 (0.15), residues: 1102 loop : -0.59 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1580 HIS 0.004 0.001 HIS I 271 PHE 0.023 0.001 PHE A1009 TYR 0.017 0.001 TYR I 294 ARG 0.008 0.000 ARG E 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 402 time to evaluate : 3.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: A 95 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7483 (ttm170) REVERT: A 125 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.5792 (pp) REVERT: A 188 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6678 (tm-30) REVERT: A 221 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: A 344 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.7702 (mp) REVERT: A 407 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8236 (mp) REVERT: A 554 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7423 (p0) REVERT: A 1189 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7202 (pp20) REVERT: A 1529 MET cc_start: 0.8033 (ttt) cc_final: 0.7774 (ttt) REVERT: A 1580 TRP cc_start: 0.7005 (OUTLIER) cc_final: 0.4018 (p-90) REVERT: A 1680 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: A 1745 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8219 (ptp-110) REVERT: A 2053 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: A 2326 ASP cc_start: 0.7657 (m-30) cc_final: 0.7396 (m-30) REVERT: B 93 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7255 (tm) REVERT: F 76 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8631 (mm) REVERT: F 171 GLU cc_start: 0.5861 (OUTLIER) cc_final: 0.5621 (pm20) REVERT: D 1061 GLU cc_start: 0.7507 (tt0) cc_final: 0.7205 (tt0) REVERT: I 382 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7666 (tt0) outliers start: 93 outliers final: 62 residues processed: 468 average time/residue: 1.4792 time to fit residues: 833.2470 Evaluate side-chains 477 residues out of total 3475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 398 time to evaluate : 3.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1745 ARG Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2011 SER Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 631 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 4.9990 chunk 333 optimal weight: 0.1980 chunk 95 optimal weight: 7.9990 chunk 288 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 322 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN A 246 GLN A 374 ASN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 727 GLN A1247 ASN A1528 ASN A1792 ASN A1880 ASN A2020 ASN A2136 ASN A2400 ASN F 385 ASN ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN D1075 ASN D1105 ASN G 58 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.154582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117514 restraints weight = 58213.336| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.43 r_work: 0.3364 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 32833 Z= 0.295 Angle : 0.585 9.349 44400 Z= 0.315 Chirality : 0.045 0.208 4821 Planarity : 0.004 0.048 5825 Dihedral : 6.688 76.906 4659 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.96 % Allowed : 23.68 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.13), residues: 3969 helix: 1.57 (0.16), residues: 1177 sheet: 0.61 (0.16), residues: 1097 loop : -0.63 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1580 HIS 0.006 0.001 HIS I 271 PHE 0.024 0.002 PHE A1009 TYR 0.020 0.002 TYR I 294 ARG 0.008 0.000 ARG E 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23820.39 seconds wall clock time: 419 minutes 3.21 seconds (25143.21 seconds total)