Starting phenix.real_space_refine on Mon Mar 18 03:43:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txo_41695/03_2024/8txo_41695_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txo_41695/03_2024/8txo_41695.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txo_41695/03_2024/8txo_41695_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txo_41695/03_2024/8txo_41695_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txo_41695/03_2024/8txo_41695_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txo_41695/03_2024/8txo_41695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txo_41695/03_2024/8txo_41695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txo_41695/03_2024/8txo_41695_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txo_41695/03_2024/8txo_41695_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 38 5.49 5 Mg 1 5.21 5 S 89 5.16 5 C 12308 2.51 5 N 3562 2.21 5 O 3794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 565": "OE1" <-> "OE2" Residue "I ASP 654": "OD1" <-> "OD2" Residue "I GLU 778": "OE1" <-> "OE2" Residue "I ASP 790": "OD1" <-> "OD2" Residue "I ASP 814": "OD1" <-> "OD2" Residue "I TYR 1231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1240": "OD1" <-> "OD2" Residue "I PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 375": "OE1" <-> "OE2" Residue "J ASP 460": "OD1" <-> "OD2" Residue "J ASP 462": "OD1" <-> "OD2" Residue "J TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 785": "OD1" <-> "OD2" Residue "J ASP 1208": "OD1" <-> "OD2" Residue "J GLU 1334": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19794 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1466 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1458 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 93 Conformer: "B" Number of residues, atoms: 206, 1458 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 93 bond proxies already assigned to first conformer: 1464 Chain: "G" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1654 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "I" Number of atoms: 7491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7491 Classifications: {'peptide': 1024} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 44, 'TRANS': 979} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 536 Unresolved non-hydrogen angles: 664 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'GLU%COO:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 21, 'PHE:plan': 1, 'GLU:plan': 30, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 312 Chain: "J" Number of atoms: 8387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1163, 8387 Classifications: {'peptide': 1163} Incomplete info: {'truncation_to_alanine': 188} Link IDs: {'PTRANS': 50, 'TRANS': 1112} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 694 Unresolved non-hydrogen angles: 859 Unresolved non-hydrogen dihedrals: 551 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 22, 'PHE:plan': 2, 'GLU:plan': 36, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 413 Chain: "N" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'DNA': 9} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 8} Chain breaks: 1 Chain: "R" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Classifications: {'RNA': 9} Modifications used: {'5*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 383 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 1, ' ZN': 2, 'S9F': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11049 SG CYS J 70 18.181 101.471 42.203 1.00 89.41 S ATOM 11063 SG CYS J 72 18.410 104.196 38.961 1.00 90.08 S ATOM 11171 SG CYS J 85 17.326 101.441 38.568 1.00 83.33 S ATOM 15940 SG CYS J 814 44.834 38.649 45.054 1.00 34.20 S ATOM 16405 SG CYS J 888 47.112 41.209 46.115 1.00 26.10 S ATOM 16450 SG CYS J 895 44.573 39.457 48.685 1.00 26.74 S ATOM 16471 SG CYS J 898 47.581 37.842 47.918 1.00 25.33 S Time building chain proxies: 11.22, per 1000 atoms: 0.57 Number of scatterers: 19794 At special positions: 0 Unit cell: (119.52, 147.74, 141.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 89 16.00 P 38 15.00 Mg 1 11.99 O 3794 8.00 N 3562 7.00 C 12308 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.92 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " Number of angles added : 6 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4812 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 30 sheets defined 33.7% alpha, 13.6% beta 15 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 8.61 Creating SS restraints... Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.862A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 155 through 158 No H-bonds generated for 'chain 'A' and resid 155 through 158' Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'G' and resid 35 through 50 Processing helix chain 'G' and resid 78 through 86 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 213 through 232 removed outlier: 4.390A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 29 through 39 Processing helix chain 'I' and resid 48 through 56 removed outlier: 3.852A pdb=" N SER I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL I 56 " --> pdb=" O ALA I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 424 through 433 removed outlier: 3.530A pdb=" N VAL I 428 " --> pdb=" O ASP I 424 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET I 429 " --> pdb=" O ILE I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 448 through 450 No H-bonds generated for 'chain 'I' and resid 448 through 450' Processing helix chain 'I' and resid 456 through 479 Processing helix chain 'I' and resid 489 through 492 No H-bonds generated for 'chain 'I' and resid 489 through 492' Processing helix chain 'I' and resid 496 through 508 removed outlier: 3.955A pdb=" N GLY I 507 " --> pdb=" O LYS I 503 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 545 through 548 No H-bonds generated for 'chain 'I' and resid 545 through 548' Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 608 through 613 removed outlier: 4.068A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 663 through 667 Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 685 Processing helix chain 'I' and resid 705 through 712 Processing helix chain 'I' and resid 738 through 740 No H-bonds generated for 'chain 'I' and resid 738 through 740' Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 844 through 846 No H-bonds generated for 'chain 'I' and resid 844 through 846' Processing helix chain 'I' and resid 859 through 864 Processing helix chain 'I' and resid 943 through 976 removed outlier: 3.545A pdb=" N LEU I 967 " --> pdb=" O GLU I 963 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY I 970 " --> pdb=" O ILE I 966 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU I 971 " --> pdb=" O LEU I 967 " (cutoff:3.500A) Processing helix chain 'I' and resid 1018 through 1037 Processing helix chain 'I' and resid 1100 through 1105 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1138 through 1150 Processing helix chain 'I' and resid 1166 through 1175 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1242 No H-bonds generated for 'chain 'I' and resid 1239 through 1242' Processing helix chain 'I' and resid 1272 through 1281 Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1298 through 1310 removed outlier: 3.574A pdb=" N LYS I1306 " --> pdb=" O THR I1302 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1333 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 59 through 62 No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 114 through 118 Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 132 through 141 Processing helix chain 'J' and resid 182 through 191 Processing helix chain 'J' and resid 194 through 206 Processing helix chain 'J' and resid 211 through 230 Processing helix chain 'J' and resid 247 through 249 No H-bonds generated for 'chain 'J' and resid 247 through 249' Processing helix chain 'J' and resid 264 through 284 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 328 through 330 No H-bonds generated for 'chain 'J' and resid 328 through 330' Processing helix chain 'J' and resid 337 through 341 Processing helix chain 'J' and resid 370 through 376 removed outlier: 3.844A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 382 Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 451 through 454 Processing helix chain 'J' and resid 474 through 483 Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 530 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.931A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 591 No H-bonds generated for 'chain 'J' and resid 589 through 591' Processing helix chain 'J' and resid 598 through 611 Processing helix chain 'J' and resid 614 through 635 Processing helix chain 'J' and resid 641 through 643 No H-bonds generated for 'chain 'J' and resid 641 through 643' Processing helix chain 'J' and resid 650 through 664 removed outlier: 4.126A pdb=" N SER J 655 " --> pdb=" O HIS J 651 " (cutoff:3.500A) Processing helix chain 'J' and resid 675 through 702 Processing helix chain 'J' and resid 721 through 728 Processing helix chain 'J' and resid 734 through 741 Processing helix chain 'J' and resid 769 through 787 removed outlier: 3.845A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR J 786 " --> pdb=" O GLY J 782 " (cutoff:3.500A) Processing helix chain 'J' and resid 790 through 804 Processing helix chain 'J' and resid 835 through 839 Processing helix chain 'J' and resid 866 through 874 Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 915 through 937 Proline residue: J 926 - end of helix removed outlier: 5.191A pdb=" N PHE J 935 " --> pdb=" O THR J 931 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS J 936 " --> pdb=" O MET J 932 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE J 937 " --> pdb=" O ARG J 933 " (cutoff:3.500A) Processing helix chain 'J' and resid 1138 through 1145 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1226 through 1243 removed outlier: 3.677A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1309 through 1314 Processing helix chain 'J' and resid 1319 through 1325 Processing helix chain 'J' and resid 1328 through 1338 Processing helix chain 'J' and resid 1347 through 1352 Processing helix chain 'J' and resid 1360 through 1371 removed outlier: 3.955A pdb=" N ALA J1364 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 23 through 28 removed outlier: 3.754A pdb=" N MET A 205 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL A 26 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'A' and resid 97 through 103 removed outlier: 6.382A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 109 through 111 removed outlier: 3.513A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 13 through 18 removed outlier: 6.917A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 170 through 172 removed outlier: 6.693A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.518A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= I, first strand: chain 'I' and resid 136 through 138 Processing sheet with id= J, first strand: chain 'I' and resid 148 through 151 Processing sheet with id= K, first strand: chain 'I' and resid 529 through 531 Processing sheet with id= L, first strand: chain 'I' and resid 603 through 607 Processing sheet with id= M, first strand: chain 'I' and resid 633 through 638 Processing sheet with id= N, first strand: chain 'I' and resid 748 through 752 removed outlier: 5.682A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 1227 through 1232 removed outlier: 6.734A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 1065 through 1067 Processing sheet with id= Q, first strand: chain 'I' and resid 68 through 75 removed outlier: 7.427A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 755 through 758 removed outlier: 6.059A pdb=" N ILE I 765 " --> pdb=" O TYR I 756 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.742A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.703A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 350 through 354 removed outlier: 3.554A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 355 through 357 removed outlier: 5.910A pdb=" N ILE J 447 " --> pdb=" O THR J 356 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'J' and resid 365 through 369 removed outlier: 6.329A pdb=" N GLU J 438 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU J 368 " --> pdb=" O GLU J 438 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL J 440 " --> pdb=" O LEU J 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'J' and resid 547 through 557 Processing sheet with id= Y, first strand: chain 'J' and resid 706 through 708 Processing sheet with id= Z, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.678A pdb=" N LYS J 983 " --> pdb=" O LYS J 959 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AB, first strand: chain 'J' and resid 1161 through 1163 Processing sheet with id= AC, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.354A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.626A pdb=" N ILE J 950 " --> pdb=" O ALA J1018 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD 690 hydrogen bonds defined for protein. 1997 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for ZD residue Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 9.00 Time building geometry restraints manager: 8.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3290 1.29 - 1.42: 4875 1.42 - 1.55: 11768 1.55 - 1.69: 78 1.69 - 1.82: 151 Bond restraints: 20162 Sorted by residual: bond pdb=" C4' DZ T 19 " pdb=" O4' DZ T 19 " ideal model delta sigma weight residual 1.680 1.271 0.409 2.00e-02 2.50e+03 4.18e+02 bond pdb=" C1' DZ T 19 " pdb=" O4' DZ T 19 " ideal model delta sigma weight residual 1.304 1.671 -0.367 2.00e-02 2.50e+03 3.37e+02 bond pdb=" C1' DZ T 19 " pdb=" C2' DZ T 19 " ideal model delta sigma weight residual 1.620 1.332 0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C15 S9F J1504 " pdb=" O31 S9F J1504 " ideal model delta sigma weight residual 1.593 1.307 0.286 2.00e-02 2.50e+03 2.05e+02 bond pdb=" C3' DZ T 19 " pdb=" C4' DZ T 19 " ideal model delta sigma weight residual 1.343 1.619 -0.276 2.00e-02 2.50e+03 1.91e+02 ... (remaining 20157 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.15: 688 106.15 - 113.12: 11142 113.12 - 120.08: 6616 120.08 - 127.05: 8845 127.05 - 134.01: 240 Bond angle restraints: 27531 Sorted by residual: angle pdb=" N GLY J1225 " pdb=" CA GLY J1225 " pdb=" C GLY J1225 " ideal model delta sigma weight residual 110.96 115.75 -4.79 1.19e+00 7.06e-01 1.62e+01 angle pdb=" N ILE I 850 " pdb=" CA ILE I 850 " pdb=" C ILE I 850 " ideal model delta sigma weight residual 113.20 109.67 3.53 9.60e-01 1.09e+00 1.35e+01 angle pdb=" N GLU J1152 " pdb=" CA GLU J1152 " pdb=" C GLU J1152 " ideal model delta sigma weight residual 109.81 117.12 -7.31 2.21e+00 2.05e-01 1.09e+01 angle pdb=" CA PHE J 461 " pdb=" C PHE J 461 " pdb=" N ASP J 462 " ideal model delta sigma weight residual 115.89 111.90 3.99 1.40e+00 5.10e-01 8.12e+00 angle pdb=" CA GLU J 235 " pdb=" CB GLU J 235 " pdb=" CG GLU J 235 " ideal model delta sigma weight residual 114.10 119.59 -5.49 2.00e+00 2.50e-01 7.54e+00 ... (remaining 27526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.72: 11484 24.72 - 49.43: 535 49.43 - 74.15: 94 74.15 - 98.87: 14 98.87 - 123.58: 1 Dihedral angle restraints: 12128 sinusoidal: 4650 harmonic: 7478 Sorted by residual: dihedral pdb=" CA ASP J 462 " pdb=" C ASP J 462 " pdb=" N GLY J 463 " pdb=" CA GLY J 463 " ideal model delta harmonic sigma weight residual 180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA PHE J 461 " pdb=" C PHE J 461 " pdb=" N ASP J 462 " pdb=" CA ASP J 462 " ideal model delta harmonic sigma weight residual -180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA SER G 49 " pdb=" C SER G 49 " pdb=" N SER G 50 " pdb=" CA SER G 50 " ideal model delta harmonic sigma weight residual -180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 12125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2513 0.043 - 0.086: 507 0.086 - 0.128: 219 0.128 - 0.171: 9 0.171 - 0.214: 1 Chirality restraints: 3249 Sorted by residual: chirality pdb=" CB ILE J 44 " pdb=" CA ILE J 44 " pdb=" CG1 ILE J 44 " pdb=" CG2 ILE J 44 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' DZ T 19 " pdb=" C2' DZ T 19 " pdb=" C4' DZ T 19 " pdb=" O3' DZ T 19 " both_signs ideal model delta sigma weight residual False -2.43 -2.58 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" C16 S9F J1504 " pdb=" C15 S9F J1504 " pdb=" C17 S9F J1504 " pdb=" O32 S9F J1504 " both_signs ideal model delta sigma weight residual False 2.50 2.65 -0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 3246 not shown) Planarity restraints: 3473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 253 " -0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO J 254 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO J 254 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO J 254 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG J 250 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO J 251 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO J 251 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO J 251 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 997 " -0.038 5.00e-02 4.00e+02 5.88e-02 5.52e+00 pdb=" N PRO J 998 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO J 998 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 998 " -0.032 5.00e-02 4.00e+02 ... (remaining 3470 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 42 2.39 - 3.01: 10691 3.01 - 3.64: 30203 3.64 - 4.27: 45587 4.27 - 4.90: 75797 Nonbonded interactions: 162320 Sorted by model distance: nonbonded pdb=" CG ASP J 462 " pdb="MG MG J1503 " model vdw 1.758 2.400 nonbonded pdb=" CB ASP J 462 " pdb="MG MG J1503 " model vdw 1.793 2.570 nonbonded pdb=" O PHE J 773 " pdb=" OG1 THR J 776 " model vdw 2.159 2.440 nonbonded pdb=" O GLY J 613 " pdb=" OG1 THR J 617 " model vdw 2.174 2.440 nonbonded pdb=" NH2 ARG I 528 " pdb=" O SER I 576 " model vdw 2.197 2.520 ... (remaining 162315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 147 or resid 149 through 157 or (r \ esid 158 through 159 and (name N or name CA or name C or name O or name CB )) or \ resid 169 through 187 or (resid 188 through 194 and (name N or name CA or name \ C or name O or name CB )) or resid 195 or (resid 196 through 197 and (name N or \ name CA or name C or name O or name CB )) or resid 198 through 233)) selection = (chain 'G' and (resid 19 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 or (resid 62 and (name N or name CA or nam \ e C or name O or name CB )) or resid 63 or (resid 64 through 68 and (name N or n \ ame CA or name C or name O or name CB )) or resid 69 or (resid 70 through 72 and \ (name N or name CA or name C or name O or name CB )) or resid 73 through 75 or \ (resid 76 through 77 and (name N or name CA or name C or name O or name CB )) or \ resid 78 through 79 or (resid 80 and (name N or name CA or name C or name O or \ name CB )) or resid 81 through 92 or (resid 93 and (name N or name CA or name C \ or name O or name CB )) or (resid 94 through 97 and (name N or name CA or name C \ or name O or name CB )) or resid 98 through 106 or (resid 107 and (name N or na \ me CA or name C or name O or name CB )) or resid 108 through 117 or (resid 118 a \ nd (name N or name CA or name C or name O or name CB )) or resid 119 or (resid 1 \ 20 and (name N or name CA or name C or name O or name CB )) or resid 121 or (res \ id 122 and (name N or name CA or name C or name O or name CB )) or resid 123 thr \ ough 126 or (resid 127 and (name N or name CA or name C or name O or name CB )) \ or resid 128 through 133 or (resid 134 through 135 and (name N or name CA or nam \ e C or name O or name CB )) or resid 136 or (resid 137 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 147 or resid 14 \ 9 through 158 or (resid 168 and (name N or name CA or name C or name O or name C \ B )) or resid 169 or (resid 170 and (name N or name CA or name C or name O or na \ me CB )) or resid 171 or (resid 172 and (name N or name CA or name C or name O o \ r name CB )) or resid 173 through 233)) } 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=0.23 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.370 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 61.650 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 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 : 0.007 0.409 20162 Z= 0.462 Angle : 0.504 7.310 27531 Z= 0.279 Chirality : 0.041 0.214 3249 Planarity : 0.004 0.080 3473 Dihedral : 14.418 123.584 7316 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.16), residues: 2581 helix: 1.41 (0.17), residues: 919 sheet: 0.60 (0.30), residues: 325 loop : -0.25 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 580 HIS 0.005 0.001 HIS J 430 PHE 0.016 0.001 PHE J 461 TYR 0.029 0.001 TYR J 723 ARG 0.009 0.000 ARG J 297 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 18 GLN cc_start: 0.7408 (mm-40) cc_final: 0.7193 (mm-40) REVERT: I 934 PHE cc_start: 0.6480 (m-80) cc_final: 0.6220 (m-80) REVERT: J 653 ILE cc_start: 0.4605 (mt) cc_final: 0.4102 (mt) REVERT: J 1370 MET cc_start: 0.4814 (mmp) cc_final: 0.4486 (ttp) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.3286 time to fit residues: 216.3790 Evaluate side-chains 257 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 0.8980 chunk 197 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 chunk 204 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 152 optimal weight: 0.2980 chunk 237 optimal weight: 7.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 41 GLN I 86 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 673 HIS I1244 HIS ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 817 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 20162 Z= 0.357 Angle : 0.634 7.855 27531 Z= 0.336 Chirality : 0.046 0.242 3249 Planarity : 0.006 0.060 3473 Dihedral : 11.484 119.064 3246 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.51 % Allowed : 9.45 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 2581 helix: 1.32 (0.17), residues: 886 sheet: 0.30 (0.29), residues: 336 loop : -0.38 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 807 HIS 0.012 0.001 HIS I 554 PHE 0.021 0.002 PHE J 461 TYR 0.022 0.002 TYR G 185 ARG 0.012 0.001 ARG I 637 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 282 time to evaluate : 3.419 Fit side-chains REVERT: A 229 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6501 (mm-30) REVERT: G 18 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7332 (mm-40) REVERT: I 808 ASN cc_start: 0.7955 (t0) cc_final: 0.7626 (t0) REVERT: J 1334 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: J 1370 MET cc_start: 0.5672 (mmp) cc_final: 0.4781 (ttm) outliers start: 46 outliers final: 31 residues processed: 314 average time/residue: 0.3188 time to fit residues: 154.1262 Evaluate side-chains 263 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 675 ASP Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1337 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 131 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 256 optimal weight: 0.7980 chunk 211 optimal weight: 0.0050 chunk 235 optimal weight: 0.0050 chunk 80 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.7610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS I 834 GLN J 276 ASN J 489 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20162 Z= 0.158 Angle : 0.492 7.934 27531 Z= 0.257 Chirality : 0.042 0.172 3249 Planarity : 0.004 0.058 3473 Dihedral : 11.105 116.848 3246 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.86 % Allowed : 12.12 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.16), residues: 2581 helix: 1.65 (0.18), residues: 891 sheet: 0.42 (0.29), residues: 331 loop : -0.24 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 115 HIS 0.005 0.001 HIS J 104 PHE 0.018 0.001 PHE J 461 TYR 0.018 0.001 TYR G 185 ARG 0.007 0.000 ARG J1330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 245 time to evaluate : 2.276 Fit side-chains REVERT: A 229 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6565 (mm-30) REVERT: I 488 MET cc_start: 0.2458 (pmm) cc_final: -0.0704 (tpt) REVERT: I 808 ASN cc_start: 0.7857 (t0) cc_final: 0.7564 (t0) REVERT: J 747 MET cc_start: 0.6162 (mmt) cc_final: 0.5776 (mmt) REVERT: J 1370 MET cc_start: 0.5760 (mmp) cc_final: 0.4783 (ttm) outliers start: 34 outliers final: 23 residues processed: 274 average time/residue: 0.3164 time to fit residues: 135.2517 Evaluate side-chains 248 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 225 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 675 ASP Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1337 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 20.0000 chunk 178 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 159 optimal weight: 30.0000 chunk 238 optimal weight: 5.9990 chunk 252 optimal weight: 30.0000 chunk 124 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 132 HIS I 677 ASN ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 20162 Z= 0.497 Angle : 0.672 15.010 27531 Z= 0.352 Chirality : 0.049 0.207 3249 Planarity : 0.006 0.070 3473 Dihedral : 11.567 112.075 3246 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.22 % Allowed : 13.82 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2581 helix: 0.88 (0.17), residues: 885 sheet: 0.03 (0.27), residues: 321 loop : -0.67 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 686 HIS 0.012 0.002 HIS I 551 PHE 0.019 0.002 PHE J 35 TYR 0.017 0.002 TYR G 185 ARG 0.005 0.001 ARG I 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 244 time to evaluate : 2.302 Fit side-chains revert: symmetry clash REVERT: I 145 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7585 (mp) REVERT: I 488 MET cc_start: 0.2772 (pmm) cc_final: 0.0162 (tpt) REVERT: I 808 ASN cc_start: 0.7994 (t0) cc_final: 0.7755 (t0) REVERT: I 1319 MET cc_start: 0.6602 (tpp) cc_final: 0.6176 (tpp) REVERT: J 1334 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6561 (mp0) REVERT: J 1370 MET cc_start: 0.5996 (mmp) cc_final: 0.5067 (ttt) outliers start: 59 outliers final: 45 residues processed: 292 average time/residue: 0.3123 time to fit residues: 143.0777 Evaluate side-chains 258 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 211 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 675 ASP Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 297 ARG Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain J residue 1351 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 210 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 0.1980 chunk 215 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 chunk 226 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN A 132 HIS ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 979 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 20162 Z= 0.159 Angle : 0.503 13.306 27531 Z= 0.260 Chirality : 0.042 0.144 3249 Planarity : 0.004 0.060 3473 Dihedral : 11.164 103.947 3246 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.08 % Allowed : 16.33 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.16), residues: 2581 helix: 1.39 (0.17), residues: 902 sheet: 0.22 (0.28), residues: 324 loop : -0.54 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 33 HIS 0.006 0.001 HIS J 104 PHE 0.018 0.001 PHE J 461 TYR 0.015 0.001 TYR G 185 ARG 0.004 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 233 time to evaluate : 2.192 Fit side-chains revert: symmetry clash REVERT: I 1131 MET cc_start: 0.7486 (mtm) cc_final: 0.7187 (ttm) REVERT: J 374 LEU cc_start: 0.7874 (tp) cc_final: 0.7556 (mm) REVERT: J 1334 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: J 1370 MET cc_start: 0.5869 (mmp) cc_final: 0.5021 (ttt) outliers start: 38 outliers final: 25 residues processed: 261 average time/residue: 0.3072 time to fit residues: 125.8567 Evaluate side-chains 242 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 216 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 675 ASP Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1337 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 252 optimal weight: 50.0000 chunk 209 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 618 GLN I 808 ASN ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20162 Z= 0.223 Angle : 0.516 13.862 27531 Z= 0.266 Chirality : 0.042 0.143 3249 Planarity : 0.004 0.061 3473 Dihedral : 11.172 95.867 3246 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.89 % Allowed : 16.71 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2581 helix: 1.44 (0.17), residues: 897 sheet: 0.11 (0.27), residues: 350 loop : -0.54 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 686 HIS 0.006 0.001 HIS J 104 PHE 0.017 0.001 PHE G 231 TYR 0.013 0.001 TYR G 185 ARG 0.004 0.000 ARG I1246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 228 time to evaluate : 2.399 Fit side-chains revert: symmetry clash REVERT: I 488 MET cc_start: 0.3219 (pmm) cc_final: 0.0744 (tpt) REVERT: J 1334 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6326 (mp0) REVERT: J 1370 MET cc_start: 0.5869 (mmp) cc_final: 0.5011 (ttt) outliers start: 53 outliers final: 41 residues processed: 269 average time/residue: 0.2900 time to fit residues: 122.8012 Evaluate side-chains 261 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 219 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 128 HIS Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 675 ASP Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain J residue 1351 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 251 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 153 optimal weight: 0.2980 chunk 116 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN J 276 ASN J 777 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20162 Z= 0.209 Angle : 0.510 13.757 27531 Z= 0.262 Chirality : 0.042 0.149 3249 Planarity : 0.004 0.061 3473 Dihedral : 11.152 77.946 3246 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.17 % Allowed : 17.37 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 2581 helix: 1.47 (0.18), residues: 902 sheet: 0.12 (0.28), residues: 334 loop : -0.54 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 686 HIS 0.005 0.001 HIS J 104 PHE 0.018 0.001 PHE G 231 TYR 0.013 0.001 TYR G 185 ARG 0.006 0.000 ARG I 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 225 time to evaluate : 2.225 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6841 (mp) REVERT: I 488 MET cc_start: 0.3536 (pmm) cc_final: 0.1186 (tpt) REVERT: J 932 MET cc_start: 0.8190 (mmt) cc_final: 0.7455 (mmt) REVERT: J 1334 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6244 (mp0) REVERT: J 1370 MET cc_start: 0.5770 (mmp) cc_final: 0.5035 (ttt) outliers start: 58 outliers final: 46 residues processed: 270 average time/residue: 0.2924 time to fit residues: 125.1861 Evaluate side-chains 263 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 215 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 128 HIS Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 675 ASP Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain J residue 1351 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 48 optimal weight: 30.0000 chunk 159 optimal weight: 50.0000 chunk 171 optimal weight: 0.0770 chunk 124 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** I 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20162 Z= 0.282 Angle : 0.553 15.446 27531 Z= 0.285 Chirality : 0.043 0.146 3249 Planarity : 0.005 0.060 3473 Dihedral : 11.308 75.593 3246 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.11 % Allowed : 17.64 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2581 helix: 1.32 (0.17), residues: 895 sheet: -0.05 (0.28), residues: 326 loop : -0.65 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 686 HIS 0.005 0.001 HIS I 551 PHE 0.015 0.002 PHE J 461 TYR 0.014 0.001 TYR J 723 ARG 0.006 0.000 ARG I 465 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 213 time to evaluate : 2.275 Fit side-chains revert: symmetry clash REVERT: I 145 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7476 (mp) REVERT: I 488 MET cc_start: 0.3786 (pmm) cc_final: 0.1721 (tpt) REVERT: J 1370 MET cc_start: 0.5943 (mmp) cc_final: 0.5224 (ttt) outliers start: 57 outliers final: 47 residues processed: 256 average time/residue: 0.3208 time to fit residues: 129.3924 Evaluate side-chains 255 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 207 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 128 HIS Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 675 ASP Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain J residue 1351 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 228 optimal weight: 4.9990 chunk 241 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 234 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 211 optimal weight: 0.9980 chunk 221 optimal weight: 0.6980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20162 Z= 0.186 Angle : 0.504 14.170 27531 Z= 0.258 Chirality : 0.041 0.143 3249 Planarity : 0.004 0.059 3473 Dihedral : 11.098 72.952 3246 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.68 % Allowed : 18.13 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2581 helix: 1.49 (0.18), residues: 904 sheet: 0.16 (0.28), residues: 337 loop : -0.59 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 686 HIS 0.005 0.001 HIS J 104 PHE 0.014 0.001 PHE G 231 TYR 0.011 0.001 TYR J 631 ARG 0.007 0.000 ARG I 465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 217 time to evaluate : 2.579 Fit side-chains revert: symmetry clash REVERT: I 488 MET cc_start: 0.3699 (pmm) cc_final: 0.1769 (tpt) REVERT: J 634 ARG cc_start: 0.7354 (mtp85) cc_final: 0.7148 (mtp85) REVERT: J 932 MET cc_start: 0.8194 (mmt) cc_final: 0.7452 (mmt) REVERT: J 1334 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6131 (mp0) REVERT: J 1370 MET cc_start: 0.6153 (mmp) cc_final: 0.5360 (ttp) outliers start: 49 outliers final: 45 residues processed: 256 average time/residue: 0.3066 time to fit residues: 124.7932 Evaluate side-chains 258 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 212 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 128 HIS Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 675 ASP Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 297 ARG Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain J residue 1351 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 260 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 207 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 159 optimal weight: 40.0000 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20162 Z= 0.291 Angle : 0.559 16.136 27531 Z= 0.288 Chirality : 0.043 0.148 3249 Planarity : 0.005 0.061 3473 Dihedral : 11.206 75.007 3246 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.11 % Allowed : 17.70 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2581 helix: 1.25 (0.17), residues: 903 sheet: 0.03 (0.28), residues: 329 loop : -0.70 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 686 HIS 0.006 0.001 HIS I 554 PHE 0.018 0.001 PHE J 461 TYR 0.011 0.001 TYR I1087 ARG 0.007 0.000 ARG I 465 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 205 time to evaluate : 2.351 Fit side-chains REVERT: I 488 MET cc_start: 0.3976 (pmm) cc_final: 0.2067 (tpt) REVERT: J 479 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: J 993 GLU cc_start: 0.4758 (tp30) cc_final: 0.4211 (tp30) REVERT: J 1334 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6322 (mp0) REVERT: J 1370 MET cc_start: 0.6368 (mmp) cc_final: 0.5479 (ttp) outliers start: 57 outliers final: 49 residues processed: 248 average time/residue: 0.3029 time to fit residues: 118.5691 Evaluate side-chains 254 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 203 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 128 HIS Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 675 ASP Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 297 ARG Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain J residue 1351 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 220 optimal weight: 30.0000 chunk 63 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 207 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.161313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.129443 restraints weight = 46221.764| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.37 r_work: 0.3491 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20162 Z= 0.150 Angle : 0.504 13.623 27531 Z= 0.259 Chirality : 0.041 0.145 3249 Planarity : 0.004 0.074 3473 Dihedral : 10.985 73.059 3246 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.46 % Allowed : 18.46 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 2581 helix: 1.48 (0.18), residues: 907 sheet: 0.17 (0.28), residues: 346 loop : -0.58 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 33 HIS 0.006 0.001 HIS J 104 PHE 0.012 0.001 PHE J 116 TYR 0.012 0.001 TYR J 631 ARG 0.012 0.000 ARG I 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4239.18 seconds wall clock time: 76 minutes 53.39 seconds (4613.39 seconds total)