Starting phenix.real_space_refine on Fri Mar 22 08:41:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psw_20466/03_2024/6psw_20466_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psw_20466/03_2024/6psw_20466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psw_20466/03_2024/6psw_20466.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psw_20466/03_2024/6psw_20466.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psw_20466/03_2024/6psw_20466_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psw_20466/03_2024/6psw_20466_trim_updated.pdb" } resolution = 3.7 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 124 5.49 5 Mg 1 5.21 5 S 136 5.16 5 C 20127 2.51 5 N 5780 2.21 5 O 6524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 136": "OE1" <-> "OE2" Residue "G GLU 193": "OE1" <-> "OE2" Residue "H ASP 15": "OD1" <-> "OD2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H ASP 120": "OD1" <-> "OD2" Residue "H TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 14": "OD1" <-> "OD2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 33": "OD1" <-> "OD2" Residue "I GLU 40": "OE1" <-> "OE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "I ASP 132": "OD1" <-> "OD2" Residue "I PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 158": "OD1" <-> "OD2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 231": "OE1" <-> "OE2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I ASP 281": "OD1" <-> "OD2" Residue "I GLU 290": "OE1" <-> "OE2" Residue "I TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 308": "OE1" <-> "OE2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I GLU 374": "OE1" <-> "OE2" Residue "I TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 412": "OE1" <-> "OE2" Residue "I ASP 423": "OD1" <-> "OD2" Residue "I ASP 427": "OD1" <-> "OD2" Residue "I ASP 434": "OD1" <-> "OD2" Residue "I ASP 446": "OD1" <-> "OD2" Residue "I ASP 516": "OD1" <-> "OD2" Residue "I ASP 549": "OD1" <-> "OD2" Residue "I TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 601": "OD1" <-> "OD2" Residue "I TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 632": "OD1" <-> "OD2" Residue "I GLU 641": "OE1" <-> "OE2" Residue "I ASP 696": "OD1" <-> "OD2" Residue "I GLU 778": "OE1" <-> "OE2" Residue "I ASP 781": "OD1" <-> "OD2" Residue "I ASP 785": "OD1" <-> "OD2" Residue "I PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 813": "OE1" <-> "OE2" Residue "I ASP 826": "OD1" <-> "OD2" Residue "I ASP 853": "OD1" <-> "OD2" Residue "I ASP 912": "OD1" <-> "OD2" Residue "I ASP 937": "OD1" <-> "OD2" Residue "I ARG 974": "NH1" <-> "NH2" Residue "I GLU 987": "OE1" <-> "OE2" Residue "I ARG 1156": "NH1" <-> "NH2" Residue "I PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1296": "OD1" <-> "OD2" Residue "I TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1341": "OD1" <-> "OD2" Residue "J ASP 18": "OD1" <-> "OD2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J ARG 53": "NH1" <-> "NH2" Residue "J PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 177": "OD1" <-> "OD2" Residue "J ASP 248": "OD1" <-> "OD2" Residue "J ASP 289": "OD1" <-> "OD2" Residue "J ARG 293": "NH1" <-> "NH2" Residue "J ASP 304": "OD1" <-> "OD2" Residue "J ASP 329": "OD1" <-> "OD2" Residue "J PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J ASP 462": "OD1" <-> "OD2" Residue "J GLU 648": "OE1" <-> "OE2" Residue "J PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 731": "NH1" <-> "NH2" Residue "J ARG 738": "NH1" <-> "NH2" Residue "J ARG 799": "NH1" <-> "NH2" Residue "J ASP 802": "OD1" <-> "OD2" Residue "J ASP 812": "OD1" <-> "OD2" Residue "J ASP 837": "OD1" <-> "OD2" Residue "J GLU 846": "OE1" <-> "OE2" Residue "J PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 981": "OE1" <-> "OE2" Residue "J GLU 987": "OE1" <-> "OE2" Residue "J TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1052": "OE1" <-> "OE2" Residue "J ASP 1073": "OD1" <-> "OD2" Residue "J ASP 1111": "OD1" <-> "OD2" Residue "J GLU 1146": "OE1" <-> "OE2" Residue "J GLU 1158": "OE1" <-> "OE2" Residue "J GLU 1188": "OE1" <-> "OE2" Residue "J PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "K ARG 3": "NH1" <-> "NH2" Residue "K ASP 8": "OD1" <-> "OD2" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K ARG 67": "NH1" <-> "NH2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "L ARG 113": "NH1" <-> "NH2" Residue "L GLU 114": "OE1" <-> "OE2" Residue "L ASP 118": "OD1" <-> "OD2" Residue "L PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 278": "OD1" <-> "OD2" Residue "L GLU 293": "OE1" <-> "OE2" Residue "L ASP 332": "OD1" <-> "OD2" Residue "L GLU 349": "OE1" <-> "OE2" Residue "L TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 417": "OD1" <-> "OD2" Residue "L ARG 441": "NH1" <-> "NH2" Residue "L GLU 481": "OE1" <-> "OE2" Residue "L ARG 584": "NH1" <-> "NH2" Residue "L ASP 612": "OD1" <-> "OD2" Residue "L ASP 613": "OD1" <-> "OD2" Residue "M ASP 250": "OD1" <-> "OD2" Residue "M ASP 258": "OD1" <-> "OD2" Residue "M GLU 261": "OE1" <-> "OE2" Residue "M ASP 280": "OD1" <-> "OD2" Residue "M GLU 286": "OE1" <-> "OE2" Residue "M GLU 319": "OE1" <-> "OE2" Residue "N GLU 4": "OE1" <-> "OE2" Residue "N TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 66": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32695 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1762 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 219} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10571 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1284} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 10460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 10460 Classifications: {'peptide': 1345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1288} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3854 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 14, 'TRANS': 458} Chain breaks: 2 Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "N" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 66} Chain: "O" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1270 Classifications: {'DNA': 62} Link IDs: {'rna3p': 61} Chain: "P" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1272 Classifications: {'DNA': 62} Link IDs: {'rna3p': 61} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14460 SG CYS J 70 76.872 99.753 110.158 1.00 33.15 S ATOM 14474 SG CYS J 72 77.146 102.675 111.995 1.00 38.61 S ATOM 14582 SG CYS J 85 74.415 101.147 113.335 1.00 42.93 S ATOM 14606 SG CYS J 88 73.523 100.283 110.077 1.00 47.24 S ATOM 20288 SG CYS J 814 73.930 38.981 83.279 1.00 26.40 S ATOM 20853 SG CYS J 888 73.547 42.857 82.747 1.00 23.18 S ATOM 20925 SG CYS J 898 75.066 40.229 80.222 1.00 16.65 S ATOM 29825 SG CYS N 40 53.649 54.250 22.072 1.00 73.58 S ATOM 29984 SG CYS N 61 56.367 55.850 24.356 1.00 81.89 S Time building chain proxies: 17.69, per 1000 atoms: 0.54 Number of scatterers: 32695 At special positions: 0 Unit cell: (163.8, 156, 166.4, 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 3 29.99 S 136 16.00 P 124 15.00 Mg 1 11.99 O 6524 8.00 N 5780 7.00 C 20127 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: 13.76 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 61 " Number of angles added : 6 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 33 sheets defined 36.9% alpha, 8.9% beta 48 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 17.46 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 removed outlier: 3.736A pdb=" N SER G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) 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 156 through 159 Processing helix chain 'G' and resid 162 through 164 No H-bonds generated for 'chain 'G' and resid 162 through 164' Processing helix chain 'G' and resid 213 through 233 Processing helix chain 'H' and resid 35 through 49 removed outlier: 3.609A pdb=" N LEU H 39 " --> pdb=" O PHE H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 87 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 228 removed outlier: 4.218A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 8 No H-bonds generated for 'chain 'I' and resid 5 through 8' Processing helix chain 'I' and resid 29 through 39 removed outlier: 4.112A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 56 removed outlier: 3.655A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 No H-bonds generated for 'chain 'I' and resid 243 through 246' Processing helix chain 'I' and resid 271 through 279 Processing helix chain 'I' and resid 319 through 328 removed outlier: 3.626A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 388 Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 436 Processing helix chain 'I' and resid 456 through 480 removed outlier: 4.314A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 541 through 543 No H-bonds generated for 'chain 'I' and resid 541 through 543' Processing helix chain 'I' and resid 609 through 612 No H-bonds generated for 'chain 'I' and resid 609 through 612' Processing helix chain 'I' and resid 647 through 649 No H-bonds generated for 'chain 'I' and resid 647 through 649' 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 688 removed outlier: 3.639A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 821 through 824 No H-bonds generated for 'chain 'I' and resid 821 through 824' Processing helix chain 'I' and resid 861 through 863 No H-bonds generated for 'chain 'I' and resid 861 through 863' Processing helix chain 'I' and resid 899 through 906 Processing helix chain 'I' and resid 943 through 980 removed outlier: 4.380A pdb=" N ALA I 977 " --> pdb=" O SER I 973 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL I 980 " --> pdb=" O ARG I 976 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1037 Processing helix chain 'I' and resid 1101 through 1105 removed outlier: 3.881A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1105' Processing helix chain 'I' and resid 1109 through 1133 removed outlier: 3.609A pdb=" N LEU I1117 " --> pdb=" O GLU I1114 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1148 Processing helix chain 'I' and resid 1168 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 1280 Processing helix chain 'I' and resid 1285 through 1291 Processing helix chain 'I' and resid 1300 through 1309 removed outlier: 3.955A pdb=" N TYR I1305 " --> pdb=" O ARG I1301 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE I1308 " --> pdb=" O MET I1304 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1330 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'J' and resid 115 through 118 No H-bonds generated for 'chain 'J' and resid 115 through 118' Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 removed outlier: 3.884A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU J 171 " --> pdb=" O ASP J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 191 removed outlier: 4.108A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 234 through 237 Processing helix chain 'J' and resid 256 through 258 No H-bonds generated for 'chain 'J' and resid 256 through 258' Processing helix chain 'J' and resid 264 through 285 removed outlier: 3.525A pdb=" N LEU J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 337 through 340 No H-bonds generated for 'chain 'J' and resid 337 through 340' Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 388 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 415 removed outlier: 4.054A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) 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 453 through 457 Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 486 through 488 No H-bonds generated for 'chain 'J' and resid 486 through 488' 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: 4.073A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 592 Processing helix chain 'J' and resid 599 through 612 Processing helix chain 'J' and resid 615 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 649 through 669 Processing helix chain 'J' and resid 675 through 702 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 740 Processing helix chain 'J' and resid 769 through 789 removed outlier: 4.016A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU J 788 " --> pdb=" O ALA J 784 " (cutoff:3.500A) Processing helix chain 'J' and resid 791 through 803 removed outlier: 3.940A pdb=" N LEU J 796 " --> pdb=" O ASN J 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 838 No H-bonds generated for 'chain 'J' and resid 835 through 838' Processing helix chain 'J' and resid 866 through 875 removed outlier: 3.675A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) 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 928 Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 1138 through 1146 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1226 through 1244 Processing helix chain 'J' and resid 1250 through 1262 removed outlier: 3.528A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG J1262 " --> pdb=" O ARG J1258 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1292 Processing helix chain 'J' and resid 1309 through 1313 Processing helix chain 'J' and resid 1319 through 1324 removed outlier: 3.792A pdb=" N SER J1324 " --> pdb=" O ILE J1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 1328 through 1338 removed outlier: 3.658A pdb=" N ALA J1336 " --> pdb=" O LEU J1332 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL J1337 " --> pdb=" O THR J1333 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1352 Processing helix chain 'J' and resid 1361 through 1373 removed outlier: 3.703A pdb=" N ALA J1364 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 13 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 55 removed outlier: 3.626A pdb=" N GLU K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.724A pdb=" N GLU K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA K 77 " --> pdb=" O GLN K 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 106 Processing helix chain 'L' and resid 115 through 135 Processing helix chain 'L' and resid 138 through 153 Processing helix chain 'L' and resid 158 through 161 No H-bonds generated for 'chain 'L' and resid 158 through 161' Processing helix chain 'L' and resid 216 through 232 Processing helix chain 'L' and resid 245 through 256 Processing helix chain 'L' and resid 263 through 289 Processing helix chain 'L' and resid 299 through 306 Processing helix chain 'L' and resid 317 through 320 No H-bonds generated for 'chain 'L' and resid 317 through 320' Processing helix chain 'L' and resid 334 through 351 Processing helix chain 'L' and resid 355 through 394 removed outlier: 4.046A pdb=" N ASN L 362 " --> pdb=" O VAL L 358 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLU L 378 " --> pdb=" O ARG L 374 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE L 390 " --> pdb=" O LEU L 386 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR L 394 " --> pdb=" O ILE L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 418 Processing helix chain 'L' and resid 427 through 445 removed outlier: 4.250A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 474 removed outlier: 4.925A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 483 through 486 No H-bonds generated for 'chain 'L' and resid 483 through 486' Processing helix chain 'L' and resid 493 through 500 Processing helix chain 'L' and resid 512 through 514 No H-bonds generated for 'chain 'L' and resid 512 through 514' Processing helix chain 'L' and resid 519 through 522 Processing helix chain 'L' and resid 531 through 550 removed outlier: 3.572A pdb=" N GLY L 550 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 553 through 562 Processing helix chain 'L' and resid 573 through 579 Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'L' and resid 605 through 610 Processing helix chain 'M' and resid 257 through 259 No H-bonds generated for 'chain 'M' and resid 257 through 259' Processing helix chain 'M' and resid 264 through 272 Processing helix chain 'M' and resid 278 through 281 No H-bonds generated for 'chain 'M' and resid 278 through 281' Processing helix chain 'M' and resid 286 through 290 Processing helix chain 'M' and resid 297 through 310 Processing helix chain 'N' and resid 5 through 26 Processing helix chain 'N' and resid 46 through 51 Processing helix chain 'N' and resid 59 through 69 Processing sheet with id= A, first strand: chain 'G' and resid 24 through 28 removed outlier: 3.868A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.552A pdb=" N VAL G 146 " --> pdb=" O VAL G 98 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.685A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 23 through 28 removed outlier: 3.777A pdb=" N ALA H 184 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 99 through 105 removed outlier: 3.663A pdb=" N MET H 142 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 58 through 60 removed outlier: 7.105A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 93 through 95 removed outlier: 3.533A pdb=" N ILE I 127 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= I, first strand: chain 'I' and resid 149 through 151 Processing sheet with id= J, first strand: chain 'I' and resid 154 through 157 Processing sheet with id= K, first strand: chain 'I' and resid 228 through 231 Processing sheet with id= L, first strand: chain 'I' and resid 238 through 240 Processing sheet with id= M, first strand: chain 'I' and resid 603 through 606 Processing sheet with id= N, first strand: chain 'I' and resid 633 through 636 Processing sheet with id= O, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.637A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.462A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 834 through 840 removed outlier: 3.520A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 887 through 889 Processing sheet with id= S, first strand: chain 'I' and resid 255 through 257 removed outlier: 5.619A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 301 through 303 removed outlier: 5.339A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 19 through 21 Processing sheet with id= V, first strand: chain 'J' and resid 104 through 106 Processing sheet with id= W, first strand: chain 'J' and resid 252 through 254 Processing sheet with id= X, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= Y, first strand: chain 'J' and resid 547 through 556 Processing sheet with id= Z, first strand: chain 'J' and resid 820 through 823 Processing sheet with id= AA, first strand: chain 'J' and resid 959 through 961 Processing sheet with id= AB, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AC, first strand: chain 'J' and resid 1024 through 1026 Processing sheet with id= AD, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 4.493A pdb=" N ALA J1097 " --> pdb=" O ILE J1080 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 1046 through 1051 Processing sheet with id= AF, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AG, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.085A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1049 hydrogen bonds defined for protein. 2958 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 222 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 91 stacking parallelities Total time for adding SS restraints: 15.03 Time building geometry restraints manager: 14.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10748 1.34 - 1.46: 7481 1.46 - 1.59: 14726 1.59 - 1.72: 251 1.72 - 1.84: 239 Bond restraints: 33445 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.842 -0.310 2.00e-02 2.50e+03 2.40e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.820 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C3 1N7 J1504 " pdb=" C4 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.731 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.712 -0.180 2.00e-02 2.50e+03 8.09e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.694 -0.152 2.00e-02 2.50e+03 5.76e+01 ... (remaining 33440 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.17: 1029 105.17 - 112.42: 17804 112.42 - 119.68: 11236 119.68 - 126.93: 15068 126.93 - 134.19: 572 Bond angle restraints: 45709 Sorted by residual: angle pdb=" N ILE N 27 " pdb=" CA ILE N 27 " pdb=" C ILE N 27 " ideal model delta sigma weight residual 106.21 113.68 -7.47 1.07e+00 8.73e-01 4.87e+01 angle pdb=" C THR L 94 " pdb=" N THR L 95 " pdb=" CA THR L 95 " ideal model delta sigma weight residual 122.56 113.32 9.24 1.50e+00 4.44e-01 3.79e+01 angle pdb=" N ILE J 490 " pdb=" CA ILE J 490 " pdb=" C ILE J 490 " ideal model delta sigma weight residual 113.20 108.82 4.38 9.60e-01 1.09e+00 2.08e+01 angle pdb=" N LEU I 237 " pdb=" CA LEU I 237 " pdb=" C LEU I 237 " ideal model delta sigma weight residual 110.91 116.10 -5.19 1.17e+00 7.31e-01 1.97e+01 angle pdb=" N ILE I1109 " pdb=" CA ILE I1109 " pdb=" C ILE I1109 " ideal model delta sigma weight residual 113.07 107.45 5.62 1.36e+00 5.41e-01 1.71e+01 ... (remaining 45704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.36: 19187 32.36 - 64.71: 1134 64.71 - 97.07: 78 97.07 - 129.42: 5 129.42 - 161.78: 5 Dihedral angle restraints: 20409 sinusoidal: 9372 harmonic: 11037 Sorted by residual: dihedral pdb=" CA PHE I 545 " pdb=" C PHE I 545 " pdb=" N GLU I 546 " pdb=" CA GLU I 546 " ideal model delta harmonic sigma weight residual -180.00 -127.47 -52.53 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA PHE I 57 " pdb=" C PHE I 57 " pdb=" N PRO I 58 " pdb=" CA PRO I 58 " ideal model delta harmonic sigma weight residual 180.00 139.27 40.73 0 5.00e+00 4.00e-02 6.64e+01 dihedral pdb=" CA VAL I 442 " pdb=" C VAL I 442 " pdb=" N ASP I 443 " pdb=" CA ASP I 443 " ideal model delta harmonic sigma weight residual -180.00 -145.49 -34.51 0 5.00e+00 4.00e-02 4.76e+01 ... (remaining 20406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4241 0.060 - 0.119: 896 0.119 - 0.179: 77 0.179 - 0.239: 7 0.239 - 0.298: 3 Chirality restraints: 5224 Sorted by residual: chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.83 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ASP I 516 " pdb=" N ASP I 516 " pdb=" C ASP I 516 " pdb=" CB ASP I 516 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C19 1N7 J1504 " pdb=" C18 1N7 J1504 " pdb=" C2 1N7 J1504 " pdb=" C3 1N7 J1504 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 5221 not shown) Planarity restraints: 5525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG I 974 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C ARG I 974 " 0.063 2.00e-02 2.50e+03 pdb=" O ARG I 974 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE I 975 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 375 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.24e+00 pdb=" C ALA L 375 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA L 375 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS L 376 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET H 51 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO H 52 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 52 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 52 " 0.041 5.00e-02 4.00e+02 ... (remaining 5522 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 391 2.57 - 3.15: 30279 3.15 - 3.73: 51571 3.73 - 4.32: 73436 4.32 - 4.90: 116059 Nonbonded interactions: 271736 Sorted by model distance: nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 1.987 2.170 nonbonded pdb=" OH TYR I 346 " pdb=" OD1 ASN I 437 " model vdw 2.023 2.440 nonbonded pdb=" OG1 THR I 216 " pdb=" OE1 GLN I 219 " model vdw 2.026 2.440 nonbonded pdb=" O ASN J 962 " pdb=" OG1 THR J 980 " model vdw 2.059 2.440 nonbonded pdb=" OH TYR I 179 " pdb=" OE2 GLU I 458 " model vdw 2.063 2.440 ... (remaining 271731 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 'G' and ((resid 6 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 158 or resid 171 through 233 or (resid 234 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'H' and ((resid 6 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 121 or (resid 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 through 228 or (resid 229 through 230 and \ (name N or name CA or name C or name O or name CB )) or resid 231 through 232 o \ r (resid 233 through 234 and (name N or name CA or name C or name O or name CB ) \ ))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.610 Check model and map are aligned: 0.550 Set scattering table: 0.320 Process input model: 105.010 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.310 33445 Z= 0.508 Angle : 0.887 9.961 45709 Z= 0.518 Chirality : 0.047 0.298 5224 Planarity : 0.005 0.075 5525 Dihedral : 18.871 161.776 13291 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 42.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.43 % Favored : 88.38 % Rotamer: Outliers : 0.40 % Allowed : 10.91 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.05 % 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: -4.03 (0.11), residues: 3805 helix: -1.94 (0.11), residues: 1474 sheet: -3.31 (0.21), residues: 382 loop : -3.18 (0.12), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP I 807 HIS 0.008 0.002 HIS J 430 PHE 0.026 0.002 PHE J1325 TYR 0.024 0.002 TYR I 810 ARG 0.007 0.001 ARG J 842 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 597 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 145 LYS cc_start: 0.9053 (tmmt) cc_final: 0.8417 (tttt) REVERT: H 58 GLU cc_start: 0.6178 (tm-30) cc_final: 0.5874 (tt0) REVERT: H 74 VAL cc_start: 0.7236 (t) cc_final: 0.6382 (m) REVERT: H 83 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8128 (mt) REVERT: H 200 LYS cc_start: 0.8866 (tttt) cc_final: 0.8592 (tttp) REVERT: I 36 GLN cc_start: 0.8021 (tp40) cc_final: 0.7591 (tp40) REVERT: I 40 GLU cc_start: 0.7788 (tt0) cc_final: 0.7512 (tt0) REVERT: I 50 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6732 (tt0) REVERT: I 277 LEU cc_start: 0.3754 (mt) cc_final: 0.3483 (mp) REVERT: I 793 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7649 (mm-30) REVERT: I 1331 ARG cc_start: 0.8471 (ttm170) cc_final: 0.8079 (mtm180) REVERT: J 295 GLU cc_start: 0.8006 (tp30) cc_final: 0.7570 (tp30) REVERT: J 337 ARG cc_start: 0.8501 (mmt-90) cc_final: 0.8293 (mmt90) REVERT: J 555 TYR cc_start: 0.8271 (m-10) cc_final: 0.7846 (m-80) REVERT: J 707 ILE cc_start: 0.8006 (pt) cc_final: 0.7658 (tt) REVERT: J 715 LYS cc_start: 0.7556 (mtpp) cc_final: 0.7275 (mptt) REVERT: J 749 LYS cc_start: 0.8358 (ptmt) cc_final: 0.8148 (mtpt) REVERT: J 785 ASP cc_start: 0.8320 (t0) cc_final: 0.8088 (t0) REVERT: J 991 THR cc_start: 0.6370 (p) cc_final: 0.6088 (p) REVERT: J 1020 TRP cc_start: 0.5491 (p90) cc_final: 0.5276 (p90) REVERT: J 1132 LYS cc_start: 0.4773 (OUTLIER) cc_final: 0.1955 (mtpt) REVERT: J 1349 GLU cc_start: 0.7702 (mp0) cc_final: 0.7271 (mt-10) REVERT: K 55 GLU cc_start: 0.6775 (pp20) cc_final: 0.6409 (pp20) REVERT: K 56 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7701 (mm-30) REVERT: L 136 GLU cc_start: 0.5627 (mt-10) cc_final: 0.3996 (mm-30) REVERT: L 143 TYR cc_start: 0.5491 (t80) cc_final: 0.4630 (t80) REVERT: L 276 MET cc_start: 0.6904 (mpp) cc_final: 0.6510 (mpp) REVERT: L 277 MET cc_start: 0.6646 (tpt) cc_final: 0.6387 (tmm) REVERT: L 297 MET cc_start: 0.1451 (ttm) cc_final: 0.0500 (mtp) REVERT: L 576 VAL cc_start: 0.7664 (t) cc_final: 0.7462 (t) REVERT: M 316 MET cc_start: 0.3865 (tpt) cc_final: 0.1676 (tmm) REVERT: N 9 TYR cc_start: 0.7758 (t80) cc_final: 0.7463 (t80) REVERT: N 65 GLN cc_start: 0.6948 (tt0) cc_final: 0.6471 (tp40) outliers start: 13 outliers final: 9 residues processed: 609 average time/residue: 0.5080 time to fit residues: 470.9832 Evaluate side-chains 387 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 376 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 330 optimal weight: 0.8980 chunk 296 optimal weight: 0.7980 chunk 164 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 306 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 228 optimal weight: 0.8980 chunk 355 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS H 128 HIS I 20 GLN ** I 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN I 832 HIS I 834 GLN ** I 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 932 GLN I1116 HIS I1135 GLN I1220 GLN J 157 GLN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 GLN J 465 GLN ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN J 594 GLN J 680 ASN J 720 ASN J 817 HIS J 910 ASN J 951 GLN J 954 ASN J1023 HIS J1249 ASN K 15 ASN L 227 GLN L 242 HIS L 271 ASN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 GLN L 600 HIS N 30 HIS N 68 GLN N 71 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33445 Z= 0.203 Angle : 0.659 9.527 45709 Z= 0.345 Chirality : 0.044 0.299 5224 Planarity : 0.005 0.074 5525 Dihedral : 18.642 160.710 5749 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.41 % Favored : 92.51 % Rotamer: Outliers : 2.90 % Allowed : 15.61 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.13), residues: 3805 helix: -0.56 (0.13), residues: 1466 sheet: -2.63 (0.24), residues: 367 loop : -2.59 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 807 HIS 0.013 0.001 HIS N 30 PHE 0.019 0.002 PHE J1165 TYR 0.017 0.001 TYR I1018 ARG 0.008 0.001 ARG J 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 521 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: G 68 TYR cc_start: 0.8696 (m-80) cc_final: 0.8139 (m-80) REVERT: G 145 LYS cc_start: 0.8998 (tmmt) cc_final: 0.8217 (tttt) REVERT: H 58 GLU cc_start: 0.5917 (tm-30) cc_final: 0.5514 (tt0) REVERT: H 83 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7890 (mt) REVERT: H 211 ILE cc_start: 0.8857 (tp) cc_final: 0.8506 (pt) REVERT: I 88 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7886 (ptp-110) REVERT: I 119 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6195 (tt0) REVERT: I 609 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7453 (tp) REVERT: I 704 MET cc_start: 0.7974 (mmm) cc_final: 0.7749 (tpp) REVERT: I 741 MET cc_start: 0.7677 (ttp) cc_final: 0.7141 (ttp) REVERT: I 974 ARG cc_start: 0.7470 (mmp80) cc_final: 0.7102 (mmp-170) REVERT: I 1137 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: I 1154 ASP cc_start: 0.6717 (p0) cc_final: 0.6459 (p0) REVERT: I 1319 MET cc_start: 0.6720 (ttm) cc_final: 0.6462 (tpp) REVERT: I 1331 ARG cc_start: 0.8378 (ttm170) cc_final: 0.8007 (mtm180) REVERT: J 165 TYR cc_start: 0.7922 (t80) cc_final: 0.7699 (t80) REVERT: J 337 ARG cc_start: 0.8280 (mmt-90) cc_final: 0.7993 (mmt90) REVERT: J 339 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8122 (mtp180) REVERT: J 443 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6930 (mp0) REVERT: J 555 TYR cc_start: 0.8208 (m-10) cc_final: 0.7856 (m-80) REVERT: J 747 MET cc_start: 0.8325 (mmm) cc_final: 0.7682 (mmm) REVERT: J 785 ASP cc_start: 0.8492 (t0) cc_final: 0.8141 (t0) REVERT: J 805 GLN cc_start: 0.8537 (pm20) cc_final: 0.8086 (pp30) REVERT: J 918 ILE cc_start: 0.8768 (pt) cc_final: 0.8202 (mt) REVERT: J 1132 LYS cc_start: 0.4701 (OUTLIER) cc_final: 0.3736 (mmtt) REVERT: J 1349 GLU cc_start: 0.7814 (mp0) cc_final: 0.7208 (mt-10) REVERT: L 105 MET cc_start: 0.8342 (ppp) cc_final: 0.8121 (ppp) REVERT: L 161 LEU cc_start: 0.5065 (OUTLIER) cc_final: 0.4852 (tp) REVERT: L 273 MET cc_start: 0.7101 (mmm) cc_final: 0.6814 (mmm) REVERT: L 277 MET cc_start: 0.6701 (tpt) cc_final: 0.6253 (tmm) REVERT: L 359 LYS cc_start: 0.4671 (OUTLIER) cc_final: 0.4447 (ttmt) REVERT: L 429 THR cc_start: 0.7593 (m) cc_final: 0.7365 (t) REVERT: M 316 MET cc_start: 0.3219 (tpt) cc_final: 0.1857 (tmm) REVERT: N 4 GLU cc_start: 0.7390 (mp0) cc_final: 0.7164 (mt-10) REVERT: N 9 TYR cc_start: 0.7536 (t80) cc_final: 0.7138 (t80) REVERT: N 17 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6288 (mmt) REVERT: N 65 GLN cc_start: 0.6830 (tt0) cc_final: 0.6528 (tp-100) REVERT: N 66 GLU cc_start: 0.7709 (mm-30) cc_final: 0.6944 (pt0) REVERT: N 72 TYR cc_start: 0.4001 (m-10) cc_final: 0.3789 (m-10) outliers start: 95 outliers final: 46 residues processed: 587 average time/residue: 0.4581 time to fit residues: 422.3189 Evaluate side-chains 454 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 400 time to evaluate : 3.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 359 LYS Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 30 HIS Chi-restraints excluded: chain N residue 58 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 chunk 241 optimal weight: 9.9990 chunk 97 optimal weight: 0.2980 chunk 355 optimal weight: 8.9990 chunk 384 optimal weight: 10.0000 chunk 316 optimal weight: 9.9990 chunk 352 optimal weight: 0.4980 chunk 121 optimal weight: 2.9990 chunk 285 optimal weight: 0.0270 overall best weight: 2.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN H 93 GLN H 147 GLN I 20 GLN I 69 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 GLN J 489 ASN J1108 GLN J1249 ASN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33445 Z= 0.266 Angle : 0.649 9.937 45709 Z= 0.340 Chirality : 0.043 0.250 5224 Planarity : 0.005 0.088 5525 Dihedral : 18.421 158.110 5742 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.12 % Favored : 91.77 % Rotamer: Outliers : 3.94 % Allowed : 18.06 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.13), residues: 3805 helix: -0.14 (0.13), residues: 1461 sheet: -2.23 (0.25), residues: 364 loop : -2.34 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 807 HIS 0.018 0.001 HIS N 30 PHE 0.022 0.002 PHE I 545 TYR 0.019 0.002 TYR L 137 ARG 0.008 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 413 time to evaluate : 3.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: G 145 LYS cc_start: 0.8964 (tmmt) cc_final: 0.8221 (ttpt) REVERT: H 32 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6620 (tp30) REVERT: H 58 GLU cc_start: 0.5952 (tm-30) cc_final: 0.5621 (tt0) REVERT: H 83 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7936 (mt) REVERT: H 211 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8485 (pt) REVERT: I 40 GLU cc_start: 0.7578 (tt0) cc_final: 0.7009 (tt0) REVERT: I 119 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6542 (tt0) REVERT: I 515 MET cc_start: 0.8679 (ttp) cc_final: 0.8295 (ttp) REVERT: I 609 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7459 (tp) REVERT: I 704 MET cc_start: 0.8063 (mmm) cc_final: 0.7792 (tpp) REVERT: I 741 MET cc_start: 0.7664 (ttp) cc_final: 0.7243 (ttp) REVERT: I 974 ARG cc_start: 0.7617 (mmp80) cc_final: 0.7161 (mmp-170) REVERT: I 1072 ASN cc_start: 0.8122 (p0) cc_final: 0.7137 (p0) REVERT: I 1137 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: I 1331 ARG cc_start: 0.8397 (ttm170) cc_final: 0.8020 (mtm180) REVERT: J 337 ARG cc_start: 0.8349 (mmt-90) cc_final: 0.8052 (mmt90) REVERT: J 339 ARG cc_start: 0.8650 (mmm-85) cc_final: 0.8216 (mtp180) REVERT: J 372 MET cc_start: 0.8688 (ttp) cc_final: 0.8440 (ttp) REVERT: J 555 TYR cc_start: 0.8232 (m-10) cc_final: 0.7884 (m-80) REVERT: J 594 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7205 (pt0) REVERT: J 805 GLN cc_start: 0.8686 (pm20) cc_final: 0.8174 (pp30) REVERT: J 918 ILE cc_start: 0.8852 (pt) cc_final: 0.8281 (mt) REVERT: J 1132 LYS cc_start: 0.4860 (OUTLIER) cc_final: 0.2284 (mmtt) REVERT: J 1189 MET cc_start: 0.6592 (mmm) cc_final: 0.6182 (ttt) REVERT: J 1282 TYR cc_start: 0.8281 (t80) cc_final: 0.8027 (t80) REVERT: J 1349 GLU cc_start: 0.7776 (mp0) cc_final: 0.7351 (mp0) REVERT: K 11 GLU cc_start: 0.6349 (tp30) cc_final: 0.6069 (tp30) REVERT: L 105 MET cc_start: 0.8350 (ppp) cc_final: 0.8050 (ppp) REVERT: L 277 MET cc_start: 0.6573 (tpt) cc_final: 0.6201 (tmm) REVERT: M 316 MET cc_start: 0.3218 (tpt) cc_final: 0.1832 (tmm) REVERT: N 4 GLU cc_start: 0.7211 (mp0) cc_final: 0.6935 (mt-10) REVERT: N 9 TYR cc_start: 0.7629 (t80) cc_final: 0.7316 (t80) REVERT: N 17 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6450 (mmt) REVERT: N 65 GLN cc_start: 0.7065 (tt0) cc_final: 0.6590 (tp-100) REVERT: N 66 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7117 (pt0) outliers start: 129 outliers final: 79 residues processed: 508 average time/residue: 0.4570 time to fit residues: 375.0272 Evaluate side-chains 453 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 365 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 27 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 351 optimal weight: 9.9990 chunk 267 optimal weight: 0.9980 chunk 184 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 chunk 238 optimal weight: 2.9990 chunk 356 optimal weight: 1.9990 chunk 377 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 chunk 338 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS H 147 GLN I 582 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 725 GLN J1279 GLN J1366 HIS ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33445 Z= 0.216 Angle : 0.612 11.185 45709 Z= 0.319 Chirality : 0.042 0.231 5224 Planarity : 0.004 0.077 5525 Dihedral : 18.139 157.010 5740 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.36 % Favored : 92.56 % Rotamer: Outliers : 4.25 % Allowed : 19.22 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.13), residues: 3805 helix: 0.15 (0.13), residues: 1463 sheet: -1.89 (0.25), residues: 367 loop : -2.17 (0.13), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 807 HIS 0.005 0.001 HIS J 430 PHE 0.017 0.001 PHE L 256 TYR 0.016 0.001 TYR J 46 ARG 0.008 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 414 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: G 145 LYS cc_start: 0.8943 (tmmt) cc_final: 0.8186 (ttpt) REVERT: H 58 GLU cc_start: 0.5959 (tm-30) cc_final: 0.5430 (tt0) REVERT: H 211 ILE cc_start: 0.8816 (tp) cc_final: 0.8485 (pt) REVERT: I 88 ARG cc_start: 0.7839 (ttm-80) cc_final: 0.7527 (ttp-110) REVERT: I 119 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6642 (tt0) REVERT: I 515 MET cc_start: 0.8523 (ttp) cc_final: 0.8151 (ttt) REVERT: I 609 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7287 (tp) REVERT: I 741 MET cc_start: 0.7670 (ttp) cc_final: 0.7383 (ttp) REVERT: I 742 TYR cc_start: 0.5029 (m-80) cc_final: 0.4595 (m-80) REVERT: I 987 GLU cc_start: 0.4818 (OUTLIER) cc_final: 0.4081 (pm20) REVERT: I 1024 GLU cc_start: 0.7828 (pp20) cc_final: 0.6701 (mm-30) REVERT: I 1066 MET cc_start: 0.7686 (mtp) cc_final: 0.7307 (mtp) REVERT: I 1072 ASN cc_start: 0.8188 (p0) cc_final: 0.7788 (p0) REVERT: I 1137 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: I 1319 MET cc_start: 0.6768 (ttm) cc_final: 0.6490 (tpp) REVERT: I 1331 ARG cc_start: 0.8394 (ttm170) cc_final: 0.7857 (mtm180) REVERT: J 155 GLU cc_start: 0.6113 (mp0) cc_final: 0.5260 (pt0) REVERT: J 158 GLN cc_start: 0.6741 (tt0) cc_final: 0.6453 (tt0) REVERT: J 337 ARG cc_start: 0.8361 (mmt-90) cc_final: 0.8146 (mmt90) REVERT: J 372 MET cc_start: 0.8692 (ttp) cc_final: 0.8375 (ttp) REVERT: J 555 TYR cc_start: 0.8248 (m-10) cc_final: 0.7733 (m-80) REVERT: J 567 THR cc_start: 0.8637 (m) cc_final: 0.8133 (p) REVERT: J 785 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8183 (m-30) REVERT: J 805 GLN cc_start: 0.8625 (pm20) cc_final: 0.8164 (pp30) REVERT: J 895 CYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8569 (p) REVERT: J 918 ILE cc_start: 0.8835 (pt) cc_final: 0.8281 (mt) REVERT: J 1132 LYS cc_start: 0.4431 (OUTLIER) cc_final: 0.3811 (mmtt) REVERT: J 1189 MET cc_start: 0.6493 (mmm) cc_final: 0.6198 (ttt) REVERT: J 1282 TYR cc_start: 0.8282 (t80) cc_final: 0.8003 (t80) REVERT: J 1341 ARG cc_start: 0.7034 (ttt-90) cc_final: 0.6763 (ttt-90) REVERT: J 1349 GLU cc_start: 0.7660 (mp0) cc_final: 0.7030 (mt-10) REVERT: J 1368 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.5918 (m-30) REVERT: K 68 GLU cc_start: 0.7870 (tp30) cc_final: 0.7621 (tp30) REVERT: L 105 MET cc_start: 0.8352 (ppp) cc_final: 0.8036 (ppp) REVERT: L 277 MET cc_start: 0.6417 (tpt) cc_final: 0.6103 (tmm) REVERT: L 390 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8322 (tp) REVERT: L 425 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6244 (m-80) REVERT: M 316 MET cc_start: 0.3052 (tpt) cc_final: 0.1632 (tmm) REVERT: N 4 GLU cc_start: 0.6984 (mp0) cc_final: 0.6705 (mt-10) REVERT: N 9 TYR cc_start: 0.7552 (t80) cc_final: 0.7214 (t80) REVERT: N 17 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6447 (mmt) REVERT: N 65 GLN cc_start: 0.7032 (tt0) cc_final: 0.6545 (tp-100) REVERT: N 66 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7178 (pt0) outliers start: 139 outliers final: 89 residues processed: 514 average time/residue: 0.4282 time to fit residues: 358.1078 Evaluate side-chains 464 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 363 time to evaluate : 3.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 987 GLU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 863 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 359 LYS Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain M residue 252 ILE Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 30 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 314 optimal weight: 1.9990 chunk 214 optimal weight: 0.0370 chunk 5 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 chunk 155 optimal weight: 0.4980 chunk 322 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 339 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS I 20 GLN ** I 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 824 GLN ** I1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33445 Z= 0.172 Angle : 0.585 12.914 45709 Z= 0.305 Chirality : 0.041 0.199 5224 Planarity : 0.004 0.073 5525 Dihedral : 17.857 155.671 5738 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 3.57 % Allowed : 20.38 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 3805 helix: 0.36 (0.14), residues: 1478 sheet: -1.64 (0.26), residues: 384 loop : -2.00 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 807 HIS 0.003 0.000 HIS J 430 PHE 0.015 0.001 PHE L 256 TYR 0.016 0.001 TYR J 679 ARG 0.010 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 419 time to evaluate : 3.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7428 (m-10) REVERT: G 137 ASN cc_start: 0.6044 (p0) cc_final: 0.5713 (p0) REVERT: H 58 GLU cc_start: 0.5875 (tm-30) cc_final: 0.5412 (tt0) REVERT: I 88 ARG cc_start: 0.7805 (ttm-80) cc_final: 0.7509 (ptp-110) REVERT: I 93 SER cc_start: 0.8768 (p) cc_final: 0.8464 (t) REVERT: I 412 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6473 (mt-10) REVERT: I 609 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7387 (tp) REVERT: I 622 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.6832 (p0) REVERT: I 741 MET cc_start: 0.7686 (ttp) cc_final: 0.7406 (ttp) REVERT: I 742 TYR cc_start: 0.4965 (m-80) cc_final: 0.4535 (m-80) REVERT: I 987 GLU cc_start: 0.4781 (OUTLIER) cc_final: 0.3999 (pm20) REVERT: I 1024 GLU cc_start: 0.7891 (pp20) cc_final: 0.6875 (mm-30) REVERT: I 1066 MET cc_start: 0.7726 (mtp) cc_final: 0.7346 (mtp) REVERT: I 1131 MET cc_start: 0.7947 (ttm) cc_final: 0.6949 (mtp) REVERT: I 1136 GLN cc_start: 0.5353 (mt0) cc_final: 0.4605 (mt0) REVERT: I 1331 ARG cc_start: 0.8405 (ttm170) cc_final: 0.7898 (mtm180) REVERT: J 155 GLU cc_start: 0.5916 (mp0) cc_final: 0.5296 (pt0) REVERT: J 158 GLN cc_start: 0.6718 (tt0) cc_final: 0.6517 (tt0) REVERT: J 327 LEU cc_start: 0.8435 (tp) cc_final: 0.8139 (mp) REVERT: J 334 LYS cc_start: 0.8115 (tptm) cc_final: 0.7854 (tttm) REVERT: J 339 ARG cc_start: 0.8674 (mmm-85) cc_final: 0.8348 (mmm-85) REVERT: J 372 MET cc_start: 0.8663 (ttp) cc_final: 0.8405 (ttp) REVERT: J 555 TYR cc_start: 0.8174 (m-10) cc_final: 0.7664 (m-80) REVERT: J 567 THR cc_start: 0.8602 (m) cc_final: 0.8091 (p) REVERT: J 747 MET cc_start: 0.8060 (mmm) cc_final: 0.7501 (mmm) REVERT: J 785 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: J 805 GLN cc_start: 0.8539 (pm20) cc_final: 0.8074 (pp30) REVERT: J 895 CYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8548 (p) REVERT: J 918 ILE cc_start: 0.8825 (pt) cc_final: 0.8271 (mt) REVERT: J 1132 LYS cc_start: 0.4406 (OUTLIER) cc_final: 0.3774 (mmtt) REVERT: J 1282 TYR cc_start: 0.8228 (t80) cc_final: 0.7958 (t80) REVERT: J 1341 ARG cc_start: 0.6929 (ttt-90) cc_final: 0.6715 (ttt-90) REVERT: J 1349 GLU cc_start: 0.7544 (mp0) cc_final: 0.6900 (mt-10) REVERT: K 11 GLU cc_start: 0.6241 (tp30) cc_final: 0.5998 (tp30) REVERT: K 67 ARG cc_start: 0.6493 (mtt-85) cc_final: 0.5610 (ttm-80) REVERT: L 105 MET cc_start: 0.8404 (ppp) cc_final: 0.8039 (ppp) REVERT: L 277 MET cc_start: 0.6468 (tpt) cc_final: 0.6111 (tmm) REVERT: L 357 GLN cc_start: 0.6809 (mt0) cc_final: 0.6258 (mm-40) REVERT: L 425 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.6211 (m-80) REVERT: L 508 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7159 (mm-30) REVERT: M 316 MET cc_start: 0.2967 (tpt) cc_final: 0.1584 (tmm) REVERT: N 4 GLU cc_start: 0.6855 (mp0) cc_final: 0.6574 (mt-10) REVERT: N 9 TYR cc_start: 0.7333 (t80) cc_final: 0.7054 (t80) REVERT: N 17 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6446 (mmt) REVERT: N 65 GLN cc_start: 0.7016 (tt0) cc_final: 0.6426 (tp-100) REVERT: N 66 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7310 (pt0) REVERT: N 72 TYR cc_start: 0.3883 (OUTLIER) cc_final: 0.3577 (m-10) outliers start: 117 outliers final: 79 residues processed: 504 average time/residue: 0.4382 time to fit residues: 360.0852 Evaluate side-chains 464 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 375 time to evaluate : 3.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 987 GLU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 733 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 863 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain M residue 252 ILE Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 58 CYS Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 127 optimal weight: 7.9990 chunk 340 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 378 optimal weight: 5.9990 chunk 314 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 798 GLN J1244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 33445 Z= 0.450 Angle : 0.745 11.634 45709 Z= 0.387 Chirality : 0.047 0.256 5224 Planarity : 0.005 0.085 5525 Dihedral : 18.261 147.743 5738 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.30 % Favored : 90.62 % Rotamer: Outliers : 4.64 % Allowed : 20.93 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.13), residues: 3805 helix: 0.02 (0.13), residues: 1464 sheet: -1.81 (0.25), residues: 399 loop : -1.96 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 433 HIS 0.009 0.001 HIS J 430 PHE 0.025 0.002 PHE N 52 TYR 0.021 0.002 TYR L 430 ARG 0.009 0.001 ARG J 220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 356 time to evaluate : 3.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: G 139 SER cc_start: 0.8536 (m) cc_final: 0.8206 (p) REVERT: H 58 GLU cc_start: 0.6195 (tm-30) cc_final: 0.5645 (tt0) REVERT: I 119 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6680 (tt0) REVERT: I 340 ASP cc_start: 0.6381 (OUTLIER) cc_final: 0.5697 (p0) REVERT: I 515 MET cc_start: 0.8203 (ttm) cc_final: 0.7862 (ttp) REVERT: I 741 MET cc_start: 0.7583 (ttp) cc_final: 0.7279 (ttp) REVERT: I 987 GLU cc_start: 0.5037 (OUTLIER) cc_final: 0.4364 (mp0) REVERT: I 1066 MET cc_start: 0.7870 (mtp) cc_final: 0.7538 (mtp) REVERT: I 1131 MET cc_start: 0.8273 (ttm) cc_final: 0.7165 (mtp) REVERT: I 1137 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: I 1331 ARG cc_start: 0.8505 (ttm170) cc_final: 0.8131 (mtm180) REVERT: J 78 LEU cc_start: 0.7928 (tp) cc_final: 0.7691 (tt) REVERT: J 155 GLU cc_start: 0.6309 (mp0) cc_final: 0.5449 (pt0) REVERT: J 368 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8931 (tt) REVERT: J 555 TYR cc_start: 0.8312 (m-10) cc_final: 0.7815 (m-80) REVERT: J 594 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7118 (pt0) REVERT: J 785 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: J 895 CYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8783 (p) REVERT: J 1040 MET cc_start: 0.4832 (mtp) cc_final: 0.4457 (ptp) REVERT: J 1132 LYS cc_start: 0.4431 (OUTLIER) cc_final: 0.3959 (mmtt) REVERT: J 1282 TYR cc_start: 0.8637 (t80) cc_final: 0.8325 (t80) REVERT: J 1349 GLU cc_start: 0.7779 (mp0) cc_final: 0.7202 (mt-10) REVERT: J 1368 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.5948 (m-30) REVERT: K 74 GLU cc_start: 0.7663 (pt0) cc_final: 0.7424 (pt0) REVERT: L 105 MET cc_start: 0.8393 (ppp) cc_final: 0.8073 (ppp) REVERT: L 329 LYS cc_start: 0.6023 (mtpt) cc_final: 0.4854 (mmtp) REVERT: L 390 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8441 (tp) REVERT: L 425 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.6370 (m-80) REVERT: M 316 MET cc_start: 0.3326 (tpt) cc_final: 0.1634 (tmm) REVERT: N 4 GLU cc_start: 0.7048 (mp0) cc_final: 0.6630 (mt-10) REVERT: N 9 TYR cc_start: 0.7814 (t80) cc_final: 0.7295 (t80) REVERT: N 65 GLN cc_start: 0.7078 (tt0) cc_final: 0.6487 (tp-100) REVERT: N 66 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7297 (pt0) REVERT: N 72 TYR cc_start: 0.4153 (OUTLIER) cc_final: 0.3709 (m-10) outliers start: 152 outliers final: 110 residues processed: 463 average time/residue: 0.4196 time to fit residues: 315.9947 Evaluate side-chains 458 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 334 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 987 GLU Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 733 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 863 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1205 GLU Chi-restraints excluded: chain J residue 1244 GLN Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 359 LYS Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 364 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 276 optimal weight: 7.9990 chunk 214 optimal weight: 0.9990 chunk 318 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 376 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 chunk 229 optimal weight: 0.0980 chunk 173 optimal weight: 0.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS ** I 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 798 GLN ** I1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33445 Z= 0.166 Angle : 0.591 9.796 45709 Z= 0.308 Chirality : 0.041 0.205 5224 Planarity : 0.004 0.069 5525 Dihedral : 17.753 151.562 5736 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.68 % Favored : 93.25 % Rotamer: Outliers : 3.54 % Allowed : 22.70 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3805 helix: 0.42 (0.14), residues: 1475 sheet: -1.52 (0.26), residues: 389 loop : -1.88 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 807 HIS 0.004 0.001 HIS I1023 PHE 0.018 0.001 PHE I 545 TYR 0.017 0.001 TYR J 679 ARG 0.007 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 400 time to evaluate : 3.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7443 (m-10) REVERT: H 58 GLU cc_start: 0.5914 (tm-30) cc_final: 0.5481 (tt0) REVERT: I 36 GLN cc_start: 0.8152 (tp40) cc_final: 0.7948 (tp40) REVERT: I 85 CYS cc_start: 0.8266 (t) cc_final: 0.7829 (m) REVERT: I 119 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6585 (tt0) REVERT: I 412 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6752 (mm-30) REVERT: I 486 THR cc_start: 0.6846 (p) cc_final: 0.6374 (m) REVERT: I 741 MET cc_start: 0.7668 (ttp) cc_final: 0.7402 (ttp) REVERT: I 742 TYR cc_start: 0.5127 (m-80) cc_final: 0.4690 (m-80) REVERT: I 1024 GLU cc_start: 0.7613 (pp20) cc_final: 0.6762 (mm-30) REVERT: I 1025 PHE cc_start: 0.7581 (t80) cc_final: 0.7274 (t80) REVERT: I 1066 MET cc_start: 0.7850 (mtp) cc_final: 0.7539 (mtp) REVERT: I 1131 MET cc_start: 0.7703 (ttm) cc_final: 0.6515 (mtp) REVERT: I 1137 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6082 (mp0) REVERT: I 1248 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.8004 (p) REVERT: I 1331 ARG cc_start: 0.8500 (ttm170) cc_final: 0.7944 (mtm180) REVERT: J 368 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8702 (tt) REVERT: J 372 MET cc_start: 0.8666 (ttp) cc_final: 0.8404 (ttp) REVERT: J 555 TYR cc_start: 0.8180 (m-10) cc_final: 0.7689 (m-80) REVERT: J 567 THR cc_start: 0.8660 (m) cc_final: 0.8240 (p) REVERT: J 785 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: J 895 CYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8506 (p) REVERT: J 918 ILE cc_start: 0.8793 (pt) cc_final: 0.8178 (mt) REVERT: J 1040 MET cc_start: 0.5063 (mtp) cc_final: 0.4668 (ptp) REVERT: J 1078 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6680 (mt) REVERT: J 1132 LYS cc_start: 0.4372 (OUTLIER) cc_final: 0.3792 (mmtt) REVERT: J 1260 MET cc_start: 0.8310 (ttm) cc_final: 0.8077 (ttm) REVERT: J 1282 TYR cc_start: 0.8274 (t80) cc_final: 0.8042 (t80) REVERT: J 1349 GLU cc_start: 0.7632 (mp0) cc_final: 0.7019 (mt-10) REVERT: K 67 ARG cc_start: 0.6449 (mtt-85) cc_final: 0.5620 (ttm-80) REVERT: L 105 MET cc_start: 0.8366 (ppp) cc_final: 0.8060 (ppp) REVERT: L 390 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8326 (tp) REVERT: L 425 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.6163 (m-80) REVERT: N 4 GLU cc_start: 0.6932 (mp0) cc_final: 0.6579 (mt-10) REVERT: N 32 ILE cc_start: 0.3586 (OUTLIER) cc_final: 0.3197 (tp) REVERT: N 65 GLN cc_start: 0.6873 (tt0) cc_final: 0.6660 (tp-100) REVERT: N 66 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7380 (pt0) outliers start: 116 outliers final: 70 residues processed: 482 average time/residue: 0.4300 time to fit residues: 338.1753 Evaluate side-chains 450 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 368 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 733 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 252 ILE Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 36 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 233 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 225 optimal weight: 0.0070 chunk 113 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 73 optimal weight: 0.0570 chunk 239 optimal weight: 10.0000 chunk 256 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 296 optimal weight: 1.9990 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS H 194 GLN I 139 ASN I 437 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 798 GLN J 158 GLN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33445 Z= 0.215 Angle : 0.606 10.308 45709 Z= 0.314 Chirality : 0.041 0.215 5224 Planarity : 0.004 0.075 5525 Dihedral : 17.682 149.553 5734 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.75 % Favored : 92.17 % Rotamer: Outliers : 3.57 % Allowed : 22.76 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3805 helix: 0.51 (0.14), residues: 1469 sheet: -1.50 (0.26), residues: 375 loop : -1.73 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J1020 HIS 0.005 0.001 HIS I1023 PHE 0.021 0.001 PHE I 545 TYR 0.016 0.001 TYR L 228 ARG 0.007 0.000 ARG J 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 368 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7418 (m-80) REVERT: G 137 ASN cc_start: 0.6253 (p0) cc_final: 0.6007 (p0) REVERT: H 58 GLU cc_start: 0.5956 (tm-30) cc_final: 0.5558 (tt0) REVERT: I 36 GLN cc_start: 0.8271 (tp40) cc_final: 0.8063 (tp40) REVERT: I 119 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6658 (tt0) REVERT: I 340 ASP cc_start: 0.6665 (OUTLIER) cc_final: 0.6040 (p0) REVERT: I 412 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6860 (mm-30) REVERT: I 486 THR cc_start: 0.6909 (p) cc_final: 0.6420 (m) REVERT: I 741 MET cc_start: 0.7613 (ttp) cc_final: 0.7295 (ttp) REVERT: I 742 TYR cc_start: 0.5178 (m-80) cc_final: 0.4695 (m-80) REVERT: I 1024 GLU cc_start: 0.7738 (pp20) cc_final: 0.7025 (mm-30) REVERT: I 1066 MET cc_start: 0.7937 (mtp) cc_final: 0.7594 (mtp) REVERT: I 1131 MET cc_start: 0.8013 (ttm) cc_final: 0.6986 (mtp) REVERT: I 1137 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.6212 (mp0) REVERT: I 1248 THR cc_start: 0.8375 (m) cc_final: 0.8152 (p) REVERT: I 1331 ARG cc_start: 0.8377 (ttm170) cc_final: 0.7878 (mtm180) REVERT: J 53 ARG cc_start: 0.7715 (ppt170) cc_final: 0.7186 (mtp180) REVERT: J 130 MET cc_start: 0.7029 (ptm) cc_final: 0.6738 (ptm) REVERT: J 372 MET cc_start: 0.8709 (ttp) cc_final: 0.8449 (ttp) REVERT: J 555 TYR cc_start: 0.8192 (m-10) cc_final: 0.7715 (m-80) REVERT: J 567 THR cc_start: 0.8636 (m) cc_final: 0.8146 (p) REVERT: J 772 TYR cc_start: 0.8593 (t80) cc_final: 0.8331 (t80) REVERT: J 785 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.7993 (m-30) REVERT: J 895 CYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8498 (p) REVERT: J 918 ILE cc_start: 0.8854 (pt) cc_final: 0.8253 (mt) REVERT: J 1040 MET cc_start: 0.5048 (mtp) cc_final: 0.4636 (ptp) REVERT: J 1078 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6129 (mt) REVERT: J 1132 LYS cc_start: 0.4315 (OUTLIER) cc_final: 0.3869 (mmtt) REVERT: J 1282 TYR cc_start: 0.8387 (t80) cc_final: 0.8069 (t80) REVERT: J 1328 THR cc_start: 0.8827 (p) cc_final: 0.8505 (m) REVERT: J 1349 GLU cc_start: 0.7701 (mp0) cc_final: 0.7041 (mt-10) REVERT: K 55 GLU cc_start: 0.6598 (pp20) cc_final: 0.6280 (pp20) REVERT: K 56 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7578 (mm-30) REVERT: L 105 MET cc_start: 0.8420 (ppp) cc_final: 0.8137 (ppp) REVERT: L 390 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8433 (tp) REVERT: L 425 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.6227 (m-80) REVERT: N 4 GLU cc_start: 0.6933 (mp0) cc_final: 0.6508 (mt-10) REVERT: N 32 ILE cc_start: 0.3623 (OUTLIER) cc_final: 0.3245 (tp) REVERT: N 65 GLN cc_start: 0.6730 (tt0) cc_final: 0.6481 (tp-100) REVERT: N 66 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7330 (pt0) outliers start: 117 outliers final: 90 residues processed: 455 average time/residue: 0.4216 time to fit residues: 314.7448 Evaluate side-chains 456 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 355 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 733 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 40 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 342 optimal weight: 5.9990 chunk 361 optimal weight: 9.9990 chunk 329 optimal weight: 0.4980 chunk 351 optimal weight: 6.9990 chunk 360 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 275 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 317 optimal weight: 6.9990 chunk 332 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33445 Z= 0.217 Angle : 0.608 11.525 45709 Z= 0.315 Chirality : 0.042 0.211 5224 Planarity : 0.004 0.071 5525 Dihedral : 17.557 147.862 5734 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.60 % Favored : 92.30 % Rotamer: Outliers : 3.51 % Allowed : 23.13 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.14), residues: 3805 helix: 0.52 (0.14), residues: 1478 sheet: -1.44 (0.26), residues: 374 loop : -1.72 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 807 HIS 0.004 0.001 HIS I1023 PHE 0.018 0.001 PHE I 545 TYR 0.015 0.001 TYR J 679 ARG 0.007 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 372 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: H 58 GLU cc_start: 0.5984 (tm-30) cc_final: 0.5546 (tt0) REVERT: I 36 GLN cc_start: 0.8261 (tp40) cc_final: 0.8040 (tp40) REVERT: I 119 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6645 (tt0) REVERT: I 340 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6023 (p0) REVERT: I 412 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6917 (mm-30) REVERT: I 445 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6935 (pt) REVERT: I 486 THR cc_start: 0.6814 (p) cc_final: 0.6381 (m) REVERT: I 681 MET cc_start: 0.8006 (mmt) cc_final: 0.7748 (mmt) REVERT: I 704 MET cc_start: 0.8085 (mmm) cc_final: 0.7814 (tpp) REVERT: I 741 MET cc_start: 0.7668 (ttp) cc_final: 0.7149 (ttp) REVERT: I 742 TYR cc_start: 0.5120 (m-80) cc_final: 0.4482 (m-80) REVERT: I 760 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.7725 (t0) REVERT: I 974 ARG cc_start: 0.7354 (mmp80) cc_final: 0.6913 (mmp-170) REVERT: I 1024 GLU cc_start: 0.7801 (pp20) cc_final: 0.7092 (mm-30) REVERT: I 1025 PHE cc_start: 0.7670 (t80) cc_final: 0.7359 (t80) REVERT: I 1066 MET cc_start: 0.7921 (mtp) cc_final: 0.7561 (mtp) REVERT: I 1131 MET cc_start: 0.7950 (ttm) cc_final: 0.6982 (mtp) REVERT: I 1137 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6195 (mp0) REVERT: I 1248 THR cc_start: 0.8354 (m) cc_final: 0.8151 (p) REVERT: I 1331 ARG cc_start: 0.8386 (ttm170) cc_final: 0.7888 (mtm180) REVERT: J 53 ARG cc_start: 0.7816 (ppt170) cc_final: 0.7156 (mtp180) REVERT: J 372 MET cc_start: 0.8636 (ttp) cc_final: 0.8342 (ttp) REVERT: J 555 TYR cc_start: 0.8181 (m-10) cc_final: 0.7710 (m-80) REVERT: J 567 THR cc_start: 0.8626 (m) cc_final: 0.8129 (p) REVERT: J 772 TYR cc_start: 0.8604 (t80) cc_final: 0.8341 (t80) REVERT: J 785 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: J 895 CYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8504 (p) REVERT: J 918 ILE cc_start: 0.8856 (pt) cc_final: 0.8234 (mt) REVERT: J 1040 MET cc_start: 0.5040 (mtp) cc_final: 0.4730 (ptp) REVERT: J 1078 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6132 (mt) REVERT: J 1132 LYS cc_start: 0.4414 (OUTLIER) cc_final: 0.3997 (mmtt) REVERT: J 1282 TYR cc_start: 0.8405 (t80) cc_final: 0.8098 (t80) REVERT: J 1328 THR cc_start: 0.8833 (p) cc_final: 0.8506 (m) REVERT: J 1349 GLU cc_start: 0.7608 (mp0) cc_final: 0.7061 (mt-10) REVERT: J 1368 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.5975 (m-30) REVERT: L 105 MET cc_start: 0.8429 (ppp) cc_final: 0.8144 (ppp) REVERT: L 167 ASP cc_start: 0.2985 (OUTLIER) cc_final: 0.2423 (t0) REVERT: L 302 PHE cc_start: -0.2804 (t80) cc_final: -0.3149 (t80) REVERT: L 329 LYS cc_start: 0.5743 (mtpt) cc_final: 0.4706 (mmtp) REVERT: L 390 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8420 (tp) REVERT: L 425 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.6230 (m-80) REVERT: M 316 MET cc_start: 0.3056 (tpt) cc_final: 0.1838 (tmm) REVERT: N 4 GLU cc_start: 0.6926 (mp0) cc_final: 0.6524 (mt-10) REVERT: N 32 ILE cc_start: 0.3551 (OUTLIER) cc_final: 0.3122 (tp) REVERT: N 65 GLN cc_start: 0.6813 (tt0) cc_final: 0.6485 (tp-100) REVERT: N 66 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7349 (pt0) outliers start: 115 outliers final: 88 residues processed: 455 average time/residue: 0.4120 time to fit residues: 306.4354 Evaluate side-chains 457 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 354 time to evaluate : 3.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 760 ASN Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 252 ILE Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 40 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 349 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 371 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 258 optimal weight: 6.9990 chunk 389 optimal weight: 10.0000 chunk 358 optimal weight: 8.9990 chunk 310 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33445 Z= 0.250 Angle : 0.634 12.381 45709 Z= 0.327 Chirality : 0.042 0.234 5224 Planarity : 0.004 0.074 5525 Dihedral : 17.570 146.759 5734 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.83 % Favored : 92.06 % Rotamer: Outliers : 3.33 % Allowed : 23.19 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3805 helix: 0.51 (0.14), residues: 1475 sheet: -1.48 (0.26), residues: 381 loop : -1.66 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 326 HIS 0.005 0.001 HIS J 430 PHE 0.016 0.001 PHE I 545 TYR 0.018 0.001 TYR L 228 ARG 0.008 0.000 ARG N 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 360 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: H 58 GLU cc_start: 0.5865 (tm-30) cc_final: 0.5461 (tt0) REVERT: I 119 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6683 (tt0) REVERT: I 340 ASP cc_start: 0.6669 (OUTLIER) cc_final: 0.6033 (p0) REVERT: I 445 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6987 (pt) REVERT: I 486 THR cc_start: 0.6854 (p) cc_final: 0.6343 (m) REVERT: I 681 MET cc_start: 0.8020 (mmt) cc_final: 0.7784 (mmt) REVERT: I 741 MET cc_start: 0.7676 (ttp) cc_final: 0.7143 (ttp) REVERT: I 742 TYR cc_start: 0.5254 (m-80) cc_final: 0.4612 (m-80) REVERT: I 974 ARG cc_start: 0.7294 (mmp80) cc_final: 0.6837 (mmp-170) REVERT: I 1024 GLU cc_start: 0.7937 (pp20) cc_final: 0.7166 (mm-30) REVERT: I 1025 PHE cc_start: 0.7716 (t80) cc_final: 0.7377 (t80) REVERT: I 1066 MET cc_start: 0.7962 (mtp) cc_final: 0.7621 (mtp) REVERT: I 1131 MET cc_start: 0.8008 (ttm) cc_final: 0.7051 (mtp) REVERT: I 1137 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: I 1248 THR cc_start: 0.8426 (m) cc_final: 0.8219 (p) REVERT: I 1319 MET cc_start: 0.6998 (tpp) cc_final: 0.6695 (tpp) REVERT: I 1331 ARG cc_start: 0.8400 (ttm170) cc_final: 0.7887 (mtm180) REVERT: J 134 ASP cc_start: 0.6509 (m-30) cc_final: 0.6279 (t0) REVERT: J 555 TYR cc_start: 0.8185 (m-10) cc_final: 0.7721 (m-80) REVERT: J 567 THR cc_start: 0.8638 (m) cc_final: 0.8133 (p) REVERT: J 785 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7380 (m-30) REVERT: J 895 CYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8518 (p) REVERT: J 918 ILE cc_start: 0.8876 (pt) cc_final: 0.8259 (mt) REVERT: J 1040 MET cc_start: 0.5086 (mtp) cc_final: 0.4785 (ptp) REVERT: J 1078 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6236 (mt) REVERT: J 1132 LYS cc_start: 0.4418 (OUTLIER) cc_final: 0.3998 (mmtt) REVERT: J 1282 TYR cc_start: 0.8449 (t80) cc_final: 0.8135 (t80) REVERT: J 1328 THR cc_start: 0.8886 (p) cc_final: 0.8521 (m) REVERT: J 1349 GLU cc_start: 0.7631 (mp0) cc_final: 0.7146 (mt-10) REVERT: J 1368 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.5976 (m-30) REVERT: L 105 MET cc_start: 0.8421 (ppp) cc_final: 0.8123 (ppp) REVERT: L 167 ASP cc_start: 0.2802 (OUTLIER) cc_final: 0.2281 (t0) REVERT: L 329 LYS cc_start: 0.5854 (mtpt) cc_final: 0.4801 (mmtp) REVERT: L 390 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8354 (tp) REVERT: L 425 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.6276 (m-80) REVERT: L 489 MET cc_start: 0.6670 (mmm) cc_final: 0.6439 (mmt) REVERT: M 316 MET cc_start: 0.2768 (tpt) cc_final: 0.1637 (tmm) REVERT: N 4 GLU cc_start: 0.6839 (mp0) cc_final: 0.6438 (mt-10) REVERT: N 32 ILE cc_start: 0.3624 (OUTLIER) cc_final: 0.3285 (tp) REVERT: N 65 GLN cc_start: 0.6726 (tt0) cc_final: 0.6490 (tp-100) REVERT: N 66 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7405 (pt0) outliers start: 109 outliers final: 90 residues processed: 442 average time/residue: 0.4182 time to fit residues: 302.3931 Evaluate side-chains 450 residues out of total 3283 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 346 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 863 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 252 ILE Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 40 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 190 optimal weight: 0.6980 chunk 246 optimal weight: 0.0970 chunk 330 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 286 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 310 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 319 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 HIS ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.152297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116075 restraints weight = 56029.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117096 restraints weight = 52289.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117304 restraints weight = 38991.453| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33445 Z= 0.214 Angle : 0.620 15.316 45709 Z= 0.320 Chirality : 0.042 0.270 5224 Planarity : 0.004 0.072 5525 Dihedral : 17.494 146.836 5734 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.49 % Favored : 92.40 % Rotamer: Outliers : 3.36 % Allowed : 23.25 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3805 helix: 0.56 (0.14), residues: 1474 sheet: -1.42 (0.26), residues: 385 loop : -1.67 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 326 HIS 0.005 0.001 HIS I1023 PHE 0.019 0.001 PHE I 545 TYR 0.015 0.001 TYR J 679 ARG 0.008 0.000 ARG N 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6885.13 seconds wall clock time: 125 minutes 0.46 seconds (7500.46 seconds total)