Starting phenix.real_space_refine on Thu Feb 22 00:33:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psv_20465/02_2024/6psv_20465_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psv_20465/02_2024/6psv_20465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psv_20465/02_2024/6psv_20465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psv_20465/02_2024/6psv_20465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psv_20465/02_2024/6psv_20465_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psv_20465/02_2024/6psv_20465_trim_updated.pdb" } resolution = 3.5 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= 0.007 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 105 5.49 5 Mg 1 5.21 5 S 136 5.16 5 C 19976 2.51 5 N 5696 2.21 5 O 6414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N GLU 4": "OE1" <-> "OE2" Residue "N GLU 13": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 62": "OD1" <-> "OD2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G ASP 118": "OD1" <-> "OD2" Residue "G GLU 204": "OE1" <-> "OE2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H ASP 135": "OD1" <-> "OD2" Residue "H TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 197": "OD1" <-> "OD2" Residue "H GLU 215": "OE1" <-> "OE2" Residue "I ARG 18": "NH1" <-> "NH2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 116": "OD1" <-> "OD2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I ASP 132": "OD1" <-> "OD2" Residue "I ASP 160": "OD1" <-> "OD2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 234": "OD1" <-> "OD2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 278": "OE1" <-> "OE2" Residue "I ASP 280": "OD1" <-> "OD2" Residue "I ASP 281": "OD1" <-> "OD2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I GLU 334": "OE1" <-> "OE2" Residue "I ASP 340": "OD1" <-> "OD2" Residue "I ASP 354": "OD1" <-> "OD2" Residue "I TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 374": "OE1" <-> "OE2" Residue "I PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 393": "OD1" <-> "OD2" Residue "I ASP 396": "OD1" <-> "OD2" Residue "I PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 424": "OD1" <-> "OD2" Residue "I ASP 434": "OD1" <-> "OD2" Residue "I ASP 443": "OD1" <-> "OD2" Residue "I GLU 477": "OE1" <-> "OE2" Residue "I ASP 483": "OD1" <-> "OD2" Residue "I TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 601": "OD1" <-> "OD2" Residue "I ASP 632": "OD1" <-> "OD2" Residue "I ASP 696": "OD1" <-> "OD2" Residue "I TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 785": "OD1" <-> "OD2" Residue "I ASP 814": "OD1" <-> "OD2" Residue "I GLU 849": "OE1" <-> "OE2" Residue "I ASP 881": "OD1" <-> "OD2" Residue "I GLU 892": "OE1" <-> "OE2" Residue "I GLU 899": "OE1" <-> "OE2" Residue "I GLU 1006": "OE1" <-> "OE2" Residue "I GLU 1012": "OE1" <-> "OE2" Residue "I GLU 1016": "OE1" <-> "OE2" Residue "I GLU 1020": "OE1" <-> "OE2" Residue "I ASP 1040": "OD1" <-> "OD2" Residue "I ASP 1041": "OD1" <-> "OD2" Residue "I ASP 1154": "OD1" <-> "OD2" Residue "I ASP 1160": "OD1" <-> "OD2" Residue "I GLU 1167": "OE1" <-> "OE2" Residue "I ASP 1188": "OD1" <-> "OD2" Residue "I TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1316": "OE1" <-> "OE2" Residue "J PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ASP 129": "OD1" <-> "OD2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J ASP 167": "OD1" <-> "OD2" Residue "J GLU 203": "OE1" <-> "OE2" Residue "J GLU 225": "OE1" <-> "OE2" Residue "J PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 248": "OD1" <-> "OD2" Residue "J ASP 284": "OD1" <-> "OD2" Residue "J GLU 301": "OE1" <-> "OE2" Residue "J ASP 304": "OD1" <-> "OD2" Residue "J PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 402": "OE1" <-> "OE2" Residue "J GLU 443": "OE1" <-> "OE2" Residue "J GLU 532": "OE1" <-> "OE2" Residue "J TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 558": "OD1" <-> "OD2" Residue "J TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 622": "OD1" <-> "OD2" Residue "J TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 660": "OE1" <-> "OE2" Residue "J ASP 691": "OD1" <-> "OD2" Residue "J ASP 699": "OD1" <-> "OD2" Residue "J GLU 704": "OE1" <-> "OE2" Residue "J ASP 710": "OD1" <-> "OD2" Residue "J PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 785": "OD1" <-> "OD2" Residue "J ARG 799": "NH1" <-> "NH2" Residue "J ASP 802": "OD1" <-> "OD2" Residue "J ASP 806": "OD1" <-> "OD2" Residue "J GLU 811": "OE1" <-> "OE2" Residue "J ASP 870": "OD1" <-> "OD2" Residue "J GLU 874": "OE1" <-> "OE2" Residue "J ASP 878": "OD1" <-> "OD2" Residue "J GLU 913": "OE1" <-> "OE2" Residue "J PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 1007": "OD1" <-> "OD2" Residue "J ASP 1021": "OD1" <-> "OD2" Residue "J ASP 1039": "OD1" <-> "OD2" Residue "J ASP 1042": "OD1" <-> "OD2" Residue "J ASP 1051": "OD1" <-> "OD2" Residue "J GLU 1052": "OE1" <-> "OE2" Residue "J ASP 1063": "OD1" <-> "OD2" Residue "J GLU 1066": "OE1" <-> "OE2" Residue "J ASP 1073": "OD1" <-> "OD2" Residue "J PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 1111": "OD1" <-> "OD2" Residue "J ASP 1133": "OD1" <-> "OD2" Residue "J ASP 1143": "OD1" <-> "OD2" Residue "J ASP 1212": "OD1" <-> "OD2" Residue "J GLU 1276": "OE1" <-> "OE2" Residue "J GLU 1293": "OE1" <-> "OE2" Residue "J TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 1305": "OD1" <-> "OD2" Residue "J GLU 1317": "OE1" <-> "OE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K GLU 41": "OE1" <-> "OE2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K ASP 65": "OD1" <-> "OD2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "K GLU 74": "OE1" <-> "OE2" Residue "L GLU 124": "OE1" <-> "OE2" Residue "L GLU 154": "OE1" <-> "OE2" Residue "L ASP 213": "OD1" <-> "OD2" Residue "L GLU 215": "OE1" <-> "OE2" Residue "L TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 267": "OD1" <-> "OD2" Residue "L TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 332": "OD1" <-> "OD2" Residue "L GLU 335": "OE1" <-> "OE2" Residue "L GLU 349": "OE1" <-> "OE2" Residue "L GLU 381": "OE1" <-> "OE2" Residue "L ASP 417": "OD1" <-> "OD2" Residue "L ASP 445": "OD1" <-> "OD2" Residue "L GLU 485": "OE1" <-> "OE2" Residue "L GLU 491": "OE1" <-> "OE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "L ASP 525": "OD1" <-> "OD2" Residue "L ASP 546": "OD1" <-> "OD2" Residue "L GLU 591": "OE1" <-> "OE2" Residue "L GLU 605": "OE1" <-> "OE2" Residue "M GLU 261": "OE1" <-> "OE2" Residue "M ASP 280": "OD1" <-> "OD2" Residue "M GLU 302": "OE1" <-> "OE2" Residue "M ASP 305": "OD1" <-> "OD2" Residue "M GLU 319": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32331 Number of models: 1 Model: "" Number of chains: 14 Chain: "N" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain: "G" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1761 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 218} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1664 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 10564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10564 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} 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: 10466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 10466 Classifications: {'peptide': 1345} Link IDs: {'CIS': 2, 'PTRANS': 55, 'TRANS': 1287} Chain breaks: 2 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: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3846 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "O" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1128 Classifications: {'DNA': 55} Link IDs: {'rna3p': 54} Chain breaks: 1 Chain: "P" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1020 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain breaks: 1 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "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: "L" 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 281 SG CYS N 37 50.579 54.739 30.098 1.00 53.11 S ATOM 438 SG CYS N 58 51.962 57.203 27.800 1.00 40.93 S ATOM 460 SG CYS N 61 49.500 57.964 30.426 1.00 43.50 S ATOM 15009 SG CYS J 70 77.842 102.200 115.823 1.00 35.44 S ATOM 15023 SG CYS J 72 75.881 105.102 115.833 1.00 36.70 S ATOM 15131 SG CYS J 85 75.065 102.412 118.264 1.00 38.52 S ATOM 15155 SG CYS J 88 73.565 102.763 114.576 1.00 37.51 S ATOM 20843 SG CYS J 814 70.542 40.018 89.557 1.00 26.84 S ATOM 21408 SG CYS J 888 70.378 43.955 88.327 1.00 18.79 S ATOM 21459 SG CYS J 895 73.507 41.742 89.304 1.00 14.85 S ATOM 21480 SG CYS J 898 71.647 40.496 86.308 1.00 16.21 S Time building chain proxies: 16.77, per 1000 atoms: 0.52 Number of scatterers: 32331 At special positions: 0 Unit cell: (159.9, 154.7, 169, 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 105 15.00 Mg 1 11.99 O 6414 8.00 N 5696 7.00 C 19976 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.88 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 61 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 58 " Number of angles added : 12 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 131 helices and 34 sheets defined 36.3% alpha, 8.5% beta 48 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 16.33 Creating SS restraints... Processing helix chain 'N' and resid 4 through 25 removed outlier: 3.512A pdb=" N SER N 10 " --> pdb=" O ASP N 6 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 51 Processing helix chain 'N' and resid 59 through 70 Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 82 through 86 Processing helix chain 'G' and resid 155 through 158 No H-bonds generated for 'chain 'G' and resid 155 through 158' Processing helix chain 'G' and resid 213 through 233 removed outlier: 4.020A pdb=" N GLN G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 78 through 86 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 230 removed outlier: 3.575A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 7 No H-bonds generated for 'chain 'I' and resid 5 through 7' Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 83 through 88 Processing helix chain 'I' and resid 206 through 212 removed outlier: 3.615A pdb=" N ILE I 209 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 Processing helix chain 'I' and resid 271 through 279 Processing helix chain 'I' and resid 289 through 294 removed outlier: 5.805A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 326 Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 390 removed outlier: 3.596A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 removed outlier: 4.255A pdb=" N ILE I 426 " --> pdb=" O LYS I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 480 removed outlier: 4.153A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 507 Processing helix chain 'I' and resid 521 through 524 No H-bonds generated for 'chain 'I' and resid 521 through 524' Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 608 through 613 removed outlier: 3.720A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 613' 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 676 through 688 removed outlier: 3.832A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) removed outlier: 4.885A 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 738 through 740 No H-bonds generated for 'chain 'I' and resid 738 through 740' 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 859 through 862 Processing helix chain 'I' and resid 897 through 905 Processing helix chain 'I' and resid 943 through 980 removed outlier: 4.272A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU I 967 " --> pdb=" O GLU I 963 " (cutoff:3.500A) Processing helix chain 'I' and resid 994 through 997 Processing helix chain 'I' and resid 1007 through 1036 Processing helix chain 'I' and resid 1101 through 1105 removed outlier: 4.244A 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 1110 through 1129 Processing helix chain 'I' and resid 1139 through 1150 removed outlier: 3.843A pdb=" N GLU I1143 " --> pdb=" O ALA I1139 " (cutoff:3.500A) Processing helix chain 'I' and resid 1166 through 1175 removed outlier: 3.721A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1186 through 1188 No H-bonds generated for 'chain 'I' and resid 1186 through 1188' 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 1273 through 1280 removed outlier: 4.207A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1298 through 1309 removed outlier: 3.504A pdb=" N TYR I1305 " --> pdb=" O ARG I1301 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS I1306 " --> pdb=" O THR I1302 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1332 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 59 through 62 No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'J' and resid 123 through 128 removed outlier: 3.582A pdb=" N LEU J 128 " --> pdb=" O ILE J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.518A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 207 Processing helix chain 'J' and resid 213 through 229 Processing helix chain 'J' and resid 234 through 237 removed outlier: 3.541A pdb=" N MET J 237 " --> pdb=" O PRO J 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 234 through 237' Processing helix chain 'J' and resid 265 through 285 Processing helix chain 'J' and resid 289 through 307 removed outlier: 3.642A pdb=" N GLU J 301 " --> pdb=" O ARG J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 341 Processing helix chain 'J' and resid 370 through 376 removed outlier: 3.648A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) 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: 3.826A pdb=" N ASP J 413 " --> pdb=" O TRP J 409 " (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 454 through 457 No H-bonds generated for 'chain 'J' and resid 454 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 513 Processing helix chain 'J' and resid 530 through 539 Processing helix chain 'J' and resid 574 through 582 removed outlier: 3.851A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ILE J 582 " --> pdb=" O ILE J 578 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 591 No H-bonds generated for 'chain 'J' and resid 589 through 591' Processing helix chain 'J' and resid 598 through 612 Processing helix chain 'J' and resid 615 through 633 removed outlier: 4.359A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET J 625 " --> pdb=" O ALA J 621 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY J 628 " --> pdb=" O ILE J 624 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 675 through 702 Processing helix chain 'J' and resid 721 through 727 removed outlier: 3.706A pdb=" N ALA J 726 " --> pdb=" O ILE J 722 " (cutoff:3.500A) Processing helix chain 'J' and resid 769 through 803 removed outlier: 3.503A pdb=" N SER J 775 " --> pdb=" O GLN J 771 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 783 " --> pdb=" O ALA J 779 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER J 793 " --> pdb=" O LYS J 789 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY J 794 " --> pdb=" O THR J 790 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG J 798 " --> pdb=" O GLY J 794 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 839 Processing helix chain 'J' and resid 866 through 875 removed outlier: 3.831A 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 924 Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1139 through 1145 Processing helix chain 'J' and resid 1217 through 1223 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 3.820A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN J1235 " --> pdb=" O ARG J1231 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1251 through 1260 removed outlier: 3.568A pdb=" N VAL J1255 " --> pdb=" O LYS J1251 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN J1259 " --> pdb=" O VAL J1255 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 removed outlier: 3.754A pdb=" N ASN J1289 " --> pdb=" O VAL J1285 " (cutoff:3.500A) Processing helix chain 'J' and resid 1311 through 1314 No H-bonds generated for 'chain 'J' and resid 1311 through 1314' Processing helix chain 'J' and resid 1320 through 1323 No H-bonds generated for 'chain 'J' and resid 1320 through 1323' Processing helix chain 'J' and resid 1328 through 1337 removed outlier: 3.630A pdb=" N ALA J1335 " --> pdb=" O VAL J1331 " (cutoff:3.500A) removed outlier: 3.627A 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 1372 removed outlier: 4.544A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 12 No H-bonds generated for 'chain 'K' and resid 9 through 12' Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 55 Processing helix chain 'K' and resid 62 through 77 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 152 Processing helix chain 'L' and resid 158 through 160 No H-bonds generated for 'chain 'L' and resid 158 through 160' Processing helix chain 'L' and resid 214 through 234 removed outlier: 3.770A pdb=" N ASP L 233 " --> pdb=" O VAL L 229 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR L 234 " --> pdb=" O VAL L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 258 removed outlier: 3.801A pdb=" N GLN L 258 " --> pdb=" O GLU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 288 Processing helix chain 'L' and resid 299 through 306 Processing helix chain 'L' and resid 327 through 329 No H-bonds generated for 'chain 'L' and resid 327 through 329' Processing helix chain 'L' and resid 334 through 351 Processing helix chain 'L' and resid 355 through 391 removed outlier: 5.183A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 417 removed outlier: 4.033A pdb=" N ASP L 417 " --> pdb=" O MET L 413 " (cutoff:3.500A) Processing helix chain 'L' and resid 421 through 423 No H-bonds generated for 'chain 'L' and resid 421 through 423' Processing helix chain 'L' and resid 427 through 445 removed outlier: 4.272A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 474 removed outlier: 3.579A pdb=" N ARG L 468 " --> pdb=" O ASN L 464 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN L 469 " --> pdb=" O ARG L 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 480 through 486 Processing helix chain 'L' and resid 493 through 500 Processing helix chain 'L' and resid 519 through 522 removed outlier: 3.639A pdb=" N PHE L 522 " --> pdb=" O LEU L 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 519 through 522' Processing helix chain 'L' and resid 531 through 550 removed outlier: 3.508A pdb=" N ALA L 535 " --> pdb=" O PRO L 531 " (cutoff:3.500A) removed outlier: 3.722A 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 removed outlier: 4.606A pdb=" N GLN L 579 " --> pdb=" O GLU L 575 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 599 removed outlier: 3.590A pdb=" N LYS L 593 " --> pdb=" O GLN L 589 " (cutoff:3.500A) Processing helix chain 'L' and resid 605 through 610 Processing helix chain 'M' and resid 251 through 253 No H-bonds generated for 'chain 'M' and resid 251 through 253' Processing helix chain 'M' and resid 264 through 273 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 308 Processing sheet with id= A, first strand: chain 'G' and resid 23 through 28 Processing sheet with id= B, first strand: chain 'G' and resid 97 through 104 Processing sheet with id= C, first strand: chain 'G' and resid 108 through 111 Processing sheet with id= D, first strand: chain 'H' and resid 23 through 28 removed outlier: 3.646A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.025A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 188 through 190 Processing sheet with id= G, first strand: chain 'H' and resid 109 through 111 Processing sheet with id= H, first strand: chain 'I' and resid 66 through 69 removed outlier: 3.552A pdb=" N ILE I 104 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 72 through 75 removed outlier: 3.847A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= K, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= L, first strand: chain 'I' and resid 148 through 151 Processing sheet with id= M, first strand: chain 'I' and resid 154 through 158 Processing sheet with id= N, first strand: chain 'I' and resid 227 through 231 Processing sheet with id= O, first strand: chain 'I' and resid 238 through 240 Processing sheet with id= P, first strand: chain 'I' and resid 603 through 606 Processing sheet with id= Q, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= R, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.099A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 798 through 804 removed outlier: 4.299A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 931 through 935 removed outlier: 6.516A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 1065 through 1067 removed outlier: 4.409A pdb=" N LYS I1065 " --> pdb=" O LEU I1235 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.967A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.549A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 103 through 106 Processing sheet with id= Y, first strand: chain 'J' and resid 252 through 254 Processing sheet with id= Z, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= AA, first strand: chain 'J' and resid 547 through 556 Processing sheet with id= AB, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.856A pdb=" N SER J 961 " --> pdb=" O GLU J 981 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AD, first strand: chain 'J' and resid 1047 through 1050 removed outlier: 3.686A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 1077 through 1079 Processing sheet with id= AF, first strand: chain 'J' and resid 1105 through 1107 Processing sheet with id= AG, first strand: chain 'J' and resid 1162 through 1165 removed outlier: 3.922A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 1279 through 1281 988 hydrogen bonds defined for protein. 2880 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 15.08 Time building geometry restraints manager: 14.91 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: 10526 1.34 - 1.46: 7293 1.46 - 1.59: 14750 1.59 - 1.71: 222 1.71 - 1.84: 244 Bond restraints: 33035 Sorted by residual: bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.838 -0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.837 -0.305 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.830 -0.298 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C19 1N7 N 102 " pdb=" C3 1N7 N 102 " 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 L 701 " pdb=" C4 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.731 -0.199 2.00e-02 2.50e+03 9.94e+01 ... (remaining 33030 not shown) Histogram of bond angle deviations from ideal: 97.15 - 104.54: 878 104.54 - 111.92: 16454 111.92 - 119.31: 11469 119.31 - 126.70: 15713 126.70 - 134.09: 567 Bond angle restraints: 45081 Sorted by residual: angle pdb=" N ASP I 516 " pdb=" CA ASP I 516 " pdb=" C ASP I 516 " ideal model delta sigma weight residual 109.96 99.93 10.03 1.50e+00 4.44e-01 4.47e+01 angle pdb=" C ILE I1096 " pdb=" N VAL I1097 " pdb=" CA VAL I1097 " ideal model delta sigma weight residual 122.96 117.39 5.57 9.50e-01 1.11e+00 3.44e+01 angle pdb=" C GLN H 194 " pdb=" N ARG H 195 " pdb=" CA ARG H 195 " ideal model delta sigma weight residual 121.70 131.55 -9.85 1.80e+00 3.09e-01 2.99e+01 angle pdb=" N GLY I 449 " pdb=" CA GLY I 449 " pdb=" C GLY I 449 " ideal model delta sigma weight residual 115.61 106.36 9.25 1.74e+00 3.30e-01 2.83e+01 angle pdb=" N VAL I1275 " pdb=" CA VAL I1275 " pdb=" C VAL I1275 " ideal model delta sigma weight residual 111.81 107.30 4.51 8.60e-01 1.35e+00 2.75e+01 ... (remaining 45076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.47: 17919 25.47 - 50.94: 2001 50.94 - 76.42: 363 76.42 - 101.89: 32 101.89 - 127.36: 4 Dihedral angle restraints: 20319 sinusoidal: 9285 harmonic: 11034 Sorted by residual: dihedral pdb=" CA LEU L 110 " pdb=" C LEU L 110 " pdb=" N LEU L 111 " pdb=" CA LEU L 111 " ideal model delta harmonic sigma weight residual 180.00 137.35 42.65 0 5.00e+00 4.00e-02 7.28e+01 dihedral pdb=" CA ARG H 12 " pdb=" C ARG H 12 " pdb=" N LEU H 13 " pdb=" CA LEU H 13 " ideal model delta harmonic sigma weight residual 0.00 38.96 -38.96 0 5.00e+00 4.00e-02 6.07e+01 dihedral pdb=" CA ASP I 81 " pdb=" C ASP I 81 " pdb=" N VAL I 82 " pdb=" CA VAL I 82 " ideal model delta harmonic sigma weight residual -180.00 -145.07 -34.93 0 5.00e+00 4.00e-02 4.88e+01 ... (remaining 20316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3870 0.056 - 0.111: 1110 0.111 - 0.167: 166 0.167 - 0.223: 14 0.223 - 0.279: 8 Chirality restraints: 5168 Sorted by residual: chirality pdb=" C19 1N7 N 102 " pdb=" C18 1N7 N 102 " pdb=" C2 1N7 N 102 " pdb=" C3 1N7 N 102 " both_signs ideal model delta sigma weight residual False -2.53 -2.81 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C15 1N7 J1504 " pdb=" C14 1N7 J1504 " pdb=" C16 1N7 J1504 " pdb=" C2 1N7 J1504 " both_signs ideal model delta sigma weight residual False -2.47 -2.74 0.27 2.00e-01 2.50e+01 1.80e+00 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 -2.79 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 5165 not shown) Planarity restraints: 5502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL I1103 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO I1104 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO I1104 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I1104 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 519 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO I 520 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO I 520 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO I 520 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 368 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO J 369 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO J 369 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 369 " -0.033 5.00e-02 4.00e+02 ... (remaining 5499 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 319 2.55 - 3.14: 28167 3.14 - 3.72: 50795 3.72 - 4.31: 72859 4.31 - 4.90: 117637 Nonbonded interactions: 269777 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 1.959 2.170 nonbonded pdb=" OH TYR I 301 " pdb=" O ARG I 332 " model vdw 2.019 2.440 nonbonded pdb=" O TRP J 115 " pdb=" OG SER J 119 " model vdw 2.054 2.440 nonbonded pdb=" OG1 THR M 263 " pdb=" OE1 GLU M 302 " model vdw 2.060 2.440 nonbonded pdb=" O LYS I 593 " pdb=" OG1 THR I 600 " model vdw 2.081 2.440 ... (remaining 269772 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 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 11 or (resid 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 94 or (resid 95 and (name N or name CA or name \ C or name O or name CB )) or resid 96 or (resid 97 and (name N or name CA or na \ me C or name O or name CB )) or resid 98 through 158 or resid 171 through 233 or \ (resid 234 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 7 through 228 or (resid 229 through 230 and (name N or nam \ e CA or name C or name O or name CB )) or resid 231 through 232 or (resid 233 th \ rough 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: 3.460 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: 0.000 Extract box with map and model: 6.530 Check model and map are aligned: 0.510 Set scattering table: 0.320 Process input model: 103.280 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 0.011 0.306 33035 Z= 0.689 Angle : 1.001 12.978 45081 Z= 0.567 Chirality : 0.052 0.279 5168 Planarity : 0.005 0.075 5502 Dihedral : 20.031 127.359 13203 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 40.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.12 % Favored : 88.75 % Rotamer: Outliers : 11.23 % Allowed : 21.05 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.43 (0.11), residues: 3804 helix: -2.46 (0.10), residues: 1508 sheet: -3.54 (0.20), residues: 436 loop : -3.20 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 434 HIS 0.011 0.002 HIS J 777 PHE 0.025 0.003 PHE H 35 TYR 0.030 0.003 TYR I 605 ARG 0.008 0.001 ARG J 610 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 367 poor density : 530 time to evaluate : 3.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 65 GLN cc_start: 0.8389 (tp40) cc_final: 0.7247 (tm-30) REVERT: G 85 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8552 (mt) REVERT: H 16 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8292 (tt) REVERT: H 23 HIS cc_start: 0.7715 (t-90) cc_final: 0.7344 (t-170) REVERT: H 123 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8298 (mm) REVERT: H 188 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: I 121 GLU cc_start: 0.7622 (tp30) cc_final: 0.7380 (tp30) REVERT: I 211 ARG cc_start: 0.6115 (mmm160) cc_final: 0.5754 (mmm160) REVERT: I 225 PHE cc_start: 0.4956 (m-80) cc_final: 0.4631 (m-80) REVERT: I 385 PHE cc_start: 0.5363 (OUTLIER) cc_final: 0.4552 (p90) REVERT: I 407 ARG cc_start: 0.7297 (tpp80) cc_final: 0.6882 (ttm170) REVERT: I 496 LYS cc_start: 0.8504 (mtpp) cc_final: 0.8294 (mmtp) REVERT: I 573 ASN cc_start: 0.8237 (m-40) cc_final: 0.7976 (m-40) REVERT: I 844 LYS cc_start: 0.6641 (pttm) cc_final: 0.6198 (pttp) REVERT: I 955 GLN cc_start: 0.8081 (tp40) cc_final: 0.7732 (tp40) REVERT: I 1180 MET cc_start: 0.9003 (ttt) cc_final: 0.8739 (ttp) REVERT: I 1197 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7449 (tp30) REVERT: J 50 LYS cc_start: 0.8545 (mttt) cc_final: 0.8144 (mttp) REVERT: J 156 ARG cc_start: 0.6484 (ptp-110) cc_final: 0.6253 (ttm170) REVERT: J 164 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: J 180 MET cc_start: 0.6707 (mtm) cc_final: 0.6339 (mtm) REVERT: J 314 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.5687 (tpt170) REVERT: J 441 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8264 (mt) REVERT: J 503 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.7913 (t) REVERT: J 532 GLU cc_start: 0.7653 (tt0) cc_final: 0.7383 (tt0) REVERT: J 554 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8351 (pt0) REVERT: J 655 SER cc_start: 0.7881 (t) cc_final: 0.7565 (p) REVERT: J 749 LYS cc_start: 0.8291 (mtmt) cc_final: 0.8052 (mtpp) REVERT: J 756 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7131 (tt0) REVERT: J 802 ASP cc_start: 0.7431 (p0) cc_final: 0.7221 (p0) REVERT: J 955 LYS cc_start: 0.6264 (tmtt) cc_final: 0.4838 (ttmt) REVERT: J 995 TYR cc_start: 0.7098 (m-80) cc_final: 0.6874 (m-10) REVERT: J 1015 GLU cc_start: 0.3041 (OUTLIER) cc_final: 0.1435 (mm-30) REVERT: J 1148 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6306 (mtt90) REVERT: J 1203 ARG cc_start: 0.6481 (ttp80) cc_final: 0.6197 (tmt-80) REVERT: J 1244 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7295 (mm110) REVERT: J 1355 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8106 (ptm160) REVERT: K 51 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7570 (mt) REVERT: L 113 ARG cc_start: 0.6763 (tpt90) cc_final: 0.6486 (tpt-90) REVERT: L 114 GLU cc_start: 0.7448 (pm20) cc_final: 0.7240 (pm20) REVERT: L 256 PHE cc_start: 0.5262 (m-10) cc_final: 0.5006 (m-80) REVERT: L 470 MET cc_start: 0.7484 (mtp) cc_final: 0.7141 (mtp) REVERT: L 476 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.7023 (ptt90) REVERT: L 524 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7431 (pp20) REVERT: L 548 LEU cc_start: 0.7352 (mt) cc_final: 0.7126 (mt) REVERT: M 284 ARG cc_start: 0.2794 (OUTLIER) cc_final: 0.2581 (mpt-90) outliers start: 367 outliers final: 243 residues processed: 842 average time/residue: 0.4897 time to fit residues: 635.8376 Evaluate side-chains 658 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 396 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 42 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 684 ASN Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 915 ASP Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1003 THR Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1058 ARG Chi-restraints excluded: chain I residue 1079 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1115 THR Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1182 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1308 ILE Chi-restraints excluded: chain I residue 1309 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 678 ARG Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 744 ARG Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 768 ASN Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 775 SER Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 789 LYS Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 878 ASP Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 908 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1015 GLU Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1094 ASP Chi-restraints excluded: chain J residue 1106 ILE Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1116 SER Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1148 ARG Chi-restraints excluded: chain J residue 1172 LYS Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1210 ILE Chi-restraints excluded: chain J residue 1226 VAL Chi-restraints excluded: chain J residue 1235 ASN Chi-restraints excluded: chain J residue 1244 GLN Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1272 SER Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1355 ARG Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 249 ILE Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 335 GLU Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 452 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 487 MET Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 598 LEU Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 285 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 328 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 304 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 226 optimal weight: 0.8980 chunk 353 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 30 HIS G 117 HIS G 132 HIS H 84 ASN H 128 HIS H 132 HIS H 186 ASN I 46 GLN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN I 314 ASN I 387 ASN I 463 GLN I 622 ASN I 649 GLN I 659 GLN I 677 ASN I 808 ASN I 856 ASN I 965 GLN I1010 GLN I1108 ASN I1116 HIS I1134 GLN ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1220 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS I1257 GLN I1268 GLN J 45 ASN J 157 GLN ** J 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN J 335 GLN J 341 ASN J 488 ASN J 680 ASN J 861 ASN J 875 ASN J 979 ASN J1023 HIS J1126 GLN J1295 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN K 62 GLN L 464 ASN ** L 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33035 Z= 0.221 Angle : 0.693 11.890 45081 Z= 0.353 Chirality : 0.045 0.302 5168 Planarity : 0.005 0.090 5502 Dihedral : 18.007 129.065 6120 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.07 % Favored : 92.88 % Rotamer: Outliers : 7.59 % Allowed : 24.76 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % 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: -3.05 (0.12), residues: 3804 helix: -1.03 (0.12), residues: 1511 sheet: -2.90 (0.21), residues: 409 loop : -2.68 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 434 HIS 0.011 0.001 HIS G 117 PHE 0.022 0.002 PHE L 316 TYR 0.019 0.002 TYR I1018 ARG 0.006 0.001 ARG I1106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 480 time to evaluate : 3.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 35 TYR cc_start: 0.7772 (m-80) cc_final: 0.7302 (m-80) REVERT: N 48 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.5276 (tmt90) REVERT: N 65 GLN cc_start: 0.8081 (tp40) cc_final: 0.7213 (tm-30) REVERT: H 16 ILE cc_start: 0.8125 (tt) cc_final: 0.7893 (tt) REVERT: H 23 HIS cc_start: 0.7367 (t-90) cc_final: 0.7110 (t-170) REVERT: H 65 LEU cc_start: 0.4747 (OUTLIER) cc_final: 0.4411 (tp) REVERT: H 86 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7893 (mtpt) REVERT: I 264 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.4847 (tm-30) REVERT: I 385 PHE cc_start: 0.5368 (OUTLIER) cc_final: 0.3952 (p90) REVERT: I 496 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8318 (mmtp) REVERT: I 841 ARG cc_start: 0.8067 (mtt90) cc_final: 0.7784 (mtt-85) REVERT: I 842 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: I 848 GLU cc_start: 0.6646 (mt-10) cc_final: 0.6443 (mt-10) REVERT: I 1061 GLN cc_start: 0.8305 (pt0) cc_final: 0.8101 (pt0) REVERT: I 1136 GLN cc_start: 0.7577 (tp40) cc_final: 0.7319 (tp40) REVERT: I 1164 PHE cc_start: 0.8258 (m-10) cc_final: 0.8027 (m-10) REVERT: I 1292 THR cc_start: 0.8748 (m) cc_final: 0.8411 (p) REVERT: J 50 LYS cc_start: 0.8353 (mttt) cc_final: 0.7861 (mttp) REVERT: J 156 ARG cc_start: 0.6413 (ptp-110) cc_final: 0.6126 (ttm110) REVERT: J 180 MET cc_start: 0.6846 (mtm) cc_final: 0.6510 (mtm) REVERT: J 188 LEU cc_start: 0.8046 (tp) cc_final: 0.7818 (tp) REVERT: J 199 GLU cc_start: 0.5959 (mt-10) cc_final: 0.5727 (mm-30) REVERT: J 201 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7662 (mt) REVERT: J 217 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6656 (tm) REVERT: J 307 LEU cc_start: 0.7836 (mt) cc_final: 0.7522 (mp) REVERT: J 423 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8434 (mp) REVERT: J 441 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8169 (mt) REVERT: J 655 SER cc_start: 0.8017 (t) cc_final: 0.7690 (p) REVERT: J 667 GLN cc_start: 0.8454 (mt0) cc_final: 0.8163 (mt0) REVERT: J 749 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7975 (mtpp) REVERT: J 756 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: J 806 ASP cc_start: 0.6715 (t0) cc_final: 0.6411 (t0) REVERT: J 849 LEU cc_start: 0.6364 (mm) cc_final: 0.5955 (mt) REVERT: J 868 TRP cc_start: 0.6692 (OUTLIER) cc_final: 0.6327 (t-100) REVERT: J 925 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7695 (tm-30) REVERT: J 955 LYS cc_start: 0.6300 (tmtt) cc_final: 0.4881 (ttmt) REVERT: K 45 LYS cc_start: 0.8492 (mmtp) cc_final: 0.8206 (mmmm) REVERT: K 51 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7583 (mt) REVERT: K 69 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.5900 (ttp-110) REVERT: L 256 PHE cc_start: 0.5078 (m-10) cc_final: 0.4834 (m-80) REVERT: L 276 MET cc_start: 0.4379 (tpp) cc_final: 0.4136 (tpp) REVERT: L 523 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8755 (mm) REVERT: M 300 LEU cc_start: 0.0314 (OUTLIER) cc_final: -0.0621 (pp) outliers start: 248 outliers final: 138 residues processed: 686 average time/residue: 0.4413 time to fit residues: 484.8176 Evaluate side-chains 552 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 399 time to evaluate : 4.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 255 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 264 GLU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 744 ARG Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 768 ASN Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1086 ASN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1235 ASN Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 523 ILE Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 196 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 294 optimal weight: 9.9990 chunk 240 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 353 optimal weight: 9.9990 chunk 382 optimal weight: 7.9990 chunk 315 optimal weight: 7.9990 chunk 350 optimal weight: 8.9990 chunk 120 optimal weight: 0.0570 chunk 283 optimal weight: 20.0000 overall best weight: 3.2106 ------------------------------------------------------------------------------- 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** ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 659 GLN I 824 GLN I 856 ASN I1220 GLN J 80 HIS J 716 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 33035 Z= 0.372 Angle : 0.725 11.985 45081 Z= 0.371 Chirality : 0.046 0.301 5168 Planarity : 0.005 0.072 5502 Dihedral : 17.629 129.941 5829 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.54 % Favored : 91.40 % Rotamer: Outliers : 8.72 % Allowed : 25.49 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % 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: -2.64 (0.13), residues: 3804 helix: -0.66 (0.13), residues: 1515 sheet: -2.60 (0.22), residues: 414 loop : -2.51 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 326 HIS 0.009 0.001 HIS J 777 PHE 0.024 0.002 PHE I 225 TYR 0.023 0.002 TYR J1186 ARG 0.006 0.001 ARG I1269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 408 time to evaluate : 3.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 48 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.5325 (tmt90) REVERT: N 65 GLN cc_start: 0.8056 (tp40) cc_final: 0.7139 (tm-30) REVERT: H 16 ILE cc_start: 0.8247 (tt) cc_final: 0.7891 (tt) REVERT: H 23 HIS cc_start: 0.7315 (t-90) cc_final: 0.7088 (t-170) REVERT: H 77 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8336 (t0) REVERT: H 104 LYS cc_start: 0.7108 (tmtt) cc_final: 0.6569 (tmtt) REVERT: I 20 GLN cc_start: 0.7785 (pp30) cc_final: 0.7579 (pp30) REVERT: I 202 ARG cc_start: 0.5558 (mtp180) cc_final: 0.5266 (mtm-85) REVERT: I 264 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.4394 (tt0) REVERT: I 496 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8267 (mmtp) REVERT: I 1314 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: J 50 LYS cc_start: 0.8444 (mttt) cc_final: 0.7981 (mttp) REVERT: J 99 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8453 (mtp85) REVERT: J 148 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6366 (tm-30) REVERT: J 156 ARG cc_start: 0.6427 (ptp-110) cc_final: 0.5969 (ttp-110) REVERT: J 180 MET cc_start: 0.6773 (mtm) cc_final: 0.6339 (mtm) REVERT: J 199 GLU cc_start: 0.5935 (mt-10) cc_final: 0.5614 (mm-30) REVERT: J 311 ARG cc_start: 0.6336 (tpt90) cc_final: 0.5914 (tpt90) REVERT: J 394 ILE cc_start: 0.8675 (mm) cc_final: 0.8388 (tt) REVERT: J 503 SER cc_start: 0.8080 (OUTLIER) cc_final: 0.7543 (t) REVERT: J 532 GLU cc_start: 0.7796 (tt0) cc_final: 0.7367 (tt0) REVERT: J 582 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8356 (mt) REVERT: J 624 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8921 (tt) REVERT: J 641 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7593 (tp) REVERT: J 655 SER cc_start: 0.7905 (t) cc_final: 0.7603 (p) REVERT: J 731 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7469 (tpt90) REVERT: J 749 LYS cc_start: 0.8304 (mtmt) cc_final: 0.7961 (mtpp) REVERT: J 756 GLU cc_start: 0.7715 (pt0) cc_final: 0.7243 (tt0) REVERT: J 802 ASP cc_start: 0.7414 (p0) cc_final: 0.7203 (p0) REVERT: J 835 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8750 (tm) REVERT: J 849 LEU cc_start: 0.6154 (mm) cc_final: 0.5761 (mt) REVERT: J 863 LEU cc_start: 0.7231 (tp) cc_final: 0.7020 (tp) REVERT: J 868 TRP cc_start: 0.6784 (OUTLIER) cc_final: 0.6204 (t-100) REVERT: J 901 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7010 (ptp90) REVERT: J 925 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7709 (tm-30) REVERT: J 1057 SER cc_start: 0.3695 (OUTLIER) cc_final: 0.3398 (p) REVERT: K 51 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7608 (mt) REVERT: K 67 ARG cc_start: 0.6425 (tmt-80) cc_final: 0.5551 (mtm-85) REVERT: L 100 MET cc_start: 0.6787 (mpp) cc_final: 0.6564 (mpp) REVERT: L 158 LEU cc_start: -0.0567 (OUTLIER) cc_final: -0.1214 (tp) REVERT: L 267 ASP cc_start: 0.5284 (p0) cc_final: 0.5055 (t70) REVERT: L 276 MET cc_start: 0.4378 (tpp) cc_final: 0.4120 (tpp) REVERT: L 277 MET cc_start: 0.5157 (tmm) cc_final: 0.4946 (tmm) REVERT: L 403 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.6990 (t0) REVERT: L 507 MET cc_start: 0.7922 (ttm) cc_final: 0.7635 (ttm) REVERT: L 523 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8713 (mm) REVERT: L 561 MET cc_start: 0.6565 (mpt) cc_final: 0.5563 (mpt) REVERT: M 284 ARG cc_start: 0.3085 (OUTLIER) cc_final: 0.2760 (mpt180) REVERT: M 300 LEU cc_start: 0.0744 (OUTLIER) cc_final: 0.0057 (pp) outliers start: 285 outliers final: 200 residues processed: 636 average time/residue: 0.4444 time to fit residues: 455.1093 Evaluate side-chains 596 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 375 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 264 GLU Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 915 ASP Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1314 GLN Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 731 ARG Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 768 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1057 SER Chi-restraints excluded: chain J residue 1086 ASN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1106 ILE Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1235 ASN Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1272 SER Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 158 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 523 ILE Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 349 optimal weight: 5.9990 chunk 266 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 39 optimal weight: 0.2980 chunk 168 optimal weight: 0.0000 chunk 237 optimal weight: 5.9990 chunk 355 optimal weight: 4.9990 chunk 376 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 336 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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** ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 725 GLN I 856 ASN I1220 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33035 Z= 0.185 Angle : 0.619 11.475 45081 Z= 0.316 Chirality : 0.042 0.267 5168 Planarity : 0.004 0.080 5502 Dihedral : 17.182 130.362 5806 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 6.79 % Allowed : 27.69 % Favored : 65.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % 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: -2.04 (0.13), residues: 3804 helix: -0.07 (0.13), residues: 1512 sheet: -2.28 (0.23), residues: 419 loop : -2.25 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 326 HIS 0.006 0.001 HIS G 23 PHE 0.019 0.001 PHE L 256 TYR 0.018 0.001 TYR I1018 ARG 0.004 0.000 ARG J 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 444 time to evaluate : 3.615 Fit side-chains revert: symmetry clash REVERT: N 6 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7159 (m-30) REVERT: N 48 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.5237 (tmt90) REVERT: N 64 TYR cc_start: 0.8112 (t80) cc_final: 0.7617 (t80) REVERT: N 65 GLN cc_start: 0.8021 (tp40) cc_final: 0.7155 (tm-30) REVERT: G 204 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: G 231 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8088 (t80) REVERT: H 13 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7744 (pp) REVERT: H 16 ILE cc_start: 0.8063 (tt) cc_final: 0.7657 (tt) REVERT: H 23 HIS cc_start: 0.7194 (t-90) cc_final: 0.6993 (t-170) REVERT: H 86 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7916 (mtpt) REVERT: I 47 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6977 (p90) REVERT: I 85 CYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7767 (m) REVERT: I 116 ASP cc_start: 0.3550 (OUTLIER) cc_final: 0.3341 (m-30) REVERT: I 335 THR cc_start: 0.6599 (p) cc_final: 0.6357 (t) REVERT: I 403 MET cc_start: 0.7381 (tmm) cc_final: 0.7144 (tpt) REVERT: I 503 LYS cc_start: 0.8205 (mtmm) cc_final: 0.7806 (mtmt) REVERT: I 515 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8488 (ttm) REVERT: I 842 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7274 (m-30) REVERT: I 1292 THR cc_start: 0.8775 (m) cc_final: 0.8431 (p) REVERT: I 1314 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: J 50 LYS cc_start: 0.8076 (mttt) cc_final: 0.7774 (mttp) REVERT: J 83 VAL cc_start: 0.7780 (p) cc_final: 0.7545 (p) REVERT: J 148 GLU cc_start: 0.7124 (tt0) cc_final: 0.6409 (tm-30) REVERT: J 156 ARG cc_start: 0.6320 (ptp-110) cc_final: 0.5790 (ttp-110) REVERT: J 158 GLN cc_start: 0.7881 (mt0) cc_final: 0.7642 (mt0) REVERT: J 217 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6645 (tm) REVERT: J 225 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6035 (tp30) REVERT: J 394 ILE cc_start: 0.8559 (mm) cc_final: 0.8343 (tt) REVERT: J 532 GLU cc_start: 0.7636 (tt0) cc_final: 0.6963 (tt0) REVERT: J 582 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8377 (mt) REVERT: J 587 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8619 (mp) REVERT: J 756 GLU cc_start: 0.7666 (pt0) cc_final: 0.7298 (tt0) REVERT: J 802 ASP cc_start: 0.7288 (p0) cc_final: 0.7008 (p0) REVERT: J 822 MET cc_start: 0.6557 (tpt) cc_final: 0.6298 (ttm) REVERT: J 849 LEU cc_start: 0.6373 (mm) cc_final: 0.6043 (mt) REVERT: J 868 TRP cc_start: 0.6779 (OUTLIER) cc_final: 0.6233 (t-100) REVERT: J 925 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7576 (tm-30) REVERT: J 1194 ARG cc_start: 0.7504 (ttp80) cc_final: 0.7267 (ttm170) REVERT: J 1329 THR cc_start: 0.8518 (t) cc_final: 0.8296 (p) REVERT: K 25 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7682 (ttm170) REVERT: K 45 LYS cc_start: 0.8393 (mmtp) cc_final: 0.8116 (mmmm) REVERT: K 51 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7691 (mt) REVERT: K 63 ILE cc_start: 0.7704 (mt) cc_final: 0.7445 (mt) REVERT: L 403 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6898 (t0) REVERT: L 557 LYS cc_start: 0.7494 (mtmm) cc_final: 0.6380 (mtmm) REVERT: L 561 MET cc_start: 0.6530 (mpt) cc_final: 0.6277 (mpt) REVERT: M 300 LEU cc_start: 0.0592 (OUTLIER) cc_final: 0.0127 (pp) outliers start: 222 outliers final: 134 residues processed: 620 average time/residue: 0.4497 time to fit residues: 444.0078 Evaluate side-chains 537 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 383 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 6 ASP Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 638 SER Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1314 GLN Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 225 GLU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 768 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1086 ASN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1235 ASN Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 313 optimal weight: 0.6980 chunk 213 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 279 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 320 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 337 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 33035 Z= 0.232 Angle : 0.632 11.973 45081 Z= 0.320 Chirality : 0.043 0.261 5168 Planarity : 0.004 0.082 5502 Dihedral : 17.000 130.284 5769 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.23 % Favored : 92.72 % Rotamer: Outliers : 7.31 % Allowed : 27.85 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % 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: -1.78 (0.13), residues: 3804 helix: 0.17 (0.14), residues: 1496 sheet: -2.03 (0.24), residues: 409 loop : -2.13 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 326 HIS 0.009 0.001 HIS J 80 PHE 0.018 0.001 PHE J 17 TYR 0.019 0.002 TYR I1018 ARG 0.004 0.000 ARG I1269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 396 time to evaluate : 3.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 48 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.5259 (tmt90) REVERT: N 64 TYR cc_start: 0.8062 (t80) cc_final: 0.7792 (t80) REVERT: N 65 GLN cc_start: 0.7973 (tp40) cc_final: 0.7119 (tm-30) REVERT: G 231 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7964 (t80) REVERT: H 10 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8206 (mmtm) REVERT: H 13 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7455 (pp) REVERT: H 16 ILE cc_start: 0.8148 (tt) cc_final: 0.7742 (tt) REVERT: H 86 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7870 (mtpt) REVERT: I 20 GLN cc_start: 0.7724 (pp30) cc_final: 0.7501 (pp30) REVERT: I 47 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.7029 (p90) REVERT: I 85 CYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7828 (m) REVERT: I 116 ASP cc_start: 0.3639 (OUTLIER) cc_final: 0.3321 (m-30) REVERT: I 163 LYS cc_start: 0.7181 (mptt) cc_final: 0.6483 (pttp) REVERT: I 327 GLN cc_start: 0.3870 (OUTLIER) cc_final: 0.2961 (pp30) REVERT: I 403 MET cc_start: 0.7310 (tmm) cc_final: 0.7042 (tpt) REVERT: I 503 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7839 (mtmt) REVERT: I 745 GLU cc_start: 0.3791 (OUTLIER) cc_final: 0.3570 (tt0) REVERT: I 842 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7270 (m-30) REVERT: I 1180 MET cc_start: 0.8753 (ttp) cc_final: 0.8391 (ttm) REVERT: I 1292 THR cc_start: 0.8845 (m) cc_final: 0.8546 (p) REVERT: I 1314 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: J 50 LYS cc_start: 0.8147 (mttt) cc_final: 0.7843 (mttp) REVERT: J 148 GLU cc_start: 0.7209 (tt0) cc_final: 0.6507 (tm-30) REVERT: J 156 ARG cc_start: 0.6274 (ptp-110) cc_final: 0.5746 (ttp-110) REVERT: J 213 LYS cc_start: 0.6551 (mtpt) cc_final: 0.5657 (tttp) REVERT: J 217 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6733 (tm) REVERT: J 225 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6077 (tp30) REVERT: J 394 ILE cc_start: 0.8571 (mm) cc_final: 0.8345 (tt) REVERT: J 443 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6671 (pp20) REVERT: J 532 GLU cc_start: 0.7669 (tt0) cc_final: 0.7111 (tt0) REVERT: J 587 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8649 (mp) REVERT: J 624 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8702 (tt) REVERT: J 756 GLU cc_start: 0.7621 (pt0) cc_final: 0.7176 (tt0) REVERT: J 802 ASP cc_start: 0.7357 (p0) cc_final: 0.7102 (p0) REVERT: J 849 LEU cc_start: 0.6299 (mm) cc_final: 0.5897 (mt) REVERT: J 868 TRP cc_start: 0.6797 (OUTLIER) cc_final: 0.6197 (t-100) REVERT: J 925 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7579 (tm-30) REVERT: J 1057 SER cc_start: 0.3901 (OUTLIER) cc_final: 0.3645 (p) REVERT: J 1106 ILE cc_start: 0.6619 (OUTLIER) cc_final: 0.6371 (pt) REVERT: J 1276 GLU cc_start: 0.5937 (OUTLIER) cc_final: 0.5470 (tt0) REVERT: J 1329 THR cc_start: 0.8539 (t) cc_final: 0.8275 (p) REVERT: K 25 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7789 (ttm170) REVERT: K 45 LYS cc_start: 0.8260 (mmtp) cc_final: 0.7501 (mmtp) REVERT: K 51 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7598 (mt) REVERT: K 63 ILE cc_start: 0.7682 (mt) cc_final: 0.7401 (mt) REVERT: K 67 ARG cc_start: 0.6305 (tmt-80) cc_final: 0.5418 (mtm-85) REVERT: L 297 MET cc_start: 0.0687 (ppp) cc_final: 0.0440 (ppp) REVERT: L 403 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7185 (t0) REVERT: L 557 LYS cc_start: 0.7437 (mtmm) cc_final: 0.6335 (mtmm) REVERT: L 561 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6445 (mpt) REVERT: M 278 ILE cc_start: 0.3816 (OUTLIER) cc_final: 0.3438 (mt) REVERT: M 284 ARG cc_start: 0.2587 (OUTLIER) cc_final: 0.1366 (mtt180) REVERT: M 300 LEU cc_start: 0.0650 (OUTLIER) cc_final: 0.0202 (pp) outliers start: 239 outliers final: 169 residues processed: 583 average time/residue: 0.4335 time to fit residues: 405.3559 Evaluate side-chains 563 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 368 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 327 GLN Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1314 GLN Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 225 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 768 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1057 SER Chi-restraints excluded: chain J residue 1086 ASN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1094 ASP Chi-restraints excluded: chain J residue 1106 ILE Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1276 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 354 THR Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 561 MET Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 278 ILE Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 126 optimal weight: 2.9990 chunk 338 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 376 optimal weight: 10.0000 chunk 312 optimal weight: 0.0010 chunk 174 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 124 optimal weight: 0.0870 chunk 197 optimal weight: 7.9990 overall best weight: 0.5564 ------------------------------------------------------------------------------- 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** H 23 HIS H 66 HIS H 186 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN I1220 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33035 Z= 0.163 Angle : 0.592 11.483 45081 Z= 0.301 Chirality : 0.041 0.248 5168 Planarity : 0.004 0.083 5502 Dihedral : 16.739 130.752 5757 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 6.27 % Allowed : 29.38 % Favored : 64.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % 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: -1.46 (0.14), residues: 3804 helix: 0.45 (0.14), residues: 1484 sheet: -1.76 (0.24), residues: 430 loop : -1.99 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 326 HIS 0.017 0.001 HIS H 66 PHE 0.019 0.001 PHE J 17 TYR 0.018 0.001 TYR I1018 ARG 0.005 0.000 ARG J 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 415 time to evaluate : 3.850 Fit side-chains REVERT: N 64 TYR cc_start: 0.8058 (t80) cc_final: 0.7754 (t80) REVERT: N 65 GLN cc_start: 0.7930 (tp40) cc_final: 0.7139 (tm-30) REVERT: G 204 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: G 231 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.8036 (t80) REVERT: H 16 ILE cc_start: 0.8109 (tt) cc_final: 0.7693 (tt) REVERT: H 65 LEU cc_start: 0.4390 (OUTLIER) cc_final: 0.4055 (tp) REVERT: H 86 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7824 (mtpt) REVERT: H 198 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8469 (mt) REVERT: I 47 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6921 (p90) REVERT: I 106 GLU cc_start: 0.3437 (mm-30) cc_final: 0.2825 (pm20) REVERT: I 116 ASP cc_start: 0.4319 (OUTLIER) cc_final: 0.3893 (m-30) REVERT: I 163 LYS cc_start: 0.7255 (mptt) cc_final: 0.6537 (pttp) REVERT: I 403 MET cc_start: 0.7346 (tmm) cc_final: 0.6982 (tpt) REVERT: I 503 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7820 (mtmt) REVERT: I 515 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8498 (ttm) REVERT: I 572 ILE cc_start: 0.8865 (mt) cc_final: 0.8639 (mt) REVERT: I 842 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7166 (m-30) REVERT: I 850 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8467 (mt) REVERT: I 905 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6063 (tp) REVERT: I 1180 MET cc_start: 0.8706 (ttp) cc_final: 0.8381 (ttm) REVERT: I 1229 TYR cc_start: 0.8664 (m-80) cc_final: 0.8342 (m-80) REVERT: J 50 LYS cc_start: 0.7910 (mttt) cc_final: 0.7589 (mttp) REVERT: J 148 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6696 (tm-30) REVERT: J 156 ARG cc_start: 0.6212 (ptp-110) cc_final: 0.5560 (ttp-110) REVERT: J 200 GLN cc_start: 0.6889 (pp30) cc_final: 0.6510 (mt0) REVERT: J 213 LYS cc_start: 0.6252 (mtpt) cc_final: 0.5610 (tttp) REVERT: J 217 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6758 (tm) REVERT: J 225 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.5881 (tp30) REVERT: J 587 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8653 (mp) REVERT: J 756 GLU cc_start: 0.7566 (pt0) cc_final: 0.7265 (tt0) REVERT: J 802 ASP cc_start: 0.7267 (p0) cc_final: 0.6985 (p0) REVERT: J 868 TRP cc_start: 0.6701 (OUTLIER) cc_final: 0.6214 (t-100) REVERT: J 925 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7614 (tm-30) REVERT: J 1276 GLU cc_start: 0.5874 (OUTLIER) cc_final: 0.5410 (tt0) REVERT: J 1329 THR cc_start: 0.8496 (t) cc_final: 0.8272 (p) REVERT: K 45 LYS cc_start: 0.8199 (mmtp) cc_final: 0.7573 (mmtp) REVERT: K 51 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7790 (mt) REVERT: L 277 MET cc_start: 0.4690 (tmm) cc_final: 0.4110 (tmm) REVERT: L 403 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7128 (t0) REVERT: L 471 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7921 (tt) REVERT: L 525 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6148 (t0) REVERT: M 284 ARG cc_start: 0.2535 (OUTLIER) cc_final: 0.1377 (mtt180) REVERT: M 300 LEU cc_start: 0.0600 (OUTLIER) cc_final: 0.0274 (pp) outliers start: 205 outliers final: 145 residues processed: 574 average time/residue: 0.4683 time to fit residues: 436.6429 Evaluate side-chains 543 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 375 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 225 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 768 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 962 ASN Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1086 ASN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1094 ASP Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1276 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 354 THR Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 525 ASP Chi-restraints excluded: chain L residue 571 TYR Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 362 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 274 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 316 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 374 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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** H 66 HIS H 132 HIS ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN I1220 GLN J1244 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN L 271 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 33035 Z= 0.224 Angle : 0.613 11.188 45081 Z= 0.311 Chirality : 0.042 0.169 5168 Planarity : 0.004 0.086 5502 Dihedral : 16.625 130.903 5740 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.89 % Favored : 93.06 % Rotamer: Outliers : 6.82 % Allowed : 29.10 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % 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: -1.38 (0.14), residues: 3804 helix: 0.53 (0.14), residues: 1484 sheet: -1.71 (0.24), residues: 421 loop : -1.95 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 326 HIS 0.004 0.001 HIS G 23 PHE 0.019 0.001 PHE J 892 TYR 0.019 0.001 TYR I1018 ARG 0.007 0.000 ARG J 978 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 387 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 48 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.5149 (tmt90) REVERT: N 64 TYR cc_start: 0.8011 (t80) cc_final: 0.7719 (t80) REVERT: G 134 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8749 (p) REVERT: G 231 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7963 (t80) REVERT: H 16 ILE cc_start: 0.8158 (tt) cc_final: 0.7736 (tt) REVERT: H 77 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8155 (t0) REVERT: H 86 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7798 (mtpt) REVERT: H 198 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8503 (mp) REVERT: I 20 GLN cc_start: 0.7704 (pp30) cc_final: 0.7442 (pp30) REVERT: I 47 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.6986 (p90) REVERT: I 106 GLU cc_start: 0.3461 (mm-30) cc_final: 0.2853 (pm20) REVERT: I 116 ASP cc_start: 0.4369 (OUTLIER) cc_final: 0.3933 (m-30) REVERT: I 403 MET cc_start: 0.7327 (tmm) cc_final: 0.6995 (tpt) REVERT: I 503 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7830 (mtmt) REVERT: I 572 ILE cc_start: 0.8901 (mt) cc_final: 0.8698 (mt) REVERT: I 842 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7228 (m-30) REVERT: I 850 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8560 (mt) REVERT: I 905 ILE cc_start: 0.6866 (OUTLIER) cc_final: 0.6233 (tp) REVERT: I 1180 MET cc_start: 0.8744 (ttp) cc_final: 0.8418 (ttm) REVERT: I 1229 TYR cc_start: 0.8705 (m-80) cc_final: 0.8372 (m-80) REVERT: I 1314 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: J 50 LYS cc_start: 0.8106 (mttt) cc_final: 0.7830 (mttp) REVERT: J 148 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6638 (tm-30) REVERT: J 156 ARG cc_start: 0.6137 (ptp-110) cc_final: 0.5391 (ttp-110) REVERT: J 200 GLN cc_start: 0.6942 (pp30) cc_final: 0.6589 (mt0) REVERT: J 213 LYS cc_start: 0.6402 (mtpt) cc_final: 0.5725 (tttp) REVERT: J 217 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6723 (tm) REVERT: J 225 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.5909 (tp30) REVERT: J 443 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6622 (pp20) REVERT: J 479 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8304 (mt-10) REVERT: J 532 GLU cc_start: 0.7629 (tt0) cc_final: 0.7085 (tt0) REVERT: J 587 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8660 (mp) REVERT: J 624 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8597 (tt) REVERT: J 756 GLU cc_start: 0.7642 (pt0) cc_final: 0.7272 (tt0) REVERT: J 802 ASP cc_start: 0.7325 (p0) cc_final: 0.7075 (p0) REVERT: J 868 TRP cc_start: 0.6787 (OUTLIER) cc_final: 0.6246 (t-100) REVERT: J 925 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7616 (tm-30) REVERT: J 1057 SER cc_start: 0.4676 (OUTLIER) cc_final: 0.4247 (p) REVERT: J 1276 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.5436 (tt0) REVERT: K 8 ASP cc_start: 0.7350 (p0) cc_final: 0.7026 (p0) REVERT: K 45 LYS cc_start: 0.8378 (mmtp) cc_final: 0.7540 (mmtp) REVERT: K 51 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7590 (mt) REVERT: K 67 ARG cc_start: 0.6491 (tmt-80) cc_final: 0.5671 (mtm-85) REVERT: K 69 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.5835 (ttp-110) REVERT: L 297 MET cc_start: 0.0772 (ppp) cc_final: 0.0510 (ppp) REVERT: L 403 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7142 (t0) REVERT: L 471 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7949 (tt) REVERT: L 525 ASP cc_start: 0.6575 (OUTLIER) cc_final: 0.6021 (t0) REVERT: L 557 LYS cc_start: 0.7253 (mtmm) cc_final: 0.7009 (mtmm) REVERT: M 278 ILE cc_start: 0.3157 (OUTLIER) cc_final: 0.2647 (mt) REVERT: M 284 ARG cc_start: 0.2554 (OUTLIER) cc_final: 0.1375 (mtt180) REVERT: M 300 LEU cc_start: 0.0450 (OUTLIER) cc_final: 0.0135 (pp) outliers start: 223 outliers final: 171 residues processed: 561 average time/residue: 0.4346 time to fit residues: 396.1626 Evaluate side-chains 565 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 366 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 915 ASP Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1028 LYS Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1314 GLN Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 225 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 768 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 962 ASN Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1057 SER Chi-restraints excluded: chain J residue 1086 ASN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1094 ASP Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1244 GLN Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1276 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 354 THR Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 525 ASP Chi-restraints excluded: chain L residue 571 TYR Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 278 ILE Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 231 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 223 optimal weight: 0.9990 chunk 112 optimal weight: 0.0470 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 238 optimal weight: 0.5980 chunk 255 optimal weight: 7.9990 chunk 185 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 294 optimal weight: 6.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 65 GLN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33035 Z= 0.204 Angle : 0.605 11.441 45081 Z= 0.307 Chirality : 0.042 0.164 5168 Planarity : 0.004 0.086 5502 Dihedral : 16.564 130.792 5737 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.73 % Favored : 93.22 % Rotamer: Outliers : 6.70 % Allowed : 29.41 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % 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: -1.26 (0.14), residues: 3804 helix: 0.59 (0.14), residues: 1485 sheet: -1.57 (0.24), residues: 426 loop : -1.88 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 326 HIS 0.011 0.001 HIS H 66 PHE 0.017 0.001 PHE J 892 TYR 0.020 0.001 TYR J1241 ARG 0.007 0.000 ARG J 978 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 380 time to evaluate : 3.703 Fit side-chains revert: symmetry clash REVERT: N 64 TYR cc_start: 0.8043 (t80) cc_final: 0.7740 (t80) REVERT: G 134 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8731 (p) REVERT: G 204 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: G 231 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8028 (t80) REVERT: H 16 ILE cc_start: 0.8201 (tt) cc_final: 0.7765 (tt) REVERT: H 86 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7792 (mtpt) REVERT: H 188 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7556 (pt0) REVERT: H 198 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8474 (mt) REVERT: I 20 GLN cc_start: 0.7705 (pp30) cc_final: 0.7497 (pp30) REVERT: I 47 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.7023 (p90) REVERT: I 106 GLU cc_start: 0.3471 (mm-30) cc_final: 0.2870 (pm20) REVERT: I 116 ASP cc_start: 0.4319 (OUTLIER) cc_final: 0.3884 (m-30) REVERT: I 403 MET cc_start: 0.7320 (tmm) cc_final: 0.6998 (tpt) REVERT: I 503 LYS cc_start: 0.8290 (mtmm) cc_final: 0.7868 (mtmt) REVERT: I 842 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7167 (m-30) REVERT: I 905 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6233 (tp) REVERT: I 1180 MET cc_start: 0.8740 (ttp) cc_final: 0.8388 (ttm) REVERT: I 1229 TYR cc_start: 0.8696 (m-80) cc_final: 0.8362 (m-80) REVERT: I 1314 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: J 50 LYS cc_start: 0.8095 (mttt) cc_final: 0.7821 (mttp) REVERT: J 148 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6862 (tm-30) REVERT: J 156 ARG cc_start: 0.6150 (ptp-110) cc_final: 0.5420 (ttp-110) REVERT: J 200 GLN cc_start: 0.6917 (pp30) cc_final: 0.6547 (mt0) REVERT: J 213 LYS cc_start: 0.6360 (mtpt) cc_final: 0.5736 (tttp) REVERT: J 225 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.5880 (tp30) REVERT: J 443 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6660 (pp20) REVERT: J 532 GLU cc_start: 0.7623 (tt0) cc_final: 0.7044 (tt0) REVERT: J 587 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8657 (mp) REVERT: J 624 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8589 (tt) REVERT: J 756 GLU cc_start: 0.7640 (pt0) cc_final: 0.7228 (tt0) REVERT: J 802 ASP cc_start: 0.7177 (p0) cc_final: 0.6902 (p0) REVERT: J 868 TRP cc_start: 0.6811 (OUTLIER) cc_final: 0.6247 (t-100) REVERT: J 925 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7624 (tm-30) REVERT: J 1057 SER cc_start: 0.4726 (OUTLIER) cc_final: 0.4313 (p) REVERT: J 1276 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.5533 (tt0) REVERT: K 45 LYS cc_start: 0.8377 (mmtp) cc_final: 0.7483 (mmtp) REVERT: K 51 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7880 (mt) REVERT: K 67 ARG cc_start: 0.6495 (tmt-80) cc_final: 0.5744 (mtm-85) REVERT: K 69 ARG cc_start: 0.7321 (ttm-80) cc_final: 0.5890 (ttp-110) REVERT: L 289 LYS cc_start: 0.5041 (mmtm) cc_final: 0.3864 (mtpp) REVERT: L 297 MET cc_start: 0.0782 (ppp) cc_final: 0.0477 (ppp) REVERT: L 403 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7188 (t0) REVERT: L 471 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7925 (tt) REVERT: L 525 ASP cc_start: 0.6695 (OUTLIER) cc_final: 0.6217 (t0) REVERT: L 557 LYS cc_start: 0.7341 (mtmm) cc_final: 0.7069 (mtmm) REVERT: M 278 ILE cc_start: 0.3164 (OUTLIER) cc_final: 0.2642 (mt) REVERT: M 284 ARG cc_start: 0.2568 (OUTLIER) cc_final: 0.1403 (mtt180) REVERT: M 304 LYS cc_start: 0.3490 (OUTLIER) cc_final: 0.2764 (mmtm) outliers start: 219 outliers final: 175 residues processed: 549 average time/residue: 0.4450 time to fit residues: 394.1239 Evaluate side-chains 570 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 369 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1028 LYS Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1314 GLN Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 225 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 768 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 962 ASN Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1057 SER Chi-restraints excluded: chain J residue 1086 ASN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1094 ASP Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1276 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 354 THR Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 525 ASP Chi-restraints excluded: chain L residue 571 TYR Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 278 ILE Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 304 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 341 optimal weight: 10.0000 chunk 359 optimal weight: 0.6980 chunk 327 optimal weight: 3.9990 chunk 349 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 274 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 315 optimal weight: 5.9990 chunk 330 optimal weight: 7.9990 chunk 348 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 65 GLN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN M 294 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33035 Z= 0.173 Angle : 0.591 11.123 45081 Z= 0.300 Chirality : 0.041 0.226 5168 Planarity : 0.004 0.085 5502 Dihedral : 16.442 130.840 5733 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.49 % Favored : 93.45 % Rotamer: Outliers : 6.21 % Allowed : 30.02 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % 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: -1.11 (0.14), residues: 3804 helix: 0.70 (0.14), residues: 1487 sheet: -1.39 (0.25), residues: 424 loop : -1.79 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 326 HIS 0.009 0.001 HIS H 66 PHE 0.017 0.001 PHE N 52 TYR 0.019 0.001 TYR I1018 ARG 0.005 0.000 ARG J 978 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 395 time to evaluate : 3.618 Fit side-chains revert: symmetry clash REVERT: N 49 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7986 (ttp-110) REVERT: N 64 TYR cc_start: 0.8040 (t80) cc_final: 0.7713 (t80) REVERT: G 134 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8824 (p) REVERT: G 204 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: G 231 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7973 (t80) REVERT: H 86 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7772 (mtpt) REVERT: H 198 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8485 (mt) REVERT: I 47 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.6977 (p90) REVERT: I 103 VAL cc_start: 0.8017 (m) cc_final: 0.7726 (p) REVERT: I 106 GLU cc_start: 0.3542 (mm-30) cc_final: 0.2981 (pm20) REVERT: I 116 ASP cc_start: 0.4515 (OUTLIER) cc_final: 0.4147 (m-30) REVERT: I 335 THR cc_start: 0.6483 (p) cc_final: 0.6249 (t) REVERT: I 403 MET cc_start: 0.7317 (tmm) cc_final: 0.6977 (tpt) REVERT: I 503 LYS cc_start: 0.8277 (mtmm) cc_final: 0.7817 (mtmt) REVERT: I 842 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7169 (m-30) REVERT: I 905 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.6170 (tp) REVERT: I 1180 MET cc_start: 0.8732 (ttp) cc_final: 0.8393 (ttm) REVERT: I 1229 TYR cc_start: 0.8592 (m-80) cc_final: 0.8230 (m-80) REVERT: I 1314 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: J 50 LYS cc_start: 0.7926 (mttt) cc_final: 0.7605 (mttp) REVERT: J 148 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: J 156 ARG cc_start: 0.6307 (ptp-110) cc_final: 0.5510 (ttp-110) REVERT: J 200 GLN cc_start: 0.6837 (pp30) cc_final: 0.6465 (mt0) REVERT: J 213 LYS cc_start: 0.6465 (mtpt) cc_final: 0.5831 (tttp) REVERT: J 225 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.5915 (tp30) REVERT: J 485 MET cc_start: 0.8877 (tpt) cc_final: 0.8410 (tpt) REVERT: J 587 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8656 (mp) REVERT: J 624 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8545 (tt) REVERT: J 756 GLU cc_start: 0.7608 (pt0) cc_final: 0.7267 (tt0) REVERT: J 757 THR cc_start: 0.9107 (t) cc_final: 0.8868 (p) REVERT: J 802 ASP cc_start: 0.7250 (p0) cc_final: 0.7015 (p0) REVERT: J 868 TRP cc_start: 0.6839 (OUTLIER) cc_final: 0.6267 (t-100) REVERT: J 925 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7731 (tm-30) REVERT: J 1057 SER cc_start: 0.4764 (OUTLIER) cc_final: 0.4370 (p) REVERT: J 1276 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5490 (tt0) REVERT: K 45 LYS cc_start: 0.8371 (mmtp) cc_final: 0.7523 (mmtp) REVERT: K 55 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7285 (tt0) REVERT: K 67 ARG cc_start: 0.6484 (tmt-80) cc_final: 0.5626 (ttp80) REVERT: L 250 LEU cc_start: 0.3289 (OUTLIER) cc_final: 0.2744 (tp) REVERT: L 289 LYS cc_start: 0.4503 (mmtm) cc_final: 0.3809 (mtpp) REVERT: L 297 MET cc_start: 0.0762 (ppp) cc_final: 0.0474 (ppp) REVERT: L 403 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7248 (t0) REVERT: L 471 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7869 (tt) REVERT: L 525 ASP cc_start: 0.6578 (OUTLIER) cc_final: 0.6247 (t0) REVERT: L 557 LYS cc_start: 0.7319 (mtmm) cc_final: 0.6295 (mtmm) REVERT: L 561 MET cc_start: 0.6958 (mpt) cc_final: 0.6132 (mpt) REVERT: M 278 ILE cc_start: 0.3112 (OUTLIER) cc_final: 0.2637 (mt) REVERT: M 284 ARG cc_start: 0.2765 (OUTLIER) cc_final: 0.1527 (mtt180) REVERT: M 304 LYS cc_start: 0.3722 (OUTLIER) cc_final: 0.2927 (mmtm) outliers start: 203 outliers final: 159 residues processed: 552 average time/residue: 0.4356 time to fit residues: 389.9968 Evaluate side-chains 559 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 376 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 302 ILE Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1314 GLN Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 225 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 768 ASN Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1021 ASP Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1057 SER Chi-restraints excluded: chain J residue 1086 ASN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1094 ASP Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1276 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 525 ASP Chi-restraints excluded: chain L residue 571 TYR Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 278 ILE Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 304 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 229 optimal weight: 2.9990 chunk 369 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 256 optimal weight: 5.9990 chunk 387 optimal weight: 8.9990 chunk 356 optimal weight: 1.9990 chunk 308 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 65 GLN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 856 ASN I 894 GLN ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 33035 Z= 0.266 Angle : 0.637 11.297 45081 Z= 0.322 Chirality : 0.043 0.196 5168 Planarity : 0.004 0.082 5502 Dihedral : 16.479 130.267 5725 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.91 % Favored : 93.03 % Rotamer: Outliers : 6.06 % Allowed : 29.83 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % 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: -1.19 (0.14), residues: 3804 helix: 0.56 (0.14), residues: 1501 sheet: -1.41 (0.26), residues: 400 loop : -1.79 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 326 HIS 0.009 0.001 HIS H 66 PHE 0.032 0.002 PHE J 172 TYR 0.027 0.002 TYR J1186 ARG 0.007 0.000 ARG J 978 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 373 time to evaluate : 3.679 Fit side-chains revert: symmetry clash REVERT: N 48 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7701 (ttt90) REVERT: N 64 TYR cc_start: 0.8039 (t80) cc_final: 0.7740 (t80) REVERT: G 231 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7991 (t80) REVERT: H 188 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7684 (pt0) REVERT: H 198 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8520 (mt) REVERT: I 20 GLN cc_start: 0.7749 (pp30) cc_final: 0.7513 (pp30) REVERT: I 47 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6935 (p90) REVERT: I 106 GLU cc_start: 0.3910 (mm-30) cc_final: 0.3282 (pm20) REVERT: I 503 LYS cc_start: 0.8278 (mtmm) cc_final: 0.7840 (mtmt) REVERT: I 749 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7914 (t70) REVERT: I 842 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: I 905 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6218 (tp) REVERT: I 976 ARG cc_start: 0.8120 (ttp-110) cc_final: 0.7584 (mtp-110) REVERT: I 1028 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6822 (mtmm) REVERT: I 1180 MET cc_start: 0.8780 (ttp) cc_final: 0.8387 (ttm) REVERT: I 1229 TYR cc_start: 0.8740 (m-80) cc_final: 0.8395 (m-80) REVERT: I 1314 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: I 1316 GLU cc_start: 0.7526 (mp0) cc_final: 0.7247 (mp0) REVERT: J 50 LYS cc_start: 0.8132 (mttt) cc_final: 0.7851 (mttp) REVERT: J 148 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6632 (tm-30) REVERT: J 156 ARG cc_start: 0.6452 (ptp-110) cc_final: 0.5797 (ttp-110) REVERT: J 164 GLN cc_start: 0.6724 (tm-30) cc_final: 0.5843 (tm-30) REVERT: J 200 GLN cc_start: 0.6955 (pp30) cc_final: 0.6592 (mt0) REVERT: J 213 LYS cc_start: 0.6491 (mtpt) cc_final: 0.5857 (tttp) REVERT: J 225 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6048 (tp30) REVERT: J 532 GLU cc_start: 0.7595 (tt0) cc_final: 0.7135 (tt0) REVERT: J 587 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8655 (mp) REVERT: J 624 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8715 (tt) REVERT: J 756 GLU cc_start: 0.7655 (pt0) cc_final: 0.7246 (tt0) REVERT: J 757 THR cc_start: 0.9091 (t) cc_final: 0.8859 (p) REVERT: J 802 ASP cc_start: 0.7241 (p0) cc_final: 0.6971 (p0) REVERT: J 849 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.6034 (mt) REVERT: J 868 TRP cc_start: 0.6963 (OUTLIER) cc_final: 0.6181 (t-100) REVERT: J 925 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7724 (tm-30) REVERT: J 1057 SER cc_start: 0.4806 (OUTLIER) cc_final: 0.4436 (p) REVERT: J 1276 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5557 (tt0) REVERT: K 67 ARG cc_start: 0.6534 (tmt-80) cc_final: 0.5742 (mtm-85) REVERT: L 277 MET cc_start: 0.4695 (tmm) cc_final: 0.4409 (ttt) REVERT: L 297 MET cc_start: 0.0601 (ppp) cc_final: 0.0304 (ppp) REVERT: L 403 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7305 (t0) REVERT: L 471 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7997 (tt) REVERT: L 557 LYS cc_start: 0.7306 (mtmm) cc_final: 0.6274 (mtmm) REVERT: L 561 MET cc_start: 0.6972 (mpt) cc_final: 0.6152 (mpt) REVERT: M 278 ILE cc_start: 0.3150 (OUTLIER) cc_final: 0.2651 (mt) REVERT: M 284 ARG cc_start: 0.2603 (OUTLIER) cc_final: 0.1392 (mtt180) REVERT: M 304 LYS cc_start: 0.3417 (OUTLIER) cc_final: 0.2651 (mmtm) outliers start: 198 outliers final: 168 residues processed: 524 average time/residue: 0.4286 time to fit residues: 364.0962 Evaluate side-chains 549 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 358 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1028 LYS Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1314 GLN Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 225 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 768 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1021 ASP Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1057 SER Chi-restraints excluded: chain J residue 1086 ASN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1094 ASP Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1276 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 278 ILE Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 304 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 245 optimal weight: 0.9980 chunk 328 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 284 optimal weight: 8.9990 chunk 45 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 chunk 309 optimal weight: 8.9990 chunk 129 optimal weight: 0.6980 chunk 317 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 65 GLN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 HIS I 856 ASN ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.176307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.143053 restraints weight = 43279.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.137809 restraints weight = 43068.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.138042 restraints weight = 53034.497| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 33035 Z= 0.261 Angle : 0.637 11.476 45081 Z= 0.323 Chirality : 0.043 0.213 5168 Planarity : 0.004 0.081 5502 Dihedral : 16.504 129.610 5725 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.10 % Favored : 92.85 % Rotamer: Outliers : 6.40 % Allowed : 29.93 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % 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: 3804 helix: 0.50 (0.14), residues: 1504 sheet: -1.41 (0.26), residues: 408 loop : -1.79 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 434 HIS 0.015 0.001 HIS H 66 PHE 0.030 0.002 PHE J 172 TYR 0.026 0.002 TYR J1186 ARG 0.009 0.000 ARG N 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7823.84 seconds wall clock time: 142 minutes 51.67 seconds (8571.67 seconds total)