Starting phenix.real_space_refine on Sun Mar 24 17:58:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re3_24432/03_2024/7re3_24432_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re3_24432/03_2024/7re3_24432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re3_24432/03_2024/7re3_24432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re3_24432/03_2024/7re3_24432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re3_24432/03_2024/7re3_24432_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re3_24432/03_2024/7re3_24432_updated.pdb" } resolution = 3.33 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= 0.009 sd= 0.100 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: 9 Type Number sf(0) Gaussians Zn 16 6.06 5 Al 4 5.89 5 P 154 5.49 5 Mg 6 5.21 5 S 302 5.16 5 C 26795 2.51 5 N 7293 2.21 5 O 8572 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 36": "OD1" <-> "OD2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D ASP 64": "OD1" <-> "OD2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 101": "OD1" <-> "OD2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 579": "NH1" <-> "NH2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 498": "OE1" <-> "OE2" Residue "F PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H ASP 78": "OD1" <-> "OD2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H ASP 163": "OD1" <-> "OD2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "G ASP 109": "OD1" <-> "OD2" Residue "G TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 336": "OD1" <-> "OD2" Residue "G PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 436": "OE1" <-> "OE2" Residue "G PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 555": "NH1" <-> "NH2" Residue "G ASP 684": "OD1" <-> "OD2" Residue "G TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 38": "OD1" <-> "OD2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "J GLU 32": "OE1" <-> "OE2" Residue "J ASP 64": "OD1" <-> "OD2" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 101": "OD1" <-> "OD2" Residue "K TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 375": "OE1" <-> "OE2" Residue "K TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 579": "NH1" <-> "NH2" Residue "L PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 128": "OE1" <-> "OE2" Residue "L PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 319": "OE1" <-> "OE2" Residue "L PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 498": "OE1" <-> "OE2" Residue "L PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43154 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1408 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1415 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 4507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4507 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 76 Chain: "F" Number of atoms: 4563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4563 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "H" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1405 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "P" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "T" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 789 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna3p': 36} Chain: "G" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "I" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "J" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1406 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "K" Number of atoms: 4507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4507 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 76 Chain: "L" Number of atoms: 4563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4563 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "Q" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "U" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 789 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 71.716 107.817 125.241 1.00 48.15 S ATOM 2495 SG CYS A 306 72.969 110.339 122.628 1.00 44.53 S ATOM 2527 SG CYS A 310 69.230 109.649 123.106 1.00 42.04 S ATOM 3935 SG CYS A 487 84.164 105.204 141.355 1.00 49.55 S ATOM 5188 SG CYS A 645 86.371 107.163 138.880 1.00 53.05 S ATOM 5194 SG CYS A 646 83.512 104.900 137.678 1.00 49.44 S ATOM 10896 SG CYS E 5 64.983 101.397 206.009 1.00214.26 S ATOM 10917 SG CYS E 8 63.948 104.559 207.246 1.00216.50 S ATOM 11055 SG CYS E 26 67.501 104.495 206.541 1.00216.99 S ATOM 11076 SG CYS E 29 66.080 102.267 209.512 1.00221.11 S ATOM 11241 SG CYS E 50 89.647 92.342 201.046 1.00222.74 S ATOM 11271 SG CYS E 55 90.295 89.014 202.792 1.00227.14 S ATOM 11404 SG CYS E 72 91.723 92.243 204.282 1.00224.64 S ATOM 10978 SG CYS E 16 70.977 92.282 205.816 1.00231.46 S ATOM 10993 SG CYS E 19 67.685 90.636 206.252 1.00236.80 S ATOM 15403 SG CYS F 5 92.499 72.975 173.413 1.00112.81 S ATOM 15424 SG CYS F 8 92.298 72.641 177.001 1.00112.92 S ATOM 15562 SG CYS F 26 94.577 75.414 175.796 1.00115.34 S ATOM 15583 SG CYS F 29 95.774 72.066 175.376 1.00114.77 S ATOM 15748 SG CYS F 50 106.308 89.273 157.575 1.00122.55 S ATOM 15778 SG CYS F 55 109.082 87.894 155.120 1.00126.81 S ATOM 15911 SG CYS F 72 110.114 88.749 158.804 1.00126.94 S ATOM 15485 SG CYS F 16 99.009 73.174 164.183 1.00111.33 S ATOM 15500 SG CYS F 19 96.770 70.039 163.475 1.00112.67 S ATOM 25306 SG CYS G 301 72.176 83.415 108.855 1.00 50.96 S ATOM 25347 SG CYS G 306 73.461 80.929 111.486 1.00 48.51 S ATOM 25379 SG CYS G 310 69.712 81.524 110.963 1.00 45.17 S ATOM 26787 SG CYS G 487 84.745 86.319 92.885 1.00 49.74 S ATOM 28040 SG CYS G 645 86.972 84.420 95.390 1.00 53.15 S ATOM 28046 SG CYS G 646 84.042 86.611 96.554 1.00 50.84 S ATOM 32331 SG CYS K 5 66.246 89.554 28.003 1.00243.70 S ATOM 32352 SG CYS K 8 65.305 86.366 26.758 1.00245.07 S ATOM 32490 SG CYS K 26 68.847 86.520 27.505 1.00242.75 S ATOM 32511 SG CYS K 29 67.405 88.708 24.514 1.00249.13 S ATOM 32676 SG CYS K 50 90.613 99.235 33.243 1.00236.04 S ATOM 32706 SG CYS K 55 91.198 102.576 31.499 1.00235.61 S ATOM 32839 SG CYS K 72 92.724 99.382 30.031 1.00234.50 S ATOM 32413 SG CYS K 16 72.005 98.818 28.251 1.00257.69 S ATOM 32428 SG CYS K 19 68.678 100.380 27.774 1.00268.30 S ATOM 36838 SG CYS L 5 92.646 118.705 60.875 1.00118.72 S ATOM 36859 SG CYS L 8 92.480 119.029 57.285 1.00119.51 S ATOM 36997 SG CYS L 26 94.813 116.316 58.521 1.00121.36 S ATOM 37018 SG CYS L 29 95.921 119.693 58.950 1.00121.71 S ATOM 37183 SG CYS L 50 106.673 102.781 76.903 1.00127.49 S ATOM 37213 SG CYS L 55 109.381 104.233 79.389 1.00133.66 S ATOM 37346 SG CYS L 72 110.478 103.399 75.718 1.00132.22 S ATOM 36920 SG CYS L 16 99.050 118.682 70.183 1.00117.47 S ATOM 36935 SG CYS L 19 96.724 121.761 70.859 1.00117.79 S Time building chain proxies: 23.17, per 1000 atoms: 0.54 Number of scatterers: 43154 At special positions: 0 Unit cell: (166.92, 192.6, 234.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 16 29.99 S 302 16.00 P 154 15.00 Al 4 13.00 Mg 6 11.99 F 12 9.00 O 8572 8.00 N 7293 7.00 C 26795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.10 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " pdb=" ZN G2000 " pdb="ZN ZN G2000 " - pdb=" ND1 HIS G 295 " pdb="ZN ZN G2000 " - pdb=" SG CYS G 310 " pdb="ZN ZN G2000 " - pdb=" SG CYS G 301 " pdb="ZN ZN G2000 " - pdb=" SG CYS G 306 " pdb=" ZN G2001 " pdb="ZN ZN G2001 " - pdb=" ND1 HIS G 642 " pdb="ZN ZN G2001 " - pdb=" SG CYS G 487 " pdb="ZN ZN G2001 " - pdb=" SG CYS G 646 " pdb="ZN ZN G2001 " - pdb=" SG CYS G 645 " pdb=" ZN K 701 " pdb="ZN ZN K 701 " - pdb=" SG CYS K 8 " pdb="ZN ZN K 701 " - pdb=" SG CYS K 5 " pdb="ZN ZN K 701 " - pdb=" SG CYS K 29 " pdb="ZN ZN K 701 " - pdb=" SG CYS K 26 " pdb=" ZN K 702 " pdb="ZN ZN K 702 " - pdb=" ND1 HIS K 75 " pdb="ZN ZN K 702 " - pdb=" SG CYS K 72 " pdb="ZN ZN K 702 " - pdb=" SG CYS K 55 " pdb="ZN ZN K 702 " - pdb=" SG CYS K 50 " pdb=" ZN K 703 " pdb="ZN ZN K 703 " - pdb=" NE2 HIS K 33 " pdb="ZN ZN K 703 " - pdb=" ND1 HIS K 39 " pdb="ZN ZN K 703 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 703 " - pdb=" SG CYS K 16 " pdb=" ZN L1000 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 8 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 26 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 29 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 5 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 75 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 55 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 72 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 50 " pdb=" ZN L1002 " pdb="ZN ZN L1002 " - pdb=" NE2 HIS L 33 " pdb="ZN ZN L1002 " - pdb=" ND1 HIS L 39 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 19 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 16 " Number of angles added : 52 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 170 helices and 34 sheets defined 36.8% alpha, 7.9% beta 68 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 17.21 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.759A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 169 through 199 removed outlier: 4.493A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG A 183 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 removed outlier: 3.752A pdb=" N SER A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 4.207A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 removed outlier: 3.826A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.773A pdb=" N LEU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.266A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 4.592A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 581 removed outlier: 3.924A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 688 through 709 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 789 Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 857 through 871 Proline residue: A 868 - end of helix removed outlier: 4.852A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 901 removed outlier: 4.097A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' Processing helix chain 'A' and resid 919 through 925 removed outlier: 3.968A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 32 through 96 removed outlier: 3.638A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.790A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.832A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.954A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 60 removed outlier: 3.707A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 33 through 98 removed outlier: 3.939A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR D 84 " --> pdb=" O ARG D 80 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N SER D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 98 " --> pdb=" O MET D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 111 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'E' and resid 28 through 36 Processing helix chain 'E' and resid 103 through 111 removed outlier: 3.964A pdb=" N ALA E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 124 removed outlier: 3.977A pdb=" N ASN E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 145 Processing helix chain 'E' and resid 261 through 273 removed outlier: 4.362A pdb=" N SER E 264 " --> pdb=" O GLU E 261 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL E 266 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ALA E 267 " --> pdb=" O SER E 264 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 272 " --> pdb=" O TYR E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 298 removed outlier: 3.926A pdb=" N ALA E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 324 Processing helix chain 'E' and resid 360 through 362 No H-bonds generated for 'chain 'E' and resid 360 through 362' Processing helix chain 'E' and resid 376 through 378 No H-bonds generated for 'chain 'E' and resid 376 through 378' Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 419 through 421 No H-bonds generated for 'chain 'E' and resid 419 through 421' Processing helix chain 'E' and resid 424 through 431 Processing helix chain 'E' and resid 446 through 452 Processing helix chain 'E' and resid 490 through 498 Processing helix chain 'E' and resid 504 through 506 No H-bonds generated for 'chain 'E' and resid 504 through 506' Processing helix chain 'E' and resid 516 through 526 removed outlier: 4.259A pdb=" N SER E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE E 525 " --> pdb=" O VAL E 521 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU E 526 " --> pdb=" O ALA E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 565 Processing helix chain 'F' and resid 27 through 36 Processing helix chain 'F' and resid 60 through 62 No H-bonds generated for 'chain 'F' and resid 60 through 62' Processing helix chain 'F' and resid 103 through 110 Processing helix chain 'F' and resid 117 through 122 Processing helix chain 'F' and resid 128 through 146 removed outlier: 3.865A pdb=" N PHE F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 274 removed outlier: 4.371A pdb=" N VAL F 266 " --> pdb=" O SER F 263 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA F 267 " --> pdb=" O SER F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 298 Processing helix chain 'F' and resid 311 through 323 Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 381 through 390 Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 424 through 431 Processing helix chain 'F' and resid 446 through 455 Processing helix chain 'F' and resid 490 through 498 Processing helix chain 'F' and resid 516 through 525 removed outlier: 4.388A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 535 No H-bonds generated for 'chain 'F' and resid 533 through 535' Processing helix chain 'F' and resid 558 through 565 Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 32 through 96 removed outlier: 3.867A pdb=" N ALA H 54 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N MET H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS H 82 " --> pdb=" O ASP H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 108 Processing helix chain 'H' and resid 117 through 124 Proline residue: H 121 - end of helix removed outlier: 3.739A pdb=" N THR H 124 " --> pdb=" O PRO H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 141 Processing helix chain 'H' and resid 177 through 179 No H-bonds generated for 'chain 'H' and resid 177 through 179' Processing helix chain 'G' and resid 4 through 12 removed outlier: 3.759A pdb=" N LEU G 8 " --> pdb=" O ALA G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 89 Processing helix chain 'G' and resid 124 through 132 Processing helix chain 'G' and resid 143 through 148 Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 169 through 199 removed outlier: 4.493A pdb=" N GLU G 180 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG G 183 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN G 184 " --> pdb=" O ARG G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 209 No H-bonds generated for 'chain 'G' and resid 207 through 209' Processing helix chain 'G' and resid 235 through 247 removed outlier: 3.751A pdb=" N SER G 239 " --> pdb=" O ASP G 235 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU G 240 " --> pdb=" O SER G 236 " (cutoff:3.500A) Proline residue: G 243 - end of helix removed outlier: 4.207A pdb=" N THR G 246 " --> pdb=" O MET G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 255 removed outlier: 3.825A pdb=" N SER G 255 " --> pdb=" O THR G 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 252 through 255' Processing helix chain 'G' and resid 257 through 259 No H-bonds generated for 'chain 'G' and resid 257 through 259' Processing helix chain 'G' and resid 276 through 286 Processing helix chain 'G' and resid 298 through 300 No H-bonds generated for 'chain 'G' and resid 298 through 300' Processing helix chain 'G' and resid 304 through 319 removed outlier: 3.773A pdb=" N LEU G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS G 309 " --> pdb=" O ARG G 305 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU G 316 " --> pdb=" O ASN G 312 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR G 319 " --> pdb=" O VAL G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 325 No H-bonds generated for 'chain 'G' and resid 323 through 325' Processing helix chain 'G' and resid 368 through 376 Processing helix chain 'G' and resid 378 through 384 Processing helix chain 'G' and resid 417 through 426 Processing helix chain 'G' and resid 448 through 458 removed outlier: 4.266A pdb=" N TYR G 455 " --> pdb=" O SER G 451 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR G 456 " --> pdb=" O ASP G 452 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG G 457 " --> pdb=" O TYR G 453 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TYR G 458 " --> pdb=" O ASP G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 466 through 479 removed outlier: 4.592A pdb=" N PHE G 471 " --> pdb=" O ARG G 467 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU G 474 " --> pdb=" O LEU G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 506 through 508 No H-bonds generated for 'chain 'G' and resid 506 through 508' Processing helix chain 'G' and resid 512 through 518 Processing helix chain 'G' and resid 521 through 531 Processing helix chain 'G' and resid 562 through 581 removed outlier: 3.923A pdb=" N THR G 567 " --> pdb=" O CYS G 563 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS G 574 " --> pdb=" O GLN G 570 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU G 575 " --> pdb=" O PHE G 571 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA G 581 " --> pdb=" O LYS G 577 " (cutoff:3.500A) Processing helix chain 'G' and resid 597 through 605 Processing helix chain 'G' and resid 628 through 637 Processing helix chain 'G' and resid 648 through 661 Processing helix chain 'G' and resid 688 through 709 Processing helix chain 'G' and resid 718 through 732 Processing helix chain 'G' and resid 739 through 752 Processing helix chain 'G' and resid 768 through 773 Processing helix chain 'G' and resid 779 through 789 Processing helix chain 'G' and resid 796 through 798 No H-bonds generated for 'chain 'G' and resid 796 through 798' Processing helix chain 'G' and resid 834 through 842 Processing helix chain 'G' and resid 857 through 871 Proline residue: G 868 - end of helix removed outlier: 4.851A pdb=" N LYS G 871 " --> pdb=" O TYR G 867 " (cutoff:3.500A) Processing helix chain 'G' and resid 875 through 901 removed outlier: 4.097A pdb=" N VAL G 880 " --> pdb=" O GLU G 876 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE G 881 " --> pdb=" O TYR G 877 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS G 882 " --> pdb=" O ALA G 878 " (cutoff:3.500A) Processing helix chain 'G' and resid 912 through 914 No H-bonds generated for 'chain 'G' and resid 912 through 914' Processing helix chain 'G' and resid 919 through 925 removed outlier: 3.969A pdb=" N MET G 924 " --> pdb=" O PHE G 920 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR G 925 " --> pdb=" O TYR G 921 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 19 removed outlier: 3.833A pdb=" N LYS I 7 " --> pdb=" O MET I 3 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS I 8 " --> pdb=" O SER I 4 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR I 9 " --> pdb=" O ASP I 5 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 40 removed outlier: 3.953A pdb=" N GLN I 31 " --> pdb=" O LYS I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 60 removed outlier: 3.706A pdb=" N VAL I 58 " --> pdb=" O SER I 54 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU I 59 " --> pdb=" O LEU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 72 No H-bonds generated for 'chain 'I' and resid 70 through 72' Processing helix chain 'J' and resid 10 through 28 Processing helix chain 'J' and resid 33 through 98 removed outlier: 3.939A pdb=" N ASP J 52 " --> pdb=" O GLU J 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS J 82 " --> pdb=" O ASP J 78 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL J 83 " --> pdb=" O LYS J 79 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR J 84 " --> pdb=" O ARG J 80 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N SER J 85 " --> pdb=" O ALA J 81 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU J 98 " --> pdb=" O MET J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 111 Processing helix chain 'J' and resid 135 through 141 Processing helix chain 'K' and resid 28 through 36 Processing helix chain 'K' and resid 103 through 111 removed outlier: 3.963A pdb=" N ALA K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 124 removed outlier: 3.978A pdb=" N ASN K 124 " --> pdb=" O TYR K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 145 Processing helix chain 'K' and resid 261 through 273 removed outlier: 4.362A pdb=" N SER K 264 " --> pdb=" O GLU K 261 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL K 266 " --> pdb=" O SER K 263 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ALA K 267 " --> pdb=" O SER K 264 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL K 272 " --> pdb=" O TYR K 269 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 298 removed outlier: 3.925A pdb=" N ALA K 292 " --> pdb=" O LYS K 288 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE K 293 " --> pdb=" O SER K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 324 Processing helix chain 'K' and resid 360 through 362 No H-bonds generated for 'chain 'K' and resid 360 through 362' Processing helix chain 'K' and resid 376 through 378 No H-bonds generated for 'chain 'K' and resid 376 through 378' Processing helix chain 'K' and resid 381 through 390 Processing helix chain 'K' and resid 419 through 421 No H-bonds generated for 'chain 'K' and resid 419 through 421' Processing helix chain 'K' and resid 424 through 431 Processing helix chain 'K' and resid 446 through 452 Processing helix chain 'K' and resid 490 through 498 Processing helix chain 'K' and resid 504 through 506 No H-bonds generated for 'chain 'K' and resid 504 through 506' Processing helix chain 'K' and resid 516 through 526 removed outlier: 4.258A pdb=" N SER K 523 " --> pdb=" O ASN K 519 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LYS K 524 " --> pdb=" O ALA K 520 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE K 525 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU K 526 " --> pdb=" O ALA K 522 " (cutoff:3.500A) Processing helix chain 'K' and resid 558 through 565 Processing helix chain 'L' and resid 27 through 36 Processing helix chain 'L' and resid 60 through 62 No H-bonds generated for 'chain 'L' and resid 60 through 62' Processing helix chain 'L' and resid 103 through 110 Processing helix chain 'L' and resid 117 through 122 Processing helix chain 'L' and resid 128 through 146 removed outlier: 3.864A pdb=" N PHE L 133 " --> pdb=" O ARG L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 274 removed outlier: 4.370A pdb=" N VAL L 266 " --> pdb=" O SER L 263 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA L 267 " --> pdb=" O SER L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 298 Processing helix chain 'L' and resid 311 through 323 Processing helix chain 'L' and resid 360 through 362 No H-bonds generated for 'chain 'L' and resid 360 through 362' Processing helix chain 'L' and resid 381 through 390 Processing helix chain 'L' and resid 419 through 421 No H-bonds generated for 'chain 'L' and resid 419 through 421' Processing helix chain 'L' and resid 424 through 431 Processing helix chain 'L' and resid 446 through 455 Processing helix chain 'L' and resid 490 through 498 Processing helix chain 'L' and resid 516 through 525 removed outlier: 4.389A pdb=" N SER L 523 " --> pdb=" O ASN L 519 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS L 524 " --> pdb=" O ALA L 520 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE L 525 " --> pdb=" O VAL L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 533 through 535 No H-bonds generated for 'chain 'L' and resid 533 through 535' Processing helix chain 'L' and resid 558 through 565 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.860A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 36 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 345 through 347 Processing sheet with id= D, first strand: chain 'A' and resid 541 through 544 Processing sheet with id= E, first strand: chain 'A' and resid 614 through 616 Processing sheet with id= F, first strand: chain 'A' and resid 666 through 668 Processing sheet with id= G, first strand: chain 'A' and resid 815 through 822 Processing sheet with id= H, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.719A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 149 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.714A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 64 through 66 Processing sheet with id= K, first strand: chain 'E' and resid 198 through 202 removed outlier: 3.679A pdb=" N GLU E 201 " --> pdb=" O VAL E 210 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 436 through 438 removed outlier: 3.708A pdb=" N MET E 436 " --> pdb=" O THR E 279 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 438 " --> pdb=" O GLN E 281 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR E 396 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LEU E 280 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR E 398 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N GLY E 282 " --> pdb=" O TYR E 398 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 530 through 532 removed outlier: 5.633A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY E 571 " --> pdb=" O VAL E 544 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE E 546 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU E 573 " --> pdb=" O PHE E 546 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 64 through 66 Processing sheet with id= O, first strand: chain 'F' and resid 185 through 188 Processing sheet with id= P, first strand: chain 'F' and resid 277 through 281 removed outlier: 6.458A pdb=" N TYR F 396 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU F 280 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR F 398 " --> pdb=" O LEU F 280 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 471 through 475 removed outlier: 6.503A pdb=" N ILE F 572 " --> pdb=" O PHE F 472 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N MET F 474 " --> pdb=" O ILE F 572 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS F 574 " --> pdb=" O MET F 474 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL F 510 " --> pdb=" O ILE F 545 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N THR F 547 " --> pdb=" O VAL F 510 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE F 512 " --> pdb=" O THR F 547 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER F 513 " --> pdb=" O GLN F 531 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 127 through 132 removed outlier: 6.816A pdb=" N LEU H 189 " --> pdb=" O ILE H 156 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE H 156 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR H 149 " --> pdb=" O ALA H 152 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 19 through 21 removed outlier: 6.861A pdb=" N VAL G 71 " --> pdb=" O GLN G 117 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLN G 117 " --> pdb=" O VAL G 71 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 36 through 38 Processing sheet with id= U, first strand: chain 'G' and resid 345 through 347 Processing sheet with id= V, first strand: chain 'G' and resid 541 through 544 Processing sheet with id= W, first strand: chain 'G' and resid 614 through 616 Processing sheet with id= X, first strand: chain 'G' and resid 666 through 668 Processing sheet with id= Y, first strand: chain 'G' and resid 815 through 822 Processing sheet with id= Z, first strand: chain 'J' and resid 127 through 132 removed outlier: 6.714A pdb=" N LEU J 189 " --> pdb=" O ILE J 156 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE J 156 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 64 through 66 Processing sheet with id= AB, first strand: chain 'K' and resid 198 through 202 removed outlier: 3.678A pdb=" N GLU K 201 " --> pdb=" O VAL K 210 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'K' and resid 436 through 438 removed outlier: 3.709A pdb=" N MET K 436 " --> pdb=" O THR K 279 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU K 438 " --> pdb=" O GLN K 281 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR K 396 " --> pdb=" O SER K 278 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU K 280 " --> pdb=" O TYR K 396 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR K 398 " --> pdb=" O LEU K 280 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N GLY K 282 " --> pdb=" O TYR K 398 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'K' and resid 530 through 532 removed outlier: 5.633A pdb=" N PHE K 511 " --> pdb=" O GLN K 531 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLY K 571 " --> pdb=" O VAL K 544 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N PHE K 546 " --> pdb=" O GLY K 571 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU K 573 " --> pdb=" O PHE K 546 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 64 through 66 Processing sheet with id= AF, first strand: chain 'L' and resid 185 through 188 Processing sheet with id= AG, first strand: chain 'L' and resid 277 through 281 removed outlier: 6.458A pdb=" N TYR L 396 " --> pdb=" O SER L 278 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU L 280 " --> pdb=" O TYR L 396 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR L 398 " --> pdb=" O LEU L 280 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 471 through 475 removed outlier: 6.504A pdb=" N ILE L 572 " --> pdb=" O PHE L 472 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N MET L 474 " --> pdb=" O ILE L 572 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS L 574 " --> pdb=" O MET L 474 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL L 510 " --> pdb=" O ILE L 545 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N THR L 547 " --> pdb=" O VAL L 510 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE L 512 " --> pdb=" O THR L 547 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER L 513 " --> pdb=" O GLN L 531 " (cutoff:3.500A) 1325 hydrogen bonds defined for protein. 3651 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 168 hydrogen bonds 336 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 15.33 Time building geometry restraints manager: 20.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9891 1.33 - 1.46: 11051 1.46 - 1.58: 22628 1.58 - 1.70: 348 1.70 - 1.83: 440 Bond restraints: 44358 Sorted by residual: bond pdb=" F2 AF3 L1005 " pdb="AL AF3 L1005 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" F1 AF3 K 706 " pdb="AL AF3 K 706 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" F3 AF3 L1005 " pdb="AL AF3 L1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" F2 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" F1 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.65e+01 ... (remaining 44353 not shown) Histogram of bond angle deviations from ideal: 87.93 - 100.04: 29 100.04 - 112.15: 23116 112.15 - 124.25: 36459 124.25 - 136.36: 1377 136.36 - 148.46: 2 Bond angle restraints: 60983 Sorted by residual: angle pdb=" CB MET D 55 " pdb=" CG MET D 55 " pdb=" SD MET D 55 " ideal model delta sigma weight residual 112.70 148.46 -35.76 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CB MET J 55 " pdb=" CG MET J 55 " pdb=" SD MET J 55 " ideal model delta sigma weight residual 112.70 148.42 -35.72 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CA GLU C 50 " pdb=" CB GLU C 50 " pdb=" CG GLU C 50 " ideal model delta sigma weight residual 114.10 130.71 -16.61 2.00e+00 2.50e-01 6.90e+01 angle pdb=" CA GLU I 50 " pdb=" CB GLU I 50 " pdb=" CG GLU I 50 " ideal model delta sigma weight residual 114.10 130.67 -16.57 2.00e+00 2.50e-01 6.86e+01 angle pdb=" CA GLU C 74 " pdb=" CB GLU C 74 " pdb=" CG GLU C 74 " ideal model delta sigma weight residual 114.10 130.59 -16.49 2.00e+00 2.50e-01 6.80e+01 ... (remaining 60978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.50: 25614 33.50 - 67.00: 1101 67.00 - 100.50: 95 100.50 - 134.01: 27 134.01 - 167.51: 2 Dihedral angle restraints: 26839 sinusoidal: 11729 harmonic: 15110 Sorted by residual: dihedral pdb=" CA LYS L 189 " pdb=" C LYS L 189 " pdb=" N ASN L 190 " pdb=" CA ASN L 190 " ideal model delta harmonic sigma weight residual -180.00 -78.48 -101.52 0 5.00e+00 4.00e-02 4.12e+02 dihedral pdb=" CA LYS F 189 " pdb=" C LYS F 189 " pdb=" N ASN F 190 " pdb=" CA ASN F 190 " ideal model delta harmonic sigma weight residual -180.00 -78.49 -101.51 0 5.00e+00 4.00e-02 4.12e+02 dihedral pdb=" CA GLN D 158 " pdb=" C GLN D 158 " pdb=" N VAL D 159 " pdb=" CA VAL D 159 " ideal model delta harmonic sigma weight residual 180.00 133.51 46.49 0 5.00e+00 4.00e-02 8.65e+01 ... (remaining 26836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 6228 0.074 - 0.148: 781 0.148 - 0.222: 55 0.222 - 0.296: 22 0.296 - 0.370: 6 Chirality restraints: 7092 Sorted by residual: chirality pdb=" C17 1N7 K 707 " pdb=" C16 1N7 K 707 " pdb=" C18 1N7 K 707 " pdb=" O3 1N7 K 707 " both_signs ideal model delta sigma weight residual False 2.40 2.77 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C17 1N7 E 707 " pdb=" C16 1N7 E 707 " pdb=" C18 1N7 E 707 " pdb=" O3 1N7 E 707 " both_signs ideal model delta sigma weight residual False 2.40 2.77 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CB ILE F 258 " pdb=" CA ILE F 258 " pdb=" CG1 ILE F 258 " pdb=" CG2 ILE F 258 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 7089 not shown) Planarity restraints: 7223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 178 " -0.550 9.50e-02 1.11e+02 2.47e-01 3.95e+01 pdb=" NE ARG F 178 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG F 178 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG F 178 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG F 178 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 178 " 0.551 9.50e-02 1.11e+02 2.47e-01 3.94e+01 pdb=" NE ARG L 178 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG L 178 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG L 178 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG L 178 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 55 " -0.442 9.50e-02 1.11e+02 1.99e-01 2.86e+01 pdb=" NE ARG G 55 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG G 55 " -0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG G 55 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG G 55 " -0.003 2.00e-02 2.50e+03 ... (remaining 7220 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 723 2.63 - 3.20: 38447 3.20 - 3.77: 70031 3.77 - 4.33: 94814 4.33 - 4.90: 149585 Nonbonded interactions: 353600 Sorted by model distance: nonbonded pdb="MG MG K 705 " pdb=" F1 AF3 K 706 " model vdw 2.063 2.120 nonbonded pdb="MG MG E 705 " pdb=" F1 AF3 E 706 " model vdw 2.064 2.120 nonbonded pdb=" O ASP F 344 " pdb=" NE2 GLN G 81 " model vdw 2.103 2.520 nonbonded pdb=" O1B ADP E 704 " pdb="MG MG E 705 " model vdw 2.119 2.170 nonbonded pdb=" O2B ADP K 704 " pdb="MG MG K 705 " model vdw 2.119 2.170 ... (remaining 353595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = (chain 'B' and (resid 7 through 22 or (resid 23 through 25 and (name N or name C \ A or name C or name O or name CB )) or resid 26 through 49 or (resid 50 through \ 54 and (name N or name CA or name C or name O or name CB )) or resid 55 through \ 191)) selection = (chain 'D' and (resid 7 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and (n \ ame N or name CA or name C or name O or name CB )) or resid 40 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 or ( \ resid 50 through 54 and (name N or name CA or name C or name O or name CB )) or \ resid 55 through 191)) selection = (chain 'H' and (resid 7 through 22 or (resid 23 through 25 and (name N or name C \ A or name C or name O or name CB )) or resid 26 through 49 or (resid 50 through \ 54 and (name N or name CA or name C or name O or name CB )) or resid 55 through \ 191)) selection = (chain 'J' and (resid 7 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and (n \ ame N or name CA or name C or name O or name CB )) or resid 40 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thro \ ugh 51 or (resid 52 through 54 and (name N or name CA or name C or name O or nam \ e CB )) or resid 55 through 191)) } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = (chain 'E' and (resid 1 through 590 or resid 701 through 706)) selection = (chain 'F' and (resid 1 through 145 or (resid 146 and (name N or name CA or name \ C or name O or name CB )) or resid 147 through 148 or (resid 149 and (name N or \ name CA or name C or name O or name CB )) or resid 150 through 172 or (resid 17 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 174 through \ 177 or (resid 178 through 179 and (name N or name CA or name C or name O or name \ CB )) or resid 180 through 185 or (resid 186 and (name N or name CA or name C o \ r name O or name CB )) or resid 187 through 222 or (resid 223 through 225 and (n \ ame N or name CA or name C or name O or name CB )) or resid 226 or (resid 227 an \ d (name N or name CA or name C or name O or name CB )) or resid 228 through 229 \ or (resid 230 and (name N or name CA or name C or name O or name CB )) or resid \ 231 through 590 or resid 1000 through 1005)) selection = (chain 'K' and (resid 1 through 590 or resid 701 through 706)) selection = (chain 'L' and (resid 1 through 145 or (resid 146 and (name N or name CA or name \ C or name O or name CB )) or resid 147 through 148 or (resid 149 and (name N or \ name CA or name C or name O or name CB )) or resid 150 through 172 or (resid 17 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 174 through \ 177 or (resid 178 through 179 and (name N or name CA or name C or name O or name \ CB )) or resid 180 through 185 or (resid 186 and (name N or name CA or name C o \ r name O or name CB )) or resid 187 through 222 or (resid 223 through 225 and (n \ ame N or name CA or name C or name O or name CB )) or resid 226 or (resid 227 an \ d (name N or name CA or name C or name O or name CB )) or resid 228 through 229 \ or (resid 230 and (name N or name CA or name C or name O or name CB )) or resid \ 231 through 590 or resid 1000 through 1005)) } ncs_group { reference = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'T' selection = chain 'U' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.040 Extract box with map and model: 9.720 Check model and map are aligned: 0.730 Set scattering table: 0.440 Process input model: 126.840 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.006 0.164 44358 Z= 0.359 Angle : 1.052 35.764 60983 Z= 0.555 Chirality : 0.051 0.370 7092 Planarity : 0.008 0.247 7223 Dihedral : 17.695 167.506 17091 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 6.67 % Allowed : 1.69 % Favored : 91.63 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.70 (0.11), residues: 5082 helix: -0.51 (0.12), residues: 1906 sheet: -0.91 (0.23), residues: 546 loop : -1.64 (0.11), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 268 HIS 0.017 0.001 HIS G 82 PHE 0.024 0.002 PHE D 147 TYR 0.033 0.002 TYR D 138 ARG 0.036 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 453 time to evaluate : 4.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7602 (mtp85) REVERT: A 124 MET cc_start: 0.8067 (mmm) cc_final: 0.7850 (mmp) REVERT: A 545 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8503 (mmmm) REVERT: A 847 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8095 (mm) REVERT: B 149 TYR cc_start: 0.8538 (t80) cc_final: 0.8301 (t80) REVERT: C 60 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7637 (mt) REVERT: D 65 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7690 (mm-40) REVERT: D 69 GLN cc_start: 0.8673 (mm110) cc_final: 0.8344 (mm-40) REVERT: D 70 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7969 (tmm) REVERT: D 158 GLN cc_start: 0.5826 (OUTLIER) cc_final: 0.4994 (mm-40) REVERT: D 168 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.6953 (pp30) REVERT: E 185 TYR cc_start: 0.4452 (m-10) cc_final: 0.4243 (m-10) REVERT: E 438 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6795 (tt) REVERT: E 459 ASN cc_start: 0.7975 (m110) cc_final: 0.7081 (p0) REVERT: E 497 ARG cc_start: 0.3523 (OUTLIER) cc_final: 0.3221 (ttm170) REVERT: F 582 TYR cc_start: 0.5037 (OUTLIER) cc_final: 0.4680 (m-80) REVERT: H 64 ASP cc_start: 0.7348 (p0) cc_final: 0.6717 (p0) REVERT: G 900 LEU cc_start: 0.8698 (tp) cc_final: 0.8333 (tt) REVERT: G 913 SER cc_start: 0.7544 (OUTLIER) cc_final: 0.7146 (m) REVERT: J 69 GLN cc_start: 0.9232 (mm110) cc_final: 0.9031 (mm110) REVERT: J 161 ASP cc_start: 0.7004 (p0) cc_final: 0.6625 (p0) REVERT: K 68 MET cc_start: 0.5086 (ppp) cc_final: 0.4265 (ppp) REVERT: K 378 MET cc_start: 0.5648 (OUTLIER) cc_final: 0.4293 (tpt) REVERT: K 482 HIS cc_start: 0.3708 (t-170) cc_final: 0.3031 (m-70) REVERT: K 486 SER cc_start: -0.0581 (OUTLIER) cc_final: -0.0827 (t) REVERT: L 122 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8594 (pp) REVERT: L 254 PRO cc_start: 0.6500 (Cg_exo) cc_final: 0.6237 (Cg_endo) REVERT: L 576 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.6376 (ptp) REVERT: L 582 TYR cc_start: 0.4180 (OUTLIER) cc_final: 0.3846 (m-80) outliers start: 292 outliers final: 28 residues processed: 621 average time/residue: 0.5596 time to fit residues: 573.0511 Evaluate side-chains 329 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 284 time to evaluate : 4.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain G residue 681 SER Chi-restraints excluded: chain G residue 913 SER Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain K residue 378 MET Chi-restraints excluded: chain K residue 486 SER Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 212 ARG Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 576 MET Chi-restraints excluded: chain L residue 582 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 437 optimal weight: 2.9990 chunk 392 optimal weight: 9.9990 chunk 217 optimal weight: 0.0970 chunk 134 optimal weight: 0.0370 chunk 264 optimal weight: 0.6980 chunk 209 optimal weight: 0.9980 chunk 406 optimal weight: 30.0000 chunk 157 optimal weight: 50.0000 chunk 246 optimal weight: 0.0570 chunk 302 optimal weight: 0.0770 chunk 470 optimal weight: 9.9990 overall best weight: 0.1932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 177 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 HIS ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN E 62 GLN E 243 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN G 177 ASN ** G 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 752 HIS G 911 ASN K 243 GLN ** K 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 354 GLN L 554 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 44358 Z= 0.148 Angle : 0.598 12.624 60983 Z= 0.305 Chirality : 0.040 0.199 7092 Planarity : 0.004 0.064 7223 Dihedral : 14.099 166.968 8060 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.23 % Favored : 94.73 % Rotamer: Outliers : 2.06 % Allowed : 7.57 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.24 (0.12), residues: 5082 helix: -0.02 (0.12), residues: 1928 sheet: -0.69 (0.23), residues: 538 loop : -1.47 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 506 HIS 0.004 0.001 HIS G 75 PHE 0.025 0.001 PHE J 49 TYR 0.019 0.001 TYR J 135 ARG 0.008 0.001 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 325 time to evaluate : 4.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 715 ILE cc_start: 0.8820 (mm) cc_final: 0.8615 (mm) REVERT: C 52 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8079 (tpt) REVERT: C 62 MET cc_start: 0.8161 (mmm) cc_final: 0.7575 (mtt) REVERT: D 65 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7547 (mm110) REVERT: D 69 GLN cc_start: 0.8685 (mm110) cc_final: 0.8164 (mm-40) REVERT: E 270 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7876 (mm110) REVERT: E 459 ASN cc_start: 0.7913 (m110) cc_final: 0.6951 (p0) REVERT: F 545 ILE cc_start: 0.7219 (mm) cc_final: 0.6583 (pt) REVERT: H 60 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7615 (tm-30) REVERT: H 64 ASP cc_start: 0.6848 (p0) cc_final: 0.6516 (p0) REVERT: G 865 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7900 (m-30) REVERT: G 900 LEU cc_start: 0.8641 (tp) cc_final: 0.8207 (tt) REVERT: I 70 LYS cc_start: 0.8567 (mmmt) cc_final: 0.8221 (mttp) REVERT: J 65 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7368 (mm110) REVERT: J 70 MET cc_start: 0.7854 (tpp) cc_final: 0.7549 (mmt) REVERT: K 68 MET cc_start: 0.5106 (ppp) cc_final: 0.4303 (ppp) REVERT: K 274 MET cc_start: 0.6436 (pmm) cc_final: 0.6040 (pmm) REVERT: K 466 ASP cc_start: 0.5027 (p0) cc_final: 0.4797 (m-30) REVERT: K 482 HIS cc_start: 0.3844 (t-170) cc_final: 0.3149 (m-70) REVERT: K 486 SER cc_start: -0.0776 (OUTLIER) cc_final: -0.1142 (t) REVERT: L 212 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6358 (pmt-80) REVERT: L 219 LEU cc_start: 0.6070 (mp) cc_final: 0.5724 (mp) REVERT: L 254 PRO cc_start: 0.6272 (Cg_exo) cc_final: 0.6064 (Cg_endo) REVERT: L 436 MET cc_start: 0.4100 (ttt) cc_final: 0.1847 (mpp) outliers start: 90 outliers final: 38 residues processed: 386 average time/residue: 0.4954 time to fit residues: 327.5870 Evaluate side-chains 314 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 270 time to evaluate : 4.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 523 SER Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 386 ASN Chi-restraints excluded: chain G residue 681 SER Chi-restraints excluded: chain G residue 865 ASP Chi-restraints excluded: chain G residue 877 TYR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 442 ARG Chi-restraints excluded: chain K residue 486 SER Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 212 ARG Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 545 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 261 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 391 optimal weight: 4.9990 chunk 320 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 471 optimal weight: 9.9990 chunk 509 optimal weight: 20.0000 chunk 419 optimal weight: 0.0470 chunk 467 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 378 optimal weight: 8.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 ASN F 270 GLN ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS G 177 ASN ** G 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 911 ASN J 158 GLN K 311 HIS ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 44358 Z= 0.186 Angle : 0.573 12.499 60983 Z= 0.291 Chirality : 0.040 0.201 7092 Planarity : 0.004 0.044 7223 Dihedral : 13.249 179.358 7989 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.65 % Favored : 94.31 % Rotamer: Outliers : 1.78 % Allowed : 9.85 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 5082 helix: 0.23 (0.12), residues: 1944 sheet: -0.62 (0.22), residues: 552 loop : -1.28 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 506 HIS 0.006 0.001 HIS G 309 PHE 0.015 0.001 PHE G 741 TYR 0.017 0.001 TYR A 32 ARG 0.007 0.000 ARG E 442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 287 time to evaluate : 4.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 ASN cc_start: 0.7476 (OUTLIER) cc_final: 0.7191 (m110) REVERT: A 715 ILE cc_start: 0.9000 (mm) cc_final: 0.8794 (mm) REVERT: A 899 MET cc_start: 0.8363 (ttm) cc_final: 0.8152 (ttm) REVERT: C 62 MET cc_start: 0.8225 (mmm) cc_final: 0.7391 (mtt) REVERT: E 474 MET cc_start: -0.0627 (tmm) cc_final: -0.0990 (tmm) REVERT: G 865 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7961 (m-30) REVERT: G 900 LEU cc_start: 0.8676 (tp) cc_final: 0.8255 (tt) REVERT: I 70 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8287 (mttp) REVERT: J 70 MET cc_start: 0.7994 (tpp) cc_final: 0.7569 (mmt) REVERT: J 158 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6393 (mm-40) REVERT: K 68 MET cc_start: 0.5225 (ppp) cc_final: 0.3851 (ppp) REVERT: K 466 ASP cc_start: 0.4899 (p0) cc_final: 0.4656 (m-30) REVERT: K 482 HIS cc_start: 0.4330 (t-170) cc_final: 0.3664 (m170) REVERT: L 219 LEU cc_start: 0.6771 (mp) cc_final: 0.6494 (mp) REVERT: L 436 MET cc_start: 0.4133 (ttt) cc_final: 0.1791 (mpp) outliers start: 78 outliers final: 48 residues processed: 348 average time/residue: 0.4909 time to fit residues: 296.7397 Evaluate side-chains 299 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 248 time to evaluate : 4.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 523 SER Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 386 ASN Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain G residue 865 ASP Chi-restraints excluded: chain G residue 877 TYR Chi-restraints excluded: chain G residue 885 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 311 HIS Chi-restraints excluded: chain K residue 442 ARG Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 370 ILE Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 545 ILE Chi-restraints excluded: chain L residue 580 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 465 optimal weight: 20.0000 chunk 354 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 316 optimal weight: 8.9990 chunk 472 optimal weight: 6.9990 chunk 500 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 448 optimal weight: 30.0000 chunk 134 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 790 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS ** E 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 GLN ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN ** G 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 911 ASN ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 GLN K 311 HIS ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 44358 Z= 0.172 Angle : 0.545 12.513 60983 Z= 0.276 Chirality : 0.039 0.193 7092 Planarity : 0.003 0.039 7223 Dihedral : 12.842 155.782 7968 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.19 % Favored : 94.77 % Rotamer: Outliers : 1.97 % Allowed : 11.11 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.12), residues: 5082 helix: 0.40 (0.12), residues: 1940 sheet: -0.52 (0.23), residues: 530 loop : -1.18 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 506 HIS 0.029 0.001 HIS K 311 PHE 0.014 0.001 PHE G 741 TYR 0.019 0.001 TYR B 135 ARG 0.006 0.000 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 264 time to evaluate : 4.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.7255 (m110) REVERT: A 715 ILE cc_start: 0.9043 (mm) cc_final: 0.8821 (mm) REVERT: A 899 MET cc_start: 0.8379 (ttm) cc_final: 0.8155 (ttm) REVERT: C 52 MET cc_start: 0.8998 (tpp) cc_final: 0.8383 (tpt) REVERT: D 70 MET cc_start: 0.8071 (tmm) cc_final: 0.7862 (tmm) REVERT: E 311 HIS cc_start: 0.2969 (m-70) cc_final: 0.2414 (m-70) REVERT: F 68 MET cc_start: 0.7372 (tpp) cc_final: 0.7053 (tpt) REVERT: F 147 LEU cc_start: 0.8473 (tp) cc_final: 0.8201 (tt) REVERT: F 474 MET cc_start: 0.7684 (ptp) cc_final: 0.7278 (pmm) REVERT: F 572 ILE cc_start: 0.4734 (OUTLIER) cc_final: 0.4223 (tt) REVERT: F 576 MET cc_start: 0.4582 (OUTLIER) cc_final: 0.3806 (mpp) REVERT: G 865 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.8022 (m-30) REVERT: G 900 LEU cc_start: 0.8593 (tp) cc_final: 0.8167 (tt) REVERT: J 70 MET cc_start: 0.8031 (tpp) cc_final: 0.7597 (mmt) REVERT: K 68 MET cc_start: 0.5276 (ppp) cc_final: 0.4007 (ppp) REVERT: K 311 HIS cc_start: 0.2657 (OUTLIER) cc_final: 0.2377 (t-90) REVERT: K 482 HIS cc_start: 0.4274 (t-170) cc_final: 0.3615 (m170) REVERT: L 429 MET cc_start: 0.6806 (ptm) cc_final: 0.6339 (ppp) REVERT: L 436 MET cc_start: 0.4399 (ttt) cc_final: 0.2049 (mpp) outliers start: 86 outliers final: 56 residues processed: 334 average time/residue: 0.4926 time to fit residues: 285.1193 Evaluate side-chains 303 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 242 time to evaluate : 4.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 386 ASN Chi-restraints excluded: chain G residue 591 THR Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain G residue 758 LEU Chi-restraints excluded: chain G residue 865 ASP Chi-restraints excluded: chain G residue 885 LEU Chi-restraints excluded: chain G residue 911 ASN Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 311 HIS Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 370 ILE Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 545 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 417 optimal weight: 9.9990 chunk 284 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 372 optimal weight: 0.9990 chunk 206 optimal weight: 10.0000 chunk 427 optimal weight: 20.0000 chunk 346 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 255 optimal weight: 50.0000 chunk 449 optimal weight: 50.0000 chunk 126 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 357 GLN A 534 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 GLN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN G 357 GLN G 497 ASN ** G 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 311 HIS ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 44358 Z= 0.386 Angle : 0.663 12.460 60983 Z= 0.341 Chirality : 0.043 0.202 7092 Planarity : 0.004 0.055 7223 Dihedral : 12.918 165.959 7968 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.24 % Favored : 93.72 % Rotamer: Outliers : 2.38 % Allowed : 11.86 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 5082 helix: 0.17 (0.12), residues: 1968 sheet: -0.64 (0.22), residues: 544 loop : -1.24 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 916 HIS 0.047 0.002 HIS K 311 PHE 0.025 0.002 PHE G 77 TYR 0.023 0.002 TYR L 149 ARG 0.008 0.001 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 252 time to evaluate : 5.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 715 ILE cc_start: 0.9048 (mm) cc_final: 0.8830 (mm) REVERT: A 899 MET cc_start: 0.8458 (ttm) cc_final: 0.8188 (ttm) REVERT: D 22 TYR cc_start: 0.5022 (t80) cc_final: 0.4404 (t80) REVERT: D 70 MET cc_start: 0.8226 (tmm) cc_final: 0.7823 (tmm) REVERT: E 311 HIS cc_start: 0.3061 (m-70) cc_final: 0.2765 (m90) REVERT: E 474 MET cc_start: -0.0129 (tmm) cc_final: -0.0351 (tmm) REVERT: F 474 MET cc_start: 0.7859 (ptp) cc_final: 0.7549 (pmm) REVERT: F 560 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6193 (ttm110) REVERT: F 572 ILE cc_start: 0.4748 (OUTLIER) cc_final: 0.4251 (tt) REVERT: G 900 LEU cc_start: 0.8574 (tp) cc_final: 0.8100 (tt) REVERT: I 70 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8390 (mttt) REVERT: J 70 MET cc_start: 0.8157 (tpp) cc_final: 0.7707 (mmt) REVERT: J 155 GLU cc_start: 0.8219 (pm20) cc_final: 0.7984 (pm20) REVERT: K 68 MET cc_start: 0.4991 (ppp) cc_final: 0.3934 (ppp) REVERT: K 274 MET cc_start: 0.6086 (pmm) cc_final: 0.5870 (pmm) REVERT: L 429 MET cc_start: 0.6579 (ptm) cc_final: 0.6360 (ppp) REVERT: L 436 MET cc_start: 0.4689 (ttt) cc_final: 0.2105 (mpp) REVERT: L 466 ASP cc_start: 0.6091 (t0) cc_final: 0.5561 (p0) outliers start: 104 outliers final: 67 residues processed: 343 average time/residue: 0.5035 time to fit residues: 297.8692 Evaluate side-chains 295 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 226 time to evaluate : 4.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain D residue 73 GLN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain F residue 81 PHE Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 560 ARG Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 386 ASN Chi-restraints excluded: chain G residue 567 THR Chi-restraints excluded: chain G residue 591 THR Chi-restraints excluded: chain G residue 592 SER Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain G residue 885 LEU Chi-restraints excluded: chain G residue 905 VAL Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 119 ILE Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 370 ILE Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 545 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 168 optimal weight: 9.9990 chunk 450 optimal weight: 30.0000 chunk 98 optimal weight: 4.9990 chunk 293 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 501 optimal weight: 8.9990 chunk 416 optimal weight: 40.0000 chunk 232 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 165 optimal weight: 7.9990 chunk 263 optimal weight: 0.8980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 GLN F 281 GLN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 44358 Z= 0.259 Angle : 0.583 12.334 60983 Z= 0.297 Chirality : 0.040 0.196 7092 Planarity : 0.003 0.042 7223 Dihedral : 12.854 176.574 7967 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.43 % Rotamer: Outliers : 2.19 % Allowed : 13.14 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.12), residues: 5082 helix: 0.32 (0.12), residues: 1964 sheet: -0.58 (0.22), residues: 528 loop : -1.16 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 182 HIS 0.010 0.001 HIS G 613 PHE 0.016 0.001 PHE G 741 TYR 0.023 0.001 TYR F 198 ARG 0.007 0.000 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 237 time to evaluate : 4.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8127 (pttp) REVERT: A 715 ILE cc_start: 0.9055 (mm) cc_final: 0.8827 (mm) REVERT: A 899 MET cc_start: 0.8545 (ttm) cc_final: 0.8324 (ttm) REVERT: D 22 TYR cc_start: 0.5121 (t80) cc_final: 0.4591 (t80) REVERT: D 70 MET cc_start: 0.8345 (tmm) cc_final: 0.8020 (tmm) REVERT: E 436 MET cc_start: 0.3953 (mtt) cc_final: 0.3640 (mtt) REVERT: F 474 MET cc_start: 0.7698 (ptp) cc_final: 0.7364 (pmm) REVERT: F 526 LEU cc_start: 0.4584 (OUTLIER) cc_final: 0.3999 (tp) REVERT: F 560 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.6116 (ttm110) REVERT: G 380 MET cc_start: 0.7913 (mmm) cc_final: 0.7691 (tpt) REVERT: I 70 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8353 (mttt) REVERT: J 70 MET cc_start: 0.8175 (tpp) cc_final: 0.7733 (mmt) REVERT: J 77 GLU cc_start: 0.8578 (pm20) cc_final: 0.8252 (pm20) REVERT: K 68 MET cc_start: 0.4969 (ppp) cc_final: 0.3934 (ppp) REVERT: L 436 MET cc_start: 0.5047 (ttt) cc_final: 0.2481 (mpp) REVERT: L 466 ASP cc_start: 0.6077 (t0) cc_final: 0.5513 (p0) outliers start: 96 outliers final: 68 residues processed: 316 average time/residue: 0.4957 time to fit residues: 273.9749 Evaluate side-chains 293 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 222 time to evaluate : 4.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain D residue 73 GLN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 560 ARG Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 386 ASN Chi-restraints excluded: chain G residue 591 THR Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain G residue 736 ASP Chi-restraints excluded: chain G residue 854 LEU Chi-restraints excluded: chain G residue 885 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 119 ILE Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 370 ILE Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 545 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 483 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 365 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 chunk 421 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 chunk 499 optimal weight: 0.0370 chunk 312 optimal weight: 7.9990 chunk 304 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 177 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN F 537 GLN ** G 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 752 HIS ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 548 GLN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 ASN L 265 ASN ** L 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 44358 Z= 0.324 Angle : 0.609 12.238 60983 Z= 0.311 Chirality : 0.042 0.200 7092 Planarity : 0.004 0.041 7223 Dihedral : 12.806 145.908 7967 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.30 % Favored : 93.66 % Rotamer: Outliers : 2.19 % Allowed : 13.78 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.12), residues: 5082 helix: 0.26 (0.12), residues: 1956 sheet: -0.64 (0.22), residues: 544 loop : -1.15 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 916 HIS 0.022 0.001 HIS E 164 PHE 0.016 0.002 PHE G 741 TYR 0.019 0.001 TYR F 198 ARG 0.006 0.001 ARG J 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 242 time to evaluate : 4.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.8042 (tmtt) cc_final: 0.7825 (tptp) REVERT: A 551 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8142 (pttp) REVERT: A 715 ILE cc_start: 0.9068 (mm) cc_final: 0.8811 (mm) REVERT: C 62 MET cc_start: 0.8192 (mmm) cc_final: 0.7651 (mtt) REVERT: D 22 TYR cc_start: 0.5098 (t80) cc_final: 0.4692 (t80) REVERT: D 70 MET cc_start: 0.8272 (tmm) cc_final: 0.8028 (tmm) REVERT: F 197 GLU cc_start: 0.7028 (mp0) cc_final: 0.6380 (mp0) REVERT: F 474 MET cc_start: 0.7914 (ptp) cc_final: 0.7642 (pmm) REVERT: F 526 LEU cc_start: 0.4585 (OUTLIER) cc_final: 0.4151 (tp) REVERT: F 572 ILE cc_start: 0.4865 (OUTLIER) cc_final: 0.4403 (tt) REVERT: G 380 MET cc_start: 0.7952 (mmm) cc_final: 0.7701 (tpt) REVERT: G 900 LEU cc_start: 0.8724 (tp) cc_final: 0.8309 (tt) REVERT: I 69 ASN cc_start: 0.8691 (t0) cc_final: 0.8370 (t0) REVERT: J 70 MET cc_start: 0.8305 (tpp) cc_final: 0.7828 (mmt) REVERT: K 68 MET cc_start: 0.4975 (ppp) cc_final: 0.3846 (ppp) REVERT: K 526 LEU cc_start: -0.0831 (OUTLIER) cc_final: -0.1041 (pp) REVERT: L 429 MET cc_start: 0.6584 (ppp) cc_final: 0.6169 (ptm) REVERT: L 436 MET cc_start: 0.4763 (ttt) cc_final: 0.2419 (mpp) REVERT: L 466 ASP cc_start: 0.6392 (t0) cc_final: 0.5717 (p0) REVERT: L 474 MET cc_start: 0.8336 (tmm) cc_final: 0.8118 (tmm) outliers start: 96 outliers final: 68 residues processed: 323 average time/residue: 0.5040 time to fit residues: 287.0329 Evaluate side-chains 292 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 220 time to evaluate : 4.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 81 PHE Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 157 GLN Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 386 ASN Chi-restraints excluded: chain G residue 591 THR Chi-restraints excluded: chain G residue 592 SER Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain G residue 736 ASP Chi-restraints excluded: chain G residue 854 LEU Chi-restraints excluded: chain G residue 885 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 119 ILE Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 526 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 370 ILE Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 545 ILE Chi-restraints excluded: chain L residue 572 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 308 optimal weight: 0.5980 chunk 199 optimal weight: 6.9990 chunk 298 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 317 optimal weight: 3.9990 chunk 340 optimal weight: 0.9980 chunk 246 optimal weight: 0.0570 chunk 46 optimal weight: 0.7980 chunk 392 optimal weight: 8.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN G 5 GLN G 9 ASN ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 548 GLN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 44358 Z= 0.148 Angle : 0.548 12.187 60983 Z= 0.276 Chirality : 0.039 0.371 7092 Planarity : 0.003 0.042 7223 Dihedral : 12.669 143.526 7963 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.78 % Favored : 95.18 % Rotamer: Outliers : 1.67 % Allowed : 14.95 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.12), residues: 5082 helix: 0.50 (0.12), residues: 1946 sheet: -0.48 (0.23), residues: 528 loop : -1.06 (0.12), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 506 HIS 0.010 0.001 HIS G 613 PHE 0.014 0.001 PHE A 652 TYR 0.020 0.001 TYR E 185 ARG 0.003 0.000 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 248 time to evaluate : 4.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8126 (pttp) REVERT: A 715 ILE cc_start: 0.9044 (mm) cc_final: 0.8775 (mm) REVERT: A 814 SER cc_start: 0.8929 (m) cc_final: 0.8595 (t) REVERT: C 62 MET cc_start: 0.8173 (mmm) cc_final: 0.7673 (mtt) REVERT: D 22 TYR cc_start: 0.5045 (t80) cc_final: 0.4810 (t80) REVERT: D 70 MET cc_start: 0.8178 (tmm) cc_final: 0.7949 (tmm) REVERT: D 73 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7880 (tm-30) REVERT: F 197 GLU cc_start: 0.7041 (mp0) cc_final: 0.6655 (mp0) REVERT: F 378 MET cc_start: 0.7667 (mmm) cc_final: 0.6196 (tmm) REVERT: F 474 MET cc_start: 0.7718 (ptp) cc_final: 0.7457 (pmm) REVERT: F 526 LEU cc_start: 0.4639 (OUTLIER) cc_final: 0.4171 (tp) REVERT: F 572 ILE cc_start: 0.4805 (OUTLIER) cc_final: 0.4343 (tt) REVERT: G 380 MET cc_start: 0.7814 (mmm) cc_final: 0.7591 (tpt) REVERT: G 902 MET cc_start: 0.7059 (tmm) cc_final: 0.6708 (ttp) REVERT: I 70 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8368 (mttt) REVERT: J 70 MET cc_start: 0.8217 (tpp) cc_final: 0.7735 (mmt) REVERT: K 68 MET cc_start: 0.5013 (ppp) cc_final: 0.3860 (ppp) REVERT: K 119 ASP cc_start: 0.3788 (OUTLIER) cc_final: 0.3354 (p0) REVERT: L 122 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8861 (pp) REVERT: L 375 GLU cc_start: 0.7872 (tp30) cc_final: 0.7545 (tp30) REVERT: L 429 MET cc_start: 0.6680 (ppp) cc_final: 0.6227 (ptm) REVERT: L 436 MET cc_start: 0.4814 (ttt) cc_final: 0.2453 (mpp) REVERT: L 466 ASP cc_start: 0.6277 (t0) cc_final: 0.5676 (p0) REVERT: L 474 MET cc_start: 0.8315 (tmm) cc_final: 0.8090 (tmm) outliers start: 73 outliers final: 50 residues processed: 314 average time/residue: 0.4800 time to fit residues: 263.4508 Evaluate side-chains 284 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 229 time to evaluate : 4.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain F residue 81 PHE Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 386 ASN Chi-restraints excluded: chain G residue 613 HIS Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 885 LEU Chi-restraints excluded: chain G residue 905 VAL Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 545 ILE Chi-restraints excluded: chain L residue 572 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 454 optimal weight: 0.8980 chunk 478 optimal weight: 20.0000 chunk 436 optimal weight: 8.9990 chunk 465 optimal weight: 20.0000 chunk 280 optimal weight: 9.9990 chunk 202 optimal weight: 0.8980 chunk 365 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 420 optimal weight: 0.0010 chunk 440 optimal weight: 0.9980 chunk 463 optimal weight: 0.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN G 9 ASN G 408 GLN ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 548 GLN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 44358 Z= 0.140 Angle : 0.541 12.088 60983 Z= 0.271 Chirality : 0.039 0.319 7092 Planarity : 0.003 0.041 7223 Dihedral : 12.530 131.559 7963 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.27 % Favored : 94.69 % Rotamer: Outliers : 1.53 % Allowed : 15.45 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.12), residues: 5082 helix: 0.67 (0.12), residues: 1952 sheet: -0.39 (0.23), residues: 536 loop : -1.06 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 506 HIS 0.023 0.001 HIS L 482 PHE 0.013 0.001 PHE G 741 TYR 0.022 0.001 TYR E 185 ARG 0.004 0.000 ARG F 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 239 time to evaluate : 4.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8213 (pttp) REVERT: A 715 ILE cc_start: 0.8993 (mm) cc_final: 0.8715 (mm) REVERT: A 814 SER cc_start: 0.8894 (m) cc_final: 0.8555 (t) REVERT: C 62 MET cc_start: 0.8151 (mmm) cc_final: 0.7874 (mtm) REVERT: D 22 TYR cc_start: 0.5012 (t80) cc_final: 0.4783 (t80) REVERT: D 70 MET cc_start: 0.8214 (tmm) cc_final: 0.7969 (tmm) REVERT: D 73 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7895 (tm-30) REVERT: F 378 MET cc_start: 0.7639 (mmm) cc_final: 0.6150 (tmm) REVERT: F 429 MET cc_start: 0.6147 (mmt) cc_final: 0.5515 (mmt) REVERT: F 474 MET cc_start: 0.7638 (ptp) cc_final: 0.7396 (pmm) REVERT: F 526 LEU cc_start: 0.4630 (OUTLIER) cc_final: 0.3976 (tp) REVERT: F 572 ILE cc_start: 0.4711 (OUTLIER) cc_final: 0.4236 (tt) REVERT: H 51 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7711 (mtm110) REVERT: H 57 ARG cc_start: 0.8325 (mpt-90) cc_final: 0.8106 (mmt-90) REVERT: G 380 MET cc_start: 0.7764 (mmm) cc_final: 0.7455 (tpt) REVERT: G 902 MET cc_start: 0.6823 (tmm) cc_final: 0.6552 (ttp) REVERT: I 70 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8316 (mttt) REVERT: J 70 MET cc_start: 0.8167 (tpp) cc_final: 0.7706 (mmt) REVERT: K 68 MET cc_start: 0.5069 (ppp) cc_final: 0.3722 (ppp) REVERT: K 119 ASP cc_start: 0.3811 (OUTLIER) cc_final: 0.3381 (p0) REVERT: L 375 GLU cc_start: 0.7849 (tp30) cc_final: 0.7479 (tp30) REVERT: L 429 MET cc_start: 0.6642 (ppp) cc_final: 0.6167 (ptm) REVERT: L 436 MET cc_start: 0.4769 (ttt) cc_final: 0.2470 (mpp) REVERT: L 466 ASP cc_start: 0.6203 (t0) cc_final: 0.5726 (p0) REVERT: L 474 MET cc_start: 0.8265 (tmm) cc_final: 0.8038 (tmm) outliers start: 67 outliers final: 48 residues processed: 301 average time/residue: 0.5029 time to fit residues: 262.7551 Evaluate side-chains 277 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 225 time to evaluate : 4.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain F residue 81 PHE Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 157 GLN Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 386 ASN Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 885 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 545 ILE Chi-restraints excluded: chain L residue 572 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 305 optimal weight: 4.9990 chunk 491 optimal weight: 4.9990 chunk 300 optimal weight: 0.8980 chunk 233 optimal weight: 20.0000 chunk 342 optimal weight: 5.9990 chunk 516 optimal weight: 10.0000 chunk 474 optimal weight: 9.9990 chunk 410 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 317 optimal weight: 3.9990 chunk 251 optimal weight: 50.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 44358 Z= 0.281 Angle : 0.591 13.033 60983 Z= 0.298 Chirality : 0.041 0.289 7092 Planarity : 0.004 0.042 7223 Dihedral : 12.583 128.642 7963 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.80 % Favored : 94.16 % Rotamer: Outliers : 1.37 % Allowed : 15.75 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.12), residues: 5082 helix: 0.57 (0.12), residues: 1946 sheet: -0.39 (0.23), residues: 498 loop : -1.09 (0.12), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 182 HIS 0.022 0.001 HIS L 482 PHE 0.016 0.001 PHE F 182 TYR 0.019 0.001 TYR L 149 ARG 0.004 0.000 ARG F 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 235 time to evaluate : 4.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8218 (pttp) REVERT: A 715 ILE cc_start: 0.9046 (mm) cc_final: 0.8774 (mm) REVERT: C 62 MET cc_start: 0.8139 (mmm) cc_final: 0.7684 (mtt) REVERT: D 70 MET cc_start: 0.8259 (tmm) cc_final: 0.7972 (tmm) REVERT: D 73 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7963 (tm-30) REVERT: F 474 MET cc_start: 0.7836 (ptp) cc_final: 0.7547 (pmm) REVERT: F 526 LEU cc_start: 0.4609 (OUTLIER) cc_final: 0.4155 (tp) REVERT: F 572 ILE cc_start: 0.4583 (OUTLIER) cc_final: 0.4122 (tt) REVERT: G 902 MET cc_start: 0.6929 (tmm) cc_final: 0.6531 (ttp) REVERT: J 70 MET cc_start: 0.8233 (tpp) cc_final: 0.7745 (mmt) REVERT: K 68 MET cc_start: 0.5021 (ppp) cc_final: 0.3745 (ppp) REVERT: K 119 ASP cc_start: 0.3768 (OUTLIER) cc_final: 0.3563 (p0) REVERT: K 257 ASN cc_start: 0.7092 (m-40) cc_final: 0.6870 (t0) REVERT: L 375 GLU cc_start: 0.7996 (tp30) cc_final: 0.7552 (tp30) REVERT: L 429 MET cc_start: 0.6601 (ppp) cc_final: 0.6034 (ptm) REVERT: L 436 MET cc_start: 0.4402 (ttt) cc_final: 0.2139 (mpp) REVERT: L 466 ASP cc_start: 0.6381 (t0) cc_final: 0.5843 (p0) outliers start: 60 outliers final: 52 residues processed: 289 average time/residue: 0.5096 time to fit residues: 255.5555 Evaluate side-chains 281 residues out of total 4460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 225 time to evaluate : 4.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain F residue 81 PHE Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 386 ASN Chi-restraints excluded: chain G residue 591 THR Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 885 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 545 ILE Chi-restraints excluded: chain L residue 572 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 326 optimal weight: 0.9990 chunk 437 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 378 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 411 optimal weight: 0.3980 chunk 172 optimal weight: 8.9990 chunk 422 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 548 GLN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.119050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.072985 restraints weight = 123944.264| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.03 r_work: 0.3066 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 44358 Z= 0.168 Angle : 0.553 12.549 60983 Z= 0.276 Chirality : 0.039 0.305 7092 Planarity : 0.003 0.042 7223 Dihedral : 12.541 127.772 7963 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 1.39 % Allowed : 15.68 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.12), residues: 5082 helix: 0.68 (0.12), residues: 1940 sheet: -0.40 (0.23), residues: 514 loop : -1.03 (0.12), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 182 HIS 0.021 0.001 HIS L 482 PHE 0.014 0.001 PHE G 741 TYR 0.031 0.001 TYR L 149 ARG 0.007 0.000 ARG G 735 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9196.08 seconds wall clock time: 167 minutes 34.77 seconds (10054.77 seconds total)