Starting phenix.real_space_refine on Mon Mar 25 21:21:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7m_37343/03_2024/8w7m_37343_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7m_37343/03_2024/8w7m_37343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7m_37343/03_2024/8w7m_37343.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7m_37343/03_2024/8w7m_37343.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7m_37343/03_2024/8w7m_37343_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7m_37343/03_2024/8w7m_37343_neut_updated.pdb" } resolution = 4.12 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= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 18 5.49 5 Mg 4 5.21 5 S 229 5.16 5 C 32459 2.51 5 N 8757 2.21 5 O 9724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 GLU 221": "OE1" <-> "OE2" Residue "2 GLU 280": "OE1" <-> "OE2" Residue "2 TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 58": "OD1" <-> "OD2" Residue "3 PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 375": "OD1" <-> "OD2" Residue "3 GLU 474": "OE1" <-> "OE2" Residue "3 ASP 741": "OD1" <-> "OD2" Residue "4 TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 562": "OE1" <-> "OE2" Residue "5 PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 329": "OE1" <-> "OE2" Residue "6 TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 213": "NH1" <-> "NH2" Residue "7 TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 427": "OD1" <-> "OD2" Residue "7 ASP 530": "OD1" <-> "OD2" Residue "7 ASP 607": "OD1" <-> "OD2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 160": "OD1" <-> "OD2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 561": "OD1" <-> "OD2" Residue "E TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 863": "OD1" <-> "OD2" Residue "G GLU 610": "OE1" <-> "OE2" Residue "G TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 694": "OD1" <-> "OD2" Residue "G PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 51196 Number of models: 1 Model: "" Number of chains: 22 Chain: "2" Number of atoms: 4955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4955 Classifications: {'peptide': 627} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 602} Chain breaks: 6 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "3" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4835 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 589} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "4" Number of atoms: 4947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4947 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 598} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 4176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4176 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 507} Chain breaks: 12 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 4837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4837 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 591} Chain breaks: 6 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 5124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5124 Classifications: {'peptide': 657} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 30, 'TRANS': 626} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1602 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 3, 'TRANS': 192} Chain breaks: 1 Chain: "B" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1617 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 1 Chain: "C" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1387 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2004 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain breaks: 2 Chain: "E" Number of atoms: 4591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4591 Classifications: {'peptide': 568} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 552} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3404 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 400} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3380 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3411 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 401} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 160 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "N" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 641 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 78} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "2" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1301 SG CYS 2 341 86.191 104.981 134.408 1.00326.76 S ATOM 1324 SG CYS 2 344 86.470 108.588 132.381 1.00328.60 S ATOM 1482 SG CYS 2 364 89.361 106.701 133.841 1.00327.66 S ATOM 1503 SG CYS 2 367 86.741 108.417 135.982 1.00331.69 S ATOM 11219 SG CYS 4 349 100.544 102.137 168.254 1.00375.19 S ATOM 11240 SG CYS 4 352 102.493 103.585 170.704 1.00369.06 S ATOM 11387 SG CYS 4 371 98.887 103.065 171.636 1.00367.10 S ATOM 11429 SG CYS 4 376 99.992 105.859 169.089 1.00360.25 S ATOM 15874 SG CYS 5 183 63.758 105.227 133.644 1.00243.31 S ATOM 15899 SG CYS 5 186 61.936 108.171 133.572 1.00253.41 S ATOM 16046 SG CYS 5 211 65.409 108.944 133.543 1.00256.56 S ATOM 16074 SG CYS 5 236 64.228 107.218 136.744 1.00265.16 S ATOM 20192 SG CYS 6 311 100.857 104.747 147.167 1.00273.32 S ATOM 20214 SG CYS 6 314 103.132 107.603 146.700 1.00270.00 S ATOM 20371 SG CYS 6 333 102.425 106.214 150.237 1.00270.21 S ATOM 20405 SG CYS 6 338 99.956 108.399 148.223 1.00285.87 S ATOM 25303 SG CYS 7 262 75.943 99.009 177.999 1.00393.18 S ATOM 25326 SG CYS 7 265 72.407 99.906 179.363 1.00387.79 S ATOM 25476 SG CYS 7 284 73.118 99.622 175.698 1.00375.91 S ATOM 25513 SG CYS 7 289 74.483 102.601 177.676 1.00384.22 S Time building chain proxies: 24.48, per 1000 atoms: 0.48 Number of scatterers: 51196 At special positions: 0 Unit cell: (150.52, 195.04, 224.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 229 16.00 P 18 15.00 Mg 4 11.99 O 9724 8.00 N 8757 7.00 C 32459 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.15 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 903 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 341 " pdb=" ZN 41003 " pdb="ZN ZN 41003 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41003 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41003 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 41003 " - pdb=" SG CYS 4 371 " pdb=" ZN 51600 " pdb="ZN ZN 51600 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 51600 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 51600 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 51600 " - pdb=" SG CYS 5 236 " pdb=" ZN 61600 " pdb="ZN ZN 61600 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61600 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 61600 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61600 " - pdb=" SG CYS 6 333 " pdb=" ZN 7 903 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 262 " Number of angles added : 30 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12180 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 236 helices and 69 sheets defined 41.1% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.94 Creating SS restraints... Processing helix chain '2' and resid 183 through 187 Processing helix chain '2' and resid 194 through 199 Processing helix chain '2' and resid 201 through 217 Processing helix chain '2' and resid 226 through 237 Processing helix chain '2' and resid 246 through 251 Processing helix chain '2' and resid 254 through 262 Processing helix chain '2' and resid 264 through 282 removed outlier: 3.734A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 288 No H-bonds generated for 'chain '2' and resid 286 through 288' Processing helix chain '2' and resid 311 through 313 No H-bonds generated for 'chain '2' and resid 311 through 313' Processing helix chain '2' and resid 436 through 442 Processing helix chain '2' and resid 478 through 487 Processing helix chain '2' and resid 493 through 500 Processing helix chain '2' and resid 509 through 520 Processing helix chain '2' and resid 549 through 559 Processing helix chain '2' and resid 573 through 577 Processing helix chain '2' and resid 595 through 598 No H-bonds generated for 'chain '2' and resid 595 through 598' Processing helix chain '2' and resid 615 through 625 Processing helix chain '2' and resid 633 through 635 No H-bonds generated for 'chain '2' and resid 633 through 635' Processing helix chain '2' and resid 652 through 654 No H-bonds generated for 'chain '2' and resid 652 through 654' Processing helix chain '2' and resid 663 through 666 No H-bonds generated for 'chain '2' and resid 663 through 666' Processing helix chain '2' and resid 671 through 676 Processing helix chain '2' and resid 689 through 706 Processing helix chain '2' and resid 746 through 751 removed outlier: 3.658A pdb=" N ARG 2 749 " --> pdb=" O GLN 2 746 " (cutoff:3.500A) Processing helix chain '2' and resid 760 through 773 Processing helix chain '2' and resid 780 through 799 removed outlier: 3.977A pdb=" N LYS 2 785 " --> pdb=" O MET 2 781 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 823 Processing helix chain '2' and resid 831 through 846 Processing helix chain '2' and resid 850 through 865 removed outlier: 6.200A pdb=" N ARG 2 855 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE 2 863 " --> pdb=" O ARG 2 859 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR 2 864 " --> pdb=" O SER 2 860 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 34 Processing helix chain '3' and resid 36 through 53 Processing helix chain '3' and resid 100 through 106 Processing helix chain '3' and resid 108 through 116 Processing helix chain '3' and resid 118 through 136 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 144 through 149 Processing helix chain '3' and resid 162 through 164 No H-bonds generated for 'chain '3' and resid 162 through 164' Processing helix chain '3' and resid 173 through 175 No H-bonds generated for 'chain '3' and resid 173 through 175' Processing helix chain '3' and resid 280 through 282 No H-bonds generated for 'chain '3' and resid 280 through 282' Processing helix chain '3' and resid 344 through 355 Processing helix chain '3' and resid 357 through 366 removed outlier: 4.489A pdb=" N PHE 3 360 " --> pdb=" O LYS 3 357 " (cutoff:3.500A) Processing helix chain '3' and resid 375 through 386 Processing helix chain '3' and resid 415 through 425 Processing helix chain '3' and resid 439 through 442 No H-bonds generated for 'chain '3' and resid 439 through 442' Processing helix chain '3' and resid 475 through 477 No H-bonds generated for 'chain '3' and resid 475 through 477' Processing helix chain '3' and resid 480 through 492 removed outlier: 3.923A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) Processing helix chain '3' and resid 529 through 532 No H-bonds generated for 'chain '3' and resid 529 through 532' Processing helix chain '3' and resid 537 through 542 Processing helix chain '3' and resid 555 through 569 Processing helix chain '3' and resid 653 through 665 Processing helix chain '3' and resid 673 through 688 Processing helix chain '3' and resid 699 through 715 Processing helix chain '3' and resid 723 through 737 Processing helix chain '4' and resid 187 through 198 Processing helix chain '4' and resid 203 through 209 Processing helix chain '4' and resid 213 through 215 No H-bonds generated for 'chain '4' and resid 213 through 215' Processing helix chain '4' and resid 218 through 222 Processing helix chain '4' and resid 225 through 236 Processing helix chain '4' and resid 245 through 250 Processing helix chain '4' and resid 252 through 263 removed outlier: 4.213A pdb=" N ASP 4 256 " --> pdb=" O LYS 4 252 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU 4 257 " --> pdb=" O GLN 4 253 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 286 Processing helix chain '4' and resid 293 through 298 Processing helix chain '4' and resid 314 through 316 No H-bonds generated for 'chain '4' and resid 314 through 316' Processing helix chain '4' and resid 319 through 321 No H-bonds generated for 'chain '4' and resid 319 through 321' Processing helix chain '4' and resid 421 through 423 No H-bonds generated for 'chain '4' and resid 421 through 423' Processing helix chain '4' and resid 503 through 514 Processing helix chain '4' and resid 516 through 526 removed outlier: 4.044A pdb=" N TYR 4 519 " --> pdb=" O GLU 4 516 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE 4 526 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 534 through 545 Processing helix chain '4' and resid 574 through 584 Processing helix chain '4' and resid 598 through 602 Processing helix chain '4' and resid 620 through 624 Processing helix chain '4' and resid 639 through 651 removed outlier: 3.903A pdb=" N GLU 4 647 " --> pdb=" O SER 4 643 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 688 through 692 Processing helix chain '4' and resid 696 through 701 Processing helix chain '4' and resid 714 through 729 Processing helix chain '4' and resid 744 through 757 Processing helix chain '4' and resid 764 through 779 Processing helix chain '4' and resid 795 through 811 Processing helix chain '4' and resid 819 through 832 Processing helix chain '5' and resid 21 through 37 Processing helix chain '5' and resid 45 through 55 Processing helix chain '5' and resid 65 through 71 Processing helix chain '5' and resid 73 through 81 Processing helix chain '5' and resid 83 through 102 Proline residue: 5 88 - end of helix Processing helix chain '5' and resid 148 through 150 No H-bonds generated for 'chain '5' and resid 148 through 150' Processing helix chain '5' and resid 153 through 155 No H-bonds generated for 'chain '5' and resid 153 through 155' Processing helix chain '5' and resid 280 through 282 No H-bonds generated for 'chain '5' and resid 280 through 282' Processing helix chain '5' and resid 351 through 362 Processing helix chain '5' and resid 366 through 373 Processing helix chain '5' and resid 382 through 393 Processing helix chain '5' and resid 420 through 432 Processing helix chain '5' and resid 468 through 471 No H-bonds generated for 'chain '5' and resid 468 through 471' Processing helix chain '5' and resid 489 through 498 removed outlier: 4.462A pdb=" N ILE 5 493 " --> pdb=" O ASP 5 489 " (cutoff:3.500A) Processing helix chain '5' and resid 545 through 549 Processing helix chain '5' and resid 562 through 576 Processing helix chain '5' and resid 596 through 609 Processing helix chain '5' and resid 616 through 635 Processing helix chain '5' and resid 650 through 667 Processing helix chain '5' and resid 674 through 692 Processing helix chain '6' and resid 106 through 120 Processing helix chain '6' and resid 135 through 146 Processing helix chain '6' and resid 155 through 172 removed outlier: 4.755A pdb=" N GLU 6 162 " --> pdb=" O LEU 6 158 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN 6 163 " --> pdb=" O SER 6 159 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY 6 164 " --> pdb=" O MET 6 160 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA 6 165 " --> pdb=" O ARG 6 161 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU 6 166 " --> pdb=" O GLU 6 162 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA 6 167 " --> pdb=" O ASN 6 163 " (cutoff:3.500A) Processing helix chain '6' and resid 174 through 197 Proline residue: 6 179 - end of helix Proline residue: 6 194 - end of helix Processing helix chain '6' and resid 281 through 283 No H-bonds generated for 'chain '6' and resid 281 through 283' Processing helix chain '6' and resid 383 through 385 No H-bonds generated for 'chain '6' and resid 383 through 385' Processing helix chain '6' and resid 407 through 410 No H-bonds generated for 'chain '6' and resid 407 through 410' Processing helix chain '6' and resid 501 through 507 Processing helix chain '6' and resid 510 through 521 Processing helix chain '6' and resid 524 through 532 Processing helix chain '6' and resid 541 through 552 Processing helix chain '6' and resid 581 through 591 Processing helix chain '6' and resid 605 through 608 No H-bonds generated for 'chain '6' and resid 605 through 608' Processing helix chain '6' and resid 627 through 631 Processing helix chain '6' and resid 646 through 658 Processing helix chain '6' and resid 685 through 687 No H-bonds generated for 'chain '6' and resid 685 through 687' Processing helix chain '6' and resid 695 through 698 No H-bonds generated for 'chain '6' and resid 695 through 698' Processing helix chain '6' and resid 703 through 708 Processing helix chain '6' and resid 721 through 736 Processing helix chain '6' and resid 738 through 741 Processing helix chain '6' and resid 748 through 760 Processing helix chain '6' and resid 767 through 784 Processing helix chain '6' and resid 797 through 814 Processing helix chain '6' and resid 821 through 835 Processing helix chain '7' and resid 14 through 27 Processing helix chain '7' and resid 62 through 71 Processing helix chain '7' and resid 82 through 95 Processing helix chain '7' and resid 102 through 108 removed outlier: 4.058A pdb=" N GLN 7 107 " --> pdb=" O VAL 7 103 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN 7 108 " --> pdb=" O SER 7 104 " (cutoff:3.500A) Processing helix chain '7' and resid 110 through 123 Processing helix chain '7' and resid 138 through 150 removed outlier: 3.913A pdb=" N ASN 7 144 " --> pdb=" O ASP 7 140 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN 7 145 " --> pdb=" O VAL 7 141 " (cutoff:3.500A) Processing helix chain '7' and resid 194 through 197 No H-bonds generated for 'chain '7' and resid 194 through 197' Processing helix chain '7' and resid 232 through 234 No H-bonds generated for 'chain '7' and resid 232 through 234' Processing helix chain '7' and resid 287 through 291 Processing helix chain '7' and resid 337 through 339 No H-bonds generated for 'chain '7' and resid 337 through 339' Processing helix chain '7' and resid 362 through 368 Processing helix chain '7' and resid 395 through 407 removed outlier: 3.709A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) Processing helix chain '7' and resid 410 through 417 Processing helix chain '7' and resid 426 through 437 Processing helix chain '7' and resid 466 through 476 Processing helix chain '7' and resid 490 through 494 Processing helix chain '7' and resid 512 through 515 No H-bonds generated for 'chain '7' and resid 512 through 515' Processing helix chain '7' and resid 531 through 542 removed outlier: 3.781A pdb=" N GLU 7 539 " --> pdb=" O THR 7 535 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL 7 540 " --> pdb=" O ALA 7 536 " (cutoff:3.500A) Processing helix chain '7' and resid 580 through 584 Processing helix chain '7' and resid 588 through 593 Processing helix chain '7' and resid 606 through 621 Processing helix chain '7' and resid 635 through 646 Processing helix chain '7' and resid 654 through 673 Processing helix chain '7' and resid 677 through 679 No H-bonds generated for 'chain '7' and resid 677 through 679' Processing helix chain '7' and resid 686 through 703 Processing helix chain '7' and resid 710 through 729 removed outlier: 4.777A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR 7 728 " --> pdb=" O LYS 7 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 22 removed outlier: 4.201A pdb=" N GLY A 6 " --> pdb=" O TYR A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 60 Processing helix chain 'A' and resid 67 through 103 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 125 through 142 Processing helix chain 'A' and resid 193 through 201 removed outlier: 4.800A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 138 through 162 removed outlier: 4.006A pdb=" N TYR B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 199 Proline residue: B 183 - end of helix Processing helix chain 'C' and resid 6 through 13 Processing helix chain 'C' and resid 28 through 31 Processing helix chain 'C' and resid 48 through 56 removed outlier: 3.992A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 97 through 100 No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 118 through 140 removed outlier: 3.608A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 168 Processing helix chain 'C' and resid 171 through 192 Processing helix chain 'D' and resid 6 through 14 Processing helix chain 'D' and resid 56 through 72 Processing helix chain 'D' and resid 81 through 106 Processing helix chain 'D' and resid 124 through 153 Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 171 through 174 No H-bonds generated for 'chain 'D' and resid 171 through 174' Processing helix chain 'D' and resid 177 through 197 Processing helix chain 'D' and resid 204 through 207 No H-bonds generated for 'chain 'D' and resid 204 through 207' Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 279 through 288 removed outlier: 4.888A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 19 removed outlier: 4.498A pdb=" N SER E 9 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 52 Processing helix chain 'E' and resid 64 through 72 Processing helix chain 'E' and resid 92 through 95 No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 100 through 103 No H-bonds generated for 'chain 'E' and resid 100 through 103' Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 224 through 240 removed outlier: 4.811A pdb=" N GLU E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 267 through 281 Processing helix chain 'E' and resid 285 through 302 Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 342 through 348 Processing helix chain 'E' and resid 353 through 366 Processing helix chain 'E' and resid 370 through 374 Processing helix chain 'E' and resid 377 through 379 No H-bonds generated for 'chain 'E' and resid 377 through 379' Processing helix chain 'E' and resid 382 through 393 removed outlier: 5.761A pdb=" N GLY E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 404 No H-bonds generated for 'chain 'E' and resid 402 through 404' Processing helix chain 'E' and resid 421 through 434 Processing helix chain 'E' and resid 462 through 484 Processing helix chain 'E' and resid 489 through 516 Processing helix chain 'E' and resid 536 through 540 Processing helix chain 'E' and resid 542 through 558 Processing helix chain 'E' and resid 605 through 615 Processing helix chain 'E' and resid 634 through 646 removed outlier: 4.793A pdb=" N SER E 638 " --> pdb=" O ARG E 634 " (cutoff:3.500A) Proline residue: E 639 - end of helix Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 724 through 731 Processing helix chain 'F' and resid 783 through 790 Processing helix chain 'F' and resid 819 through 844 Processing helix chain 'F' and resid 849 through 875 Processing helix chain 'F' and resid 879 through 888 Processing helix chain 'F' and resid 892 through 904 Processing helix chain 'F' and resid 908 through 922 Processing helix chain 'G' and resid 671 through 679 Processing helix chain 'G' and resid 724 through 731 Processing helix chain 'G' and resid 783 through 789 Processing helix chain 'G' and resid 819 through 843 Processing helix chain 'G' and resid 851 through 876 Processing helix chain 'G' and resid 879 through 887 Processing helix chain 'G' and resid 892 through 904 Processing helix chain 'G' and resid 908 through 923 Processing helix chain 'H' and resid 602 through 604 No H-bonds generated for 'chain 'H' and resid 602 through 604' Processing helix chain 'H' and resid 671 through 679 Processing helix chain 'H' and resid 724 through 731 Processing helix chain 'H' and resid 783 through 789 Processing helix chain 'H' and resid 819 through 842 Processing helix chain 'H' and resid 851 through 876 Processing helix chain 'H' and resid 879 through 888 Processing helix chain 'H' and resid 892 through 904 Processing helix chain 'H' and resid 908 through 923 Processing helix chain 'N' and resid 14 through 25 Proline residue: N 19 - end of helix Processing helix chain 'N' and resid 35 through 47 Processing helix chain 'N' and resid 55 through 68 Processing helix chain 'N' and resid 80 through 94 Processing sheet with id= A, first strand: chain '2' and resid 241 through 243 removed outlier: 6.353A pdb=" N HIS 2 294 " --> pdb=" O LEU 2 242 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '2' and resid 405 through 411 removed outlier: 3.794A pdb=" N ARG 2 326 " --> pdb=" O THR 2 389 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLN 2 391 " --> pdb=" O VAL 2 324 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL 2 324 " --> pdb=" O GLN 2 391 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE 2 429 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS 2 431 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE 2 451 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN 2 433 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR 2 449 " --> pdb=" O ASN 2 433 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 338 through 341 removed outlier: 4.718A pdb=" N LYS 2 338 " --> pdb=" O ASN 2 376 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 539 through 543 removed outlier: 6.866A pdb=" N ILE 2 679 " --> pdb=" O LEU 2 540 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU 2 542 " --> pdb=" O ILE 2 679 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N CYS 2 681 " --> pdb=" O LEU 2 542 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain '2' and resid 563 through 565 removed outlier: 6.683A pdb=" N VAL 2 603 " --> pdb=" O VAL 2 564 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain '2' and resid 578 through 581 Processing sheet with id= G, first strand: chain '2' and resid 629 through 631 Processing sheet with id= H, first strand: chain '2' and resid 331 through 337 removed outlier: 5.962A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 95 through 99 removed outlier: 6.410A pdb=" N LYS 3 154 " --> pdb=" O ILE 3 96 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE 3 98 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER 3 156 " --> pdb=" O ILE 3 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '3' and resid 165 through 167 removed outlier: 8.222A pdb=" N LEU 3 166 " --> pdb=" O LEU 3 179 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER 3 181 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS 3 178 " --> pdb=" O PHE 3 298 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE 3 298 " --> pdb=" O LYS 3 178 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL 3 297 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLY 3 323 " --> pdb=" O VAL 3 297 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS 3 299 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ILE 3 321 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU 3 301 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR 3 319 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 185 through 187 Processing sheet with id= L, first strand: chain '3' and resid 194 through 196 Processing sheet with id= M, first strand: chain '3' and resid 201 through 203 Processing sheet with id= N, first strand: chain '3' and resid 545 through 549 removed outlier: 6.766A pdb=" N VAL 3 512 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N MET 3 407 " --> pdb=" O VAL 3 512 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ALA 3 514 " --> pdb=" O MET 3 407 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA 3 516 " --> pdb=" O GLY 3 409 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '3' and resid 444 through 447 Processing sheet with id= P, first strand: chain '3' and resid 494 through 499 removed outlier: 3.809A pdb=" N LYS 3 499 " --> pdb=" O ILE 3 502 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '4' and resid 240 through 244 removed outlier: 6.871A pdb=" N LYS 4 302 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU 4 243 " --> pdb=" O LYS 4 302 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG 4 304 " --> pdb=" O LEU 4 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '4' and resid 414 through 420 removed outlier: 6.198A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR 4 438 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL 4 463 " --> pdb=" O THR 4 438 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG 4 440 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL 4 461 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE 4 442 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR 4 459 " --> pdb=" O ILE 4 442 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '4' and resid 355 through 359 Processing sheet with id= T, first strand: chain '4' and resid 704 through 706 removed outlier: 3.558A pdb=" N CYS 4 567 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE 4 564 " --> pdb=" O ILE 4 671 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '4' and resid 603 through 606 Processing sheet with id= V, first strand: chain '4' and resid 653 through 658 Processing sheet with id= W, first strand: chain '4' and resid 339 through 344 removed outlier: 6.772A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '5' and resid 60 through 64 removed outlier: 6.134A pdb=" N GLN 5 136 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL 5 63 " --> pdb=" O GLN 5 136 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE 5 138 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain '5' and resid 273 through 279 removed outlier: 3.845A pdb=" N SER 5 168 " --> pdb=" O LYS 5 257 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN 5 259 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ILE 5 166 " --> pdb=" O GLN 5 259 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR 5 290 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE 5 297 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE 5 330 " --> pdb=" O ILE 5 297 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER 5 299 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE 5 328 " --> pdb=" O SER 5 299 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR 5 301 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '5' and resid 173 through 175 Processing sheet with id= AA, first strand: chain '5' and resid 189 through 193 Processing sheet with id= AB, first strand: chain '5' and resid 411 through 414 removed outlier: 6.419A pdb=" N VAL 5 519 " --> pdb=" O VAL 5 412 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU 5 414 " --> pdb=" O VAL 5 519 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA 5 521 " --> pdb=" O LEU 5 414 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain '6' and resid 150 through 154 removed outlier: 6.310A pdb=" N GLN 6 264 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE 6 153 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER 6 266 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain '6' and resid 376 through 382 removed outlier: 6.694A pdb=" N GLN 6 362 " --> pdb=" O VAL 6 294 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL 6 294 " --> pdb=" O GLN 6 362 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL 6 400 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA 6 456 " --> pdb=" O VAL 6 400 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE 6 402 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE 6 454 " --> pdb=" O ILE 6 402 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL 6 404 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE 6 452 " --> pdb=" O VAL 6 404 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '6' and resid 301 through 303 Processing sheet with id= AF, first strand: chain '6' and resid 309 through 311 Processing sheet with id= AG, first strand: chain '6' and resid 711 through 715 removed outlier: 5.778A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain '6' and resid 610 through 614 Processing sheet with id= AI, first strand: chain '6' and resid 661 through 663 Processing sheet with id= AJ, first strand: chain '7' and resid 77 through 81 removed outlier: 5.986A pdb=" N PHE 7 201 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE 7 80 " --> pdb=" O PHE 7 201 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR 7 203 " --> pdb=" O ILE 7 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain '7' and resid 330 through 336 removed outlier: 3.678A pdb=" N ARG 7 247 " --> pdb=" O LYS 7 314 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN 7 316 " --> pdb=" O ILE 7 245 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE 7 245 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN 7 237 " --> pdb=" O PHE 7 355 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE 7 354 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ALA 7 378 " --> pdb=" O ILE 7 354 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU 7 356 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU 7 376 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ALA 7 358 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR 7 374 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '7' and resid 252 through 254 Processing sheet with id= AM, first strand: chain '7' and resid 257 through 262 removed outlier: 3.758A pdb=" N CYS 7 262 " --> pdb=" O TYR 7 267 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR 7 267 " --> pdb=" O CYS 7 262 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '7' and resid 596 through 598 removed outlier: 6.782A pdb=" N ILE 7 563 " --> pdb=" O VAL 7 456 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LEU 7 458 " --> pdb=" O ILE 7 563 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA 7 565 " --> pdb=" O LEU 7 458 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '7' and resid 495 through 498 Processing sheet with id= AP, first strand: chain '7' and resid 546 through 548 Processing sheet with id= AQ, first strand: chain 'A' and resid 162 through 166 Processing sheet with id= AR, first strand: chain 'A' and resid 172 through 175 Processing sheet with id= AS, first strand: chain 'B' and resid 68 through 72 Processing sheet with id= AT, first strand: chain 'C' and resid 43 through 47 Processing sheet with id= AU, first strand: chain 'D' and resid 227 through 231 Processing sheet with id= AV, first strand: chain 'D' and resid 258 through 260 Processing sheet with id= AW, first strand: chain 'E' and resid 56 through 61 removed outlier: 7.074A pdb=" N LEU E 27 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL E 59 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE E 29 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE E 61 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL E 31 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N SER E 80 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE E 30 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU E 82 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N SER E 32 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL E 84 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP E 119 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU E 83 " --> pdb=" O ASP E 119 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TYR E 121 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'E' and resid 316 through 322 removed outlier: 3.768A pdb=" N GLY E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'E' and resid 525 through 530 removed outlier: 7.716A pdb=" N CYS E 528 " --> pdb=" O PRO E 566 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL E 568 " --> pdb=" O CYS E 528 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU E 530 " --> pdb=" O VAL E 568 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA E 570 " --> pdb=" O LEU E 530 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER E 571 " --> pdb=" O LEU E 580 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'F' and resid 526 through 530 removed outlier: 6.444A pdb=" N THR F 504 " --> pdb=" O TYR F 493 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TYR F 493 " --> pdb=" O THR F 504 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS F 506 " --> pdb=" O ARG F 491 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG F 491 " --> pdb=" O LYS F 506 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'F' and resid 536 through 540 Processing sheet with id= BB, first strand: chain 'F' and resid 578 through 583 removed outlier: 6.822A pdb=" N GLY F 591 " --> pdb=" O THR F 579 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL F 581 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE F 589 " --> pdb=" O VAL F 581 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ALA F 583 " --> pdb=" O ARG F 587 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG F 587 " --> pdb=" O ALA F 583 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR F 592 " --> pdb=" O TYR F 596 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR F 596 " --> pdb=" O THR F 592 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASN F 601 " --> pdb=" O PRO F 606 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'F' and resid 624 through 631 Processing sheet with id= BD, first strand: chain 'F' and resid 686 through 689 removed outlier: 3.520A pdb=" N LEU F 707 " --> pdb=" O PRO F 695 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU F 722 " --> pdb=" O LEU F 704 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU F 706 " --> pdb=" O PRO F 720 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER F 708 " --> pdb=" O TRP F 718 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TRP F 718 " --> pdb=" O SER F 708 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'F' and resid 772 through 775 removed outlier: 6.097A pdb=" N ILE F 755 " --> pdb=" O PRO F 744 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'G' and resid 491 through 493 Processing sheet with id= BG, first strand: chain 'G' and resid 543 through 547 Processing sheet with id= BH, first strand: chain 'G' and resid 609 through 611 removed outlier: 4.591A pdb=" N TYR G 596 " --> pdb=" O THR G 592 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR G 592 " --> pdb=" O TYR G 596 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER G 580 " --> pdb=" O GLY G 591 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'G' and resid 615 through 621 removed outlier: 6.204A pdb=" N VAL G 628 " --> pdb=" O VAL G 616 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU G 618 " --> pdb=" O PHE G 626 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE G 626 " --> pdb=" O LEU G 618 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA G 620 " --> pdb=" O ARG G 624 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG G 624 " --> pdb=" O ALA G 620 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLU G 642 " --> pdb=" O TYR G 650 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR G 650 " --> pdb=" O GLU G 642 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'G' and resid 686 through 689 removed outlier: 6.748A pdb=" N LEU G 706 " --> pdb=" O PRO G 720 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SER G 708 " --> pdb=" O TRP G 718 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TRP G 718 " --> pdb=" O SER G 708 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'G' and resid 740 through 748 removed outlier: 6.992A pdb=" N ASN G 753 " --> pdb=" O LEU G 745 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU G 747 " --> pdb=" O THR G 751 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR G 751 " --> pdb=" O LEU G 747 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'H' and resid 527 through 530 removed outlier: 3.820A pdb=" N THR H 495 " --> pdb=" O VAL H 502 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR H 504 " --> pdb=" O TYR H 493 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR H 493 " --> pdb=" O THR H 504 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS H 506 " --> pdb=" O ARG H 491 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ARG H 491 " --> pdb=" O LYS H 506 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'H' and resid 536 through 539 Processing sheet with id= BN, first strand: chain 'H' and resid 578 through 583 removed outlier: 6.905A pdb=" N GLY H 591 " --> pdb=" O THR H 579 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL H 581 " --> pdb=" O ILE H 589 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE H 589 " --> pdb=" O VAL H 581 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA H 583 " --> pdb=" O ARG H 587 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ARG H 587 " --> pdb=" O ALA H 583 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN H 601 " --> pdb=" O PRO H 606 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'H' and resid 684 through 687 removed outlier: 6.937A pdb=" N PHE H 698 " --> pdb=" O LYS H 685 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU H 687 " --> pdb=" O CYS H 696 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N CYS H 696 " --> pdb=" O LEU H 687 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY H 699 " --> pdb=" O THR H 703 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR H 703 " --> pdb=" O GLY H 699 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU H 722 " --> pdb=" O LEU H 704 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU H 706 " --> pdb=" O PRO H 720 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N SER H 708 " --> pdb=" O TRP H 718 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TRP H 718 " --> pdb=" O SER H 708 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'H' and resid 771 through 775 removed outlier: 5.270A pdb=" N ILE H 755 " --> pdb=" O PRO H 744 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'H' and resid 615 through 621 removed outlier: 6.561A pdb=" N VAL H 628 " --> pdb=" O VAL H 616 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU H 618 " --> pdb=" O PHE H 626 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE H 626 " --> pdb=" O LEU H 618 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA H 620 " --> pdb=" O ARG H 624 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG H 624 " --> pdb=" O ALA H 620 " (cutoff:3.500A) 2093 hydrogen bonds defined for protein. 5961 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.57 Time building geometry restraints manager: 23.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 16969 1.36 - 1.51: 13406 1.51 - 1.65: 21388 1.65 - 1.80: 223 1.80 - 1.95: 146 Bond restraints: 52132 Sorted by residual: bond pdb=" N THR E 594 " pdb=" CA THR E 594 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.09e-02 8.42e+03 8.94e+00 bond pdb=" N GLU 7 634 " pdb=" CA GLU 7 634 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.46e-02 4.69e+03 8.81e+00 bond pdb=" N ILE 3 91 " pdb=" CA ILE 3 91 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.20e-02 6.94e+03 8.29e+00 bond pdb=" N ILE 7 230 " pdb=" CA ILE 7 230 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.22e-02 6.72e+03 8.27e+00 bond pdb=" N ILE 7 220 " pdb=" CA ILE 7 220 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.08e+00 ... (remaining 52127 not shown) Histogram of bond angle deviations from ideal: 96.97 - 104.87: 858 104.87 - 112.78: 28882 112.78 - 120.69: 22766 120.69 - 128.59: 17764 128.59 - 136.50: 287 Bond angle restraints: 70557 Sorted by residual: angle pdb=" C ASP 3 280 " pdb=" CA ASP 3 280 " pdb=" CB ASP 3 280 " ideal model delta sigma weight residual 116.54 110.86 5.68 1.15e+00 7.56e-01 2.44e+01 angle pdb=" N PRO 7 626 " pdb=" CA PRO 7 626 " pdb=" C PRO 7 626 " ideal model delta sigma weight residual 111.14 104.32 6.82 1.56e+00 4.11e-01 1.91e+01 angle pdb=" N ILE E 524 " pdb=" CA ILE E 524 " pdb=" C ILE E 524 " ideal model delta sigma weight residual 113.53 109.25 4.28 9.80e-01 1.04e+00 1.91e+01 angle pdb=" C ASN H 622 " pdb=" CA ASN H 622 " pdb=" CB ASN H 622 " ideal model delta sigma weight residual 116.63 111.71 4.92 1.16e+00 7.43e-01 1.80e+01 angle pdb=" CA VAL 7 633 " pdb=" C VAL 7 633 " pdb=" O VAL 7 633 " ideal model delta sigma weight residual 121.59 117.38 4.21 1.03e+00 9.43e-01 1.67e+01 ... (remaining 70552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 31236 34.86 - 69.72: 512 69.72 - 104.58: 73 104.58 - 139.44: 3 139.44 - 174.31: 2 Dihedral angle restraints: 31826 sinusoidal: 13076 harmonic: 18750 Sorted by residual: dihedral pdb=" C5' ADP 31001 " pdb=" O5' ADP 31001 " pdb=" PA ADP 31001 " pdb=" O2A ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 114.31 -174.31 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP 31001 " pdb=" O3A ADP 31001 " pdb=" PA ADP 31001 " pdb=" PB ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 83.64 -143.64 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" O1B ADP 31001 " pdb=" O3A ADP 31001 " pdb=" PB ADP 31001 " pdb=" PA ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 61.27 -121.28 1 2.00e+01 2.50e-03 3.65e+01 ... (remaining 31823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 6655 0.045 - 0.091: 976 0.091 - 0.136: 415 0.136 - 0.181: 15 0.181 - 0.227: 4 Chirality restraints: 8065 Sorted by residual: chirality pdb=" CA ILE E 595 " pdb=" N ILE E 595 " pdb=" C ILE E 595 " pdb=" CB ILE E 595 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ILE 7 220 " pdb=" N ILE 7 220 " pdb=" C ILE 7 220 " pdb=" CB ILE 7 220 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CA ILE E 601 " pdb=" N ILE E 601 " pdb=" C ILE E 601 " pdb=" CB ILE E 601 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 8062 not shown) Planarity restraints: 9000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS 7 620 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C HIS 7 620 " 0.036 2.00e-02 2.50e+03 pdb=" O HIS 7 620 " -0.014 2.00e-02 2.50e+03 pdb=" N MET 7 621 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA 3 368 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO 3 369 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO 3 369 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO 3 369 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 5 87 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO 5 88 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO 5 88 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO 5 88 " -0.026 5.00e-02 4.00e+02 ... (remaining 8997 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 506 2.44 - 3.05: 40595 3.05 - 3.67: 88731 3.67 - 4.28: 128803 4.28 - 4.90: 202952 Nonbonded interactions: 461587 Sorted by model distance: nonbonded pdb=" O1B AGS 41001 " pdb="MG MG 41002 " model vdw 1.822 2.170 nonbonded pdb=" O2A AGS 41001 " pdb="MG MG 41002 " model vdw 1.847 2.170 nonbonded pdb="MG MG 7 901 " pdb=" O3B AGS 7 902 " model vdw 1.861 2.170 nonbonded pdb=" O PRO G 481 " pdb=" OG1 THR G 495 " model vdw 1.898 2.440 nonbonded pdb="MG MG 7 901 " pdb=" O3A AGS 7 902 " model vdw 1.900 2.170 ... (remaining 461582 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 'F' and (resid 474 through 663 or resid 670 through 789 or (resid 790 and \ (name N or name CA or name C or name O or name CB )) or resid 814 through 892 o \ r (resid 893 through 894 and (name N or name CA or name C or name O or name CB ) \ ) or resid 895 through 901 or (resid 902 and (name N or name CA or name C or nam \ e O or name CB )) or resid 903 through 911 or (resid 912 and (name N or name CA \ or name C or name O or name CB )) or resid 913 through 923)) selection = (chain 'G' and (resid 474 through 789 or (resid 790 and (name N or name CA or na \ me C or name O or name CB )) or resid 814 through 901 or (resid 902 and (name N \ or name CA or name C or name O or name CB )) or resid 903 through 909 or (resid \ 910 and (name N or name CA or name C or name O or name CB )) or resid 911 throug \ h 923)) selection = (chain 'H' and (resid 474 through 663 or resid 670 through 892 or (resid 893 thr \ ough 894 and (name N or name CA or name C or name O or name CB )) or resid 895 t \ hrough 909 or (resid 910 and (name N or name CA or name C or name O or name CB ) \ ) or resid 911 or (resid 912 and (name N or name CA or name C or name O or name \ CB )) or resid 913 through 923)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.360 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: 20.700 Check model and map are aligned: 0.670 Set scattering table: 0.460 Process input model: 142.540 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 52132 Z= 0.205 Angle : 0.576 10.259 70557 Z= 0.343 Chirality : 0.039 0.227 8065 Planarity : 0.004 0.055 9000 Dihedral : 14.047 174.306 19646 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.53 % Rotamer: Outliers : 0.55 % Allowed : 0.19 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.11), residues: 6264 helix: 1.04 (0.10), residues: 2701 sheet: -1.37 (0.16), residues: 1019 loop : -0.75 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 53 HIS 0.005 0.001 HIS 4 386 PHE 0.021 0.001 PHE 3 543 TYR 0.022 0.001 TYR G 862 ARG 0.012 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 6.107 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: 2 783 MET cc_start: 0.8773 (mtp) cc_final: 0.8399 (mtp) REVERT: 3 386 MET cc_start: 0.9044 (tpp) cc_final: 0.8775 (tpp) REVERT: 3 407 MET cc_start: 0.9321 (pmm) cc_final: 0.9091 (pmm) REVERT: 5 65 MET cc_start: 0.9639 (mmp) cc_final: 0.9116 (mmm) REVERT: 5 182 MET cc_start: 0.9651 (tpp) cc_final: 0.9271 (tpp) REVERT: 5 252 ASP cc_start: 0.8970 (m-30) cc_final: 0.8535 (p0) REVERT: 5 276 MET cc_start: 0.9004 (mpp) cc_final: 0.8712 (mpp) REVERT: 6 143 MET cc_start: 0.9542 (tpt) cc_final: 0.9304 (tpp) REVERT: 6 629 MET cc_start: 0.9557 (mmp) cc_final: 0.9223 (mmm) REVERT: 7 64 MET cc_start: 0.9310 (mmp) cc_final: 0.8837 (mmm) REVERT: 7 222 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8174 (m) REVERT: 7 498 MET cc_start: 0.9527 (tpt) cc_final: 0.9239 (tpp) REVERT: 7 541 MET cc_start: 0.9446 (ptm) cc_final: 0.8800 (ppp) REVERT: 7 623 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.6542 (t0) REVERT: 7 652 MET cc_start: 0.6895 (ppp) cc_final: 0.6421 (ppp) REVERT: 7 707 MET cc_start: 0.9336 (ppp) cc_final: 0.9080 (ppp) REVERT: A 100 MET cc_start: 0.9321 (mmt) cc_final: 0.8842 (mmm) REVERT: C 16 PHE cc_start: 0.9454 (m-80) cc_final: 0.9162 (m-80) REVERT: C 159 ASN cc_start: 0.8424 (t0) cc_final: 0.8010 (t0) REVERT: C 191 MET cc_start: 0.9394 (tmm) cc_final: 0.9169 (tmm) REVERT: D 84 MET cc_start: 0.9400 (mpp) cc_final: 0.9168 (mpp) REVERT: E 44 MET cc_start: 0.9531 (mtp) cc_final: 0.9175 (mtp) REVERT: E 362 MET cc_start: 0.9698 (tmm) cc_final: 0.9056 (tmm) REVERT: F 477 MET cc_start: 0.9279 (mmm) cc_final: 0.9013 (mmm) REVERT: F 778 MET cc_start: 0.8928 (mmp) cc_final: 0.7971 (mmm) REVERT: G 778 MET cc_start: 0.8660 (mmp) cc_final: 0.8443 (mmm) REVERT: H 477 MET cc_start: 0.8543 (mmm) cc_final: 0.8304 (mmm) REVERT: H 778 MET cc_start: 0.9026 (mmp) cc_final: 0.8391 (mmp) REVERT: N 65 GLN cc_start: 0.8570 (tp40) cc_final: 0.8295 (tp-100) outliers start: 31 outliers final: 11 residues processed: 205 average time/residue: 0.6607 time to fit residues: 239.3258 Evaluate side-chains 167 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 8.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 533 optimal weight: 0.7980 chunk 479 optimal weight: 10.0000 chunk 265 optimal weight: 30.0000 chunk 163 optimal weight: 8.9990 chunk 323 optimal weight: 20.0000 chunk 255 optimal weight: 3.9990 chunk 495 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 301 optimal weight: 0.4980 chunk 368 optimal weight: 9.9990 chunk 573 optimal weight: 30.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 653 ASN ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 46 GLN 3 151 HIS 3 349 ASN 3 365 GLN 3 673 GLN 3 677 ASN 4 263 ASN 4 327 ASN 4 386 HIS 4 726 ASN 5 145 GLN 5 273 ASN 6 649 GLN 6 659 GLN 7 209 GLN ** 7 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS D 160 GLN D 186 HIS E 354 ASN E 395 ASN ** E 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN E 550 ASN F 622 ASN F 843 ASN F 852 ASN F 877 GLN ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 852 ASN H 877 GLN ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 52132 Z= 0.216 Angle : 0.573 10.897 70557 Z= 0.299 Chirality : 0.041 0.174 8065 Planarity : 0.004 0.042 9000 Dihedral : 6.901 165.453 7088 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.34 % Favored : 96.62 % Rotamer: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.11), residues: 6264 helix: 1.25 (0.10), residues: 2750 sheet: -1.10 (0.16), residues: 1041 loop : -0.40 (0.13), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 743 HIS 0.009 0.001 HIS 4 354 PHE 0.030 0.002 PHE 6 584 TYR 0.024 0.002 TYR H 922 ARG 0.005 0.001 ARG F 868 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 171 time to evaluate : 6.014 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: 2 783 MET cc_start: 0.8849 (mtp) cc_final: 0.8542 (mtp) REVERT: 4 272 MET cc_start: 0.9755 (ttp) cc_final: 0.9505 (ptp) REVERT: 5 65 MET cc_start: 0.9633 (mmp) cc_final: 0.9175 (mmm) REVERT: 5 252 ASP cc_start: 0.8962 (m-30) cc_final: 0.8601 (p0) REVERT: 5 393 MET cc_start: 0.9144 (tpp) cc_final: 0.8247 (tpp) REVERT: 6 143 MET cc_start: 0.9609 (tpt) cc_final: 0.9343 (tpp) REVERT: 6 629 MET cc_start: 0.9620 (mmp) cc_final: 0.9251 (mmm) REVERT: 6 709 PHE cc_start: 0.9114 (m-10) cc_final: 0.8813 (m-80) REVERT: 7 64 MET cc_start: 0.9357 (mmp) cc_final: 0.8980 (mmm) REVERT: 7 529 MET cc_start: 0.8331 (tmm) cc_final: 0.7840 (tmm) REVERT: 7 541 MET cc_start: 0.9202 (ptm) cc_final: 0.8959 (ptm) REVERT: 7 652 MET cc_start: 0.7487 (ppp) cc_final: 0.7135 (ppp) REVERT: A 100 MET cc_start: 0.9291 (mmt) cc_final: 0.8883 (mmm) REVERT: C 16 PHE cc_start: 0.9428 (m-80) cc_final: 0.9095 (m-80) REVERT: C 159 ASN cc_start: 0.8463 (t0) cc_final: 0.8017 (t0) REVERT: D 129 MET cc_start: 0.9299 (mmp) cc_final: 0.9065 (mmm) REVERT: E 1 MET cc_start: 0.8600 (tmm) cc_final: 0.8320 (tmm) REVERT: E 44 MET cc_start: 0.9496 (mtp) cc_final: 0.9058 (mtp) REVERT: E 362 MET cc_start: 0.9702 (tmm) cc_final: 0.9098 (tmm) REVERT: E 366 MET cc_start: 0.9243 (mmp) cc_final: 0.8885 (mmm) REVERT: E 380 MET cc_start: 0.9029 (mmp) cc_final: 0.8629 (mmm) REVERT: F 477 MET cc_start: 0.9272 (mmm) cc_final: 0.8966 (mmm) REVERT: F 774 MET cc_start: 0.8910 (mpp) cc_final: 0.8612 (mpp) REVERT: F 778 MET cc_start: 0.8643 (mmp) cc_final: 0.8040 (mmm) REVERT: H 477 MET cc_start: 0.8571 (mmm) cc_final: 0.8304 (mmm) REVERT: H 778 MET cc_start: 0.9055 (mmp) cc_final: 0.8327 (mmm) REVERT: N 65 GLN cc_start: 0.8931 (tp40) cc_final: 0.8573 (tp-100) outliers start: 6 outliers final: 2 residues processed: 177 average time/residue: 0.5558 time to fit residues: 177.1313 Evaluate side-chains 156 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 5.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 318 optimal weight: 8.9990 chunk 178 optimal weight: 20.0000 chunk 477 optimal weight: 0.7980 chunk 390 optimal weight: 0.1980 chunk 158 optimal weight: 0.6980 chunk 574 optimal weight: 2.9990 chunk 621 optimal weight: 5.9990 chunk 512 optimal weight: 1.9990 chunk 570 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 461 optimal weight: 0.0770 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 151 HIS 3 673 GLN 3 677 ASN 4 196 ASN 4 253 GLN ** 4 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 726 ASN 6 458 HIS 6 649 GLN ** 7 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN C 103 HIS D 160 GLN E 22 HIS E 77 ASN E 360 HIS ** E 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 510 GLN G 563 HIS ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 52132 Z= 0.158 Angle : 0.529 8.892 70557 Z= 0.273 Chirality : 0.041 0.221 8065 Planarity : 0.004 0.055 9000 Dihedral : 6.772 166.821 7088 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.13 % Rotamer: Outliers : 0.04 % Allowed : 2.61 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.11), residues: 6264 helix: 1.45 (0.10), residues: 2739 sheet: -0.94 (0.16), residues: 1078 loop : -0.21 (0.13), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 566 HIS 0.007 0.001 HIS 4 354 PHE 0.031 0.001 PHE 6 584 TYR 0.022 0.001 TYR H 922 ARG 0.012 0.000 ARG F 868 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 6.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8823 (mtp) cc_final: 0.8510 (mtp) REVERT: 3 261 MET cc_start: 0.8756 (tpt) cc_final: 0.8305 (tpp) REVERT: 3 386 MET cc_start: 0.9148 (tpt) cc_final: 0.8676 (tpp) REVERT: 3 462 MET cc_start: 0.9554 (mmp) cc_final: 0.9324 (mmp) REVERT: 3 478 MET cc_start: 0.8753 (tpt) cc_final: 0.8414 (tpp) REVERT: 4 272 MET cc_start: 0.9829 (ttp) cc_final: 0.9557 (ptm) REVERT: 4 314 MET cc_start: 0.8068 (ppp) cc_final: 0.7560 (ppp) REVERT: 5 65 MET cc_start: 0.9597 (mmp) cc_final: 0.9173 (mmm) REVERT: 5 252 ASP cc_start: 0.8920 (m-30) cc_final: 0.8599 (p0) REVERT: 5 256 LEU cc_start: 0.9756 (mt) cc_final: 0.9471 (mt) REVERT: 5 276 MET cc_start: 0.9155 (mpp) cc_final: 0.8905 (pmm) REVERT: 5 393 MET cc_start: 0.9140 (tpp) cc_final: 0.8309 (tpp) REVERT: 5 404 MET cc_start: 0.8998 (tmm) cc_final: 0.8759 (tmm) REVERT: 6 143 MET cc_start: 0.9614 (tpt) cc_final: 0.9403 (tpp) REVERT: 6 313 MET cc_start: 0.9548 (ptm) cc_final: 0.9244 (ptt) REVERT: 6 629 MET cc_start: 0.9632 (mmp) cc_final: 0.9197 (mmm) REVERT: 6 709 PHE cc_start: 0.9151 (m-10) cc_final: 0.8815 (m-80) REVERT: 7 64 MET cc_start: 0.9357 (mmp) cc_final: 0.8947 (mmm) REVERT: 7 459 MET cc_start: 0.9435 (tpt) cc_final: 0.9169 (tpp) REVERT: 7 498 MET cc_start: 0.9455 (tpt) cc_final: 0.9227 (tpp) REVERT: 7 529 MET cc_start: 0.8529 (tmm) cc_final: 0.8070 (tmm) REVERT: 7 541 MET cc_start: 0.9171 (ptm) cc_final: 0.8951 (ptm) REVERT: A 79 MET cc_start: 0.9714 (mtm) cc_final: 0.9359 (ptp) REVERT: A 100 MET cc_start: 0.9337 (mmt) cc_final: 0.8872 (mmm) REVERT: C 16 PHE cc_start: 0.9386 (m-80) cc_final: 0.9000 (m-80) REVERT: C 159 ASN cc_start: 0.8532 (t0) cc_final: 0.8067 (t0) REVERT: D 103 MET cc_start: 0.9529 (mmp) cc_final: 0.9298 (mmm) REVERT: E 1 MET cc_start: 0.8565 (tmm) cc_final: 0.8162 (tmm) REVERT: E 44 MET cc_start: 0.9475 (mtp) cc_final: 0.9100 (mtp) REVERT: E 362 MET cc_start: 0.9674 (tmm) cc_final: 0.9141 (tmm) REVERT: E 380 MET cc_start: 0.8989 (mmp) cc_final: 0.8562 (mmm) REVERT: F 477 MET cc_start: 0.9250 (mmm) cc_final: 0.8977 (mmm) REVERT: F 778 MET cc_start: 0.8703 (mmp) cc_final: 0.8114 (mmm) REVERT: H 477 MET cc_start: 0.8645 (mmm) cc_final: 0.8365 (mmm) REVERT: H 774 MET cc_start: 0.8514 (mpp) cc_final: 0.8164 (mpp) REVERT: H 778 MET cc_start: 0.8993 (mmp) cc_final: 0.8278 (mmm) REVERT: N 65 GLN cc_start: 0.9023 (tp40) cc_final: 0.8695 (tp-100) outliers start: 2 outliers final: 1 residues processed: 179 average time/residue: 0.5606 time to fit residues: 180.2265 Evaluate side-chains 161 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 6.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 568 optimal weight: 2.9990 chunk 432 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 386 optimal weight: 10.0000 chunk 577 optimal weight: 6.9990 chunk 610 optimal weight: 0.8980 chunk 301 optimal weight: 4.9990 chunk 546 optimal weight: 20.0000 chunk 164 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 417 GLN 3 532 ASN 3 673 GLN 3 677 ASN ** 4 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 726 ASN 5 49 GLN 5 53 ASN 5 145 GLN 6 683 ASN ** 7 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 ASN E 436 ASN ** E 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 678 ASN ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 52132 Z= 0.204 Angle : 0.524 8.563 70557 Z= 0.273 Chirality : 0.039 0.178 8065 Planarity : 0.004 0.048 9000 Dihedral : 6.740 171.304 7088 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.84 % Rotamer: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 6264 helix: 1.58 (0.10), residues: 2746 sheet: -0.87 (0.16), residues: 1074 loop : -0.19 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 74 HIS 0.005 0.001 HIS 4 354 PHE 0.047 0.001 PHE N 78 TYR 0.020 0.001 TYR H 501 ARG 0.015 0.000 ARG F 868 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 5.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8853 (mtp) cc_final: 0.8457 (mtt) REVERT: 3 261 MET cc_start: 0.8876 (tpt) cc_final: 0.8596 (tpp) REVERT: 3 383 LEU cc_start: 0.9758 (mt) cc_final: 0.9557 (mt) REVERT: 3 386 MET cc_start: 0.9216 (tpt) cc_final: 0.8703 (tpp) REVERT: 3 462 MET cc_start: 0.9608 (mmp) cc_final: 0.9392 (mmm) REVERT: 3 478 MET cc_start: 0.8746 (tpt) cc_final: 0.8391 (tpp) REVERT: 4 272 MET cc_start: 0.9825 (ttp) cc_final: 0.9548 (ptm) REVERT: 4 314 MET cc_start: 0.8229 (ppp) cc_final: 0.7405 (ppp) REVERT: 4 847 MET cc_start: 0.8465 (ppp) cc_final: 0.8060 (mmm) REVERT: 5 65 MET cc_start: 0.9592 (mmp) cc_final: 0.9192 (mmm) REVERT: 5 252 ASP cc_start: 0.8974 (m-30) cc_final: 0.8635 (p0) REVERT: 5 393 MET cc_start: 0.9129 (tpp) cc_final: 0.8240 (tpp) REVERT: 5 404 MET cc_start: 0.9048 (tmm) cc_final: 0.8796 (tmm) REVERT: 6 143 MET cc_start: 0.9593 (tpt) cc_final: 0.9375 (tpp) REVERT: 6 313 MET cc_start: 0.9596 (ptm) cc_final: 0.9244 (ptm) REVERT: 6 629 MET cc_start: 0.9616 (mmp) cc_final: 0.9146 (mmm) REVERT: 6 709 PHE cc_start: 0.9163 (m-10) cc_final: 0.8798 (m-80) REVERT: 7 64 MET cc_start: 0.9393 (mmp) cc_final: 0.8970 (mmm) REVERT: 7 448 MET cc_start: 0.8690 (tpt) cc_final: 0.8356 (tpt) REVERT: 7 498 MET cc_start: 0.9457 (tpt) cc_final: 0.9234 (tpp) REVERT: 7 529 MET cc_start: 0.8562 (tmm) cc_final: 0.7974 (tmm) REVERT: 7 541 MET cc_start: 0.9161 (ptm) cc_final: 0.8896 (ptm) REVERT: A 100 MET cc_start: 0.9378 (mmt) cc_final: 0.8914 (mmm) REVERT: C 16 PHE cc_start: 0.9433 (m-80) cc_final: 0.9054 (m-80) REVERT: C 159 ASN cc_start: 0.8580 (t0) cc_final: 0.8106 (t0) REVERT: D 103 MET cc_start: 0.9547 (mmp) cc_final: 0.9326 (mmm) REVERT: D 277 MET cc_start: 0.9709 (mmm) cc_final: 0.9235 (mmm) REVERT: E 1 MET cc_start: 0.8586 (tmm) cc_final: 0.8114 (tmm) REVERT: E 44 MET cc_start: 0.9491 (mtp) cc_final: 0.9037 (mtp) REVERT: E 362 MET cc_start: 0.9694 (tmm) cc_final: 0.9059 (tmm) REVERT: E 380 MET cc_start: 0.8971 (mmp) cc_final: 0.8559 (mmm) REVERT: F 477 MET cc_start: 0.9248 (mmm) cc_final: 0.8953 (mmm) REVERT: F 778 MET cc_start: 0.8693 (mmp) cc_final: 0.8156 (mmm) REVERT: H 774 MET cc_start: 0.8651 (mpp) cc_final: 0.8335 (mpp) REVERT: H 778 MET cc_start: 0.8941 (mmp) cc_final: 0.8244 (mmm) REVERT: N 65 GLN cc_start: 0.9049 (tp40) cc_final: 0.8737 (tp-100) REVERT: N 81 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7933 (pp30) outliers start: 2 outliers final: 0 residues processed: 171 average time/residue: 0.5683 time to fit residues: 174.4159 Evaluate side-chains 156 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 6.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 508 optimal weight: 10.0000 chunk 346 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 454 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 521 optimal weight: 8.9990 chunk 422 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 311 optimal weight: 7.9990 chunk 548 optimal weight: 20.0000 chunk 154 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 350 ASN ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 726 ASN 5 53 ASN ** 7 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN A 90 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 ASN F 761 HIS F 916 ASN G 678 ASN ** H 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 753 ASN H 915 ASN ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 52132 Z= 0.250 Angle : 0.558 9.421 70557 Z= 0.290 Chirality : 0.039 0.171 8065 Planarity : 0.004 0.048 9000 Dihedral : 6.811 173.118 7088 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 6264 helix: 1.58 (0.10), residues: 2736 sheet: -0.88 (0.16), residues: 1084 loop : -0.16 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 74 HIS 0.012 0.001 HIS G 629 PHE 0.021 0.001 PHE 6 584 TYR 0.023 0.001 TYR H 862 ARG 0.015 0.000 ARG F 868 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 6.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8920 (mtp) cc_final: 0.8555 (mtp) REVERT: 3 261 MET cc_start: 0.8915 (tpt) cc_final: 0.8612 (tpp) REVERT: 3 383 LEU cc_start: 0.9774 (mt) cc_final: 0.9559 (mt) REVERT: 3 386 MET cc_start: 0.9257 (tpt) cc_final: 0.8716 (tpp) REVERT: 3 407 MET cc_start: 0.9478 (pmm) cc_final: 0.9240 (pmm) REVERT: 3 462 MET cc_start: 0.9651 (mmp) cc_final: 0.9439 (mmm) REVERT: 3 478 MET cc_start: 0.8749 (tpt) cc_final: 0.8466 (tpp) REVERT: 4 272 MET cc_start: 0.9810 (ttp) cc_final: 0.9535 (ptm) REVERT: 4 314 MET cc_start: 0.8361 (ppp) cc_final: 0.7598 (ppp) REVERT: 4 847 MET cc_start: 0.8538 (ppp) cc_final: 0.8140 (mmm) REVERT: 5 65 MET cc_start: 0.9594 (mmp) cc_final: 0.9178 (mmm) REVERT: 5 252 ASP cc_start: 0.9039 (m-30) cc_final: 0.8610 (p0) REVERT: 5 393 MET cc_start: 0.9062 (tpp) cc_final: 0.8049 (tpp) REVERT: 5 404 MET cc_start: 0.9178 (tmm) cc_final: 0.8753 (tmm) REVERT: 5 485 MET cc_start: 0.8503 (mmm) cc_final: 0.8204 (mmm) REVERT: 5 552 MET cc_start: 0.9801 (tpp) cc_final: 0.9360 (tpp) REVERT: 6 313 MET cc_start: 0.9641 (ptm) cc_final: 0.9309 (ptm) REVERT: 6 629 MET cc_start: 0.9682 (mmp) cc_final: 0.9262 (mmm) REVERT: 6 709 PHE cc_start: 0.9135 (m-10) cc_final: 0.8720 (m-80) REVERT: 7 64 MET cc_start: 0.9422 (mmp) cc_final: 0.9001 (mmm) REVERT: 7 448 MET cc_start: 0.8831 (tpt) cc_final: 0.8509 (tpt) REVERT: 7 498 MET cc_start: 0.9458 (tpt) cc_final: 0.9226 (tpp) REVERT: 7 529 MET cc_start: 0.8503 (tmm) cc_final: 0.8073 (tmm) REVERT: 7 541 MET cc_start: 0.9153 (ptm) cc_final: 0.8897 (ptm) REVERT: A 100 MET cc_start: 0.9417 (mmt) cc_final: 0.8979 (mmm) REVERT: C 159 ASN cc_start: 0.8604 (t0) cc_final: 0.8083 (t0) REVERT: E 1 MET cc_start: 0.8594 (tmm) cc_final: 0.8129 (tmm) REVERT: E 44 MET cc_start: 0.9489 (mtp) cc_final: 0.9061 (mtp) REVERT: E 362 MET cc_start: 0.9677 (tmm) cc_final: 0.9083 (tmm) REVERT: E 380 MET cc_start: 0.8993 (mmp) cc_final: 0.8578 (mmm) REVERT: F 477 MET cc_start: 0.9257 (mmm) cc_final: 0.9011 (mmm) REVERT: F 778 MET cc_start: 0.8542 (mmp) cc_final: 0.8038 (mmm) REVERT: H 477 MET cc_start: 0.8684 (mmm) cc_final: 0.8407 (mmm) REVERT: H 774 MET cc_start: 0.8770 (mpp) cc_final: 0.8493 (mpp) REVERT: H 778 MET cc_start: 0.8806 (mmp) cc_final: 0.8106 (mmm) REVERT: N 36 ASP cc_start: 0.9556 (p0) cc_final: 0.9123 (p0) REVERT: N 65 GLN cc_start: 0.9130 (tp40) cc_final: 0.8806 (tp-100) REVERT: N 78 PHE cc_start: 0.9534 (m-10) cc_final: 0.9177 (m-10) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.5762 time to fit residues: 172.9096 Evaluate side-chains 155 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 5.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 205 optimal weight: 10.0000 chunk 550 optimal weight: 20.0000 chunk 120 optimal weight: 0.8980 chunk 358 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 611 optimal weight: 0.8980 chunk 507 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 202 optimal weight: 0.8980 chunk 321 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 666 ASN ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 676 ASN 5 49 GLN ** 7 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN G 678 ASN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 52132 Z= 0.147 Angle : 0.503 7.284 70557 Z= 0.261 Chirality : 0.040 0.245 8065 Planarity : 0.004 0.048 9000 Dihedral : 6.737 170.626 7088 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 0.02 % Allowed : 1.68 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.11), residues: 6264 helix: 1.67 (0.10), residues: 2743 sheet: -0.71 (0.16), residues: 1056 loop : -0.08 (0.13), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 6 356 HIS 0.013 0.001 HIS E 126 PHE 0.027 0.001 PHE 6 584 TYR 0.020 0.001 TYR G 922 ARG 0.006 0.000 ARG 6 770 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 6.293 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: 2 783 MET cc_start: 0.8857 (mtp) cc_final: 0.8460 (mtp) REVERT: 3 383 LEU cc_start: 0.9758 (mt) cc_final: 0.9542 (mt) REVERT: 3 386 MET cc_start: 0.9184 (tpt) cc_final: 0.8624 (tpp) REVERT: 3 462 MET cc_start: 0.9598 (mmp) cc_final: 0.9343 (mmm) REVERT: 3 478 MET cc_start: 0.8818 (tpt) cc_final: 0.8401 (tpp) REVERT: 4 314 MET cc_start: 0.8271 (ppp) cc_final: 0.7547 (ppp) REVERT: 4 847 MET cc_start: 0.8514 (ppp) cc_final: 0.8127 (mmm) REVERT: 5 65 MET cc_start: 0.9556 (mmp) cc_final: 0.9199 (mmm) REVERT: 5 252 ASP cc_start: 0.9007 (m-30) cc_final: 0.8651 (p0) REVERT: 5 276 MET cc_start: 0.9073 (pmm) cc_final: 0.8873 (pmm) REVERT: 5 393 MET cc_start: 0.9066 (tpp) cc_final: 0.8014 (tpp) REVERT: 5 404 MET cc_start: 0.9187 (tmm) cc_final: 0.8753 (tmm) REVERT: 5 485 MET cc_start: 0.8625 (mmm) cc_final: 0.8226 (mmp) REVERT: 5 552 MET cc_start: 0.9828 (tpp) cc_final: 0.9412 (tpp) REVERT: 6 313 MET cc_start: 0.9615 (ptm) cc_final: 0.9276 (ptm) REVERT: 6 629 MET cc_start: 0.9708 (mmp) cc_final: 0.9299 (mmm) REVERT: 7 64 MET cc_start: 0.9429 (mmp) cc_final: 0.9016 (mmm) REVERT: 7 448 MET cc_start: 0.8828 (tpt) cc_final: 0.8516 (tpt) REVERT: 7 459 MET cc_start: 0.9457 (tpt) cc_final: 0.9176 (tpp) REVERT: 7 498 MET cc_start: 0.9408 (tpt) cc_final: 0.9179 (tpp) REVERT: 7 529 MET cc_start: 0.8533 (tmm) cc_final: 0.8160 (tmm) REVERT: 7 541 MET cc_start: 0.9121 (ptm) cc_final: 0.8896 (ptm) REVERT: A 79 MET cc_start: 0.9715 (mtm) cc_final: 0.9417 (ptp) REVERT: A 100 MET cc_start: 0.9366 (mmt) cc_final: 0.8923 (mmm) REVERT: C 16 PHE cc_start: 0.9426 (m-80) cc_final: 0.9029 (m-80) REVERT: C 159 ASN cc_start: 0.8658 (t0) cc_final: 0.8146 (t0) REVERT: D 103 MET cc_start: 0.9562 (mmp) cc_final: 0.9334 (mmm) REVERT: D 277 MET cc_start: 0.9693 (mmm) cc_final: 0.9179 (mmm) REVERT: E 1 MET cc_start: 0.8504 (tmm) cc_final: 0.7991 (tmm) REVERT: E 44 MET cc_start: 0.9478 (mtp) cc_final: 0.9050 (mtp) REVERT: E 362 MET cc_start: 0.9677 (tmm) cc_final: 0.9139 (tmm) REVERT: E 380 MET cc_start: 0.8998 (mmp) cc_final: 0.8526 (mmm) REVERT: F 477 MET cc_start: 0.9222 (mmm) cc_final: 0.8947 (mmm) REVERT: F 778 MET cc_start: 0.8590 (mmp) cc_final: 0.8041 (mmm) REVERT: H 774 MET cc_start: 0.8778 (mpp) cc_final: 0.8529 (mpp) REVERT: H 778 MET cc_start: 0.8786 (mmp) cc_final: 0.8097 (mmm) REVERT: H 821 MET cc_start: 0.8797 (ttt) cc_final: 0.8323 (tpp) REVERT: N 65 GLN cc_start: 0.9096 (tp40) cc_final: 0.8777 (tp-100) outliers start: 1 outliers final: 1 residues processed: 170 average time/residue: 0.5919 time to fit residues: 179.8363 Evaluate side-chains 158 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 5.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 589 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 348 optimal weight: 7.9990 chunk 446 optimal weight: 0.1980 chunk 345 optimal weight: 20.0000 chunk 514 optimal weight: 5.9990 chunk 341 optimal weight: 0.0770 chunk 609 optimal weight: 9.9990 chunk 381 optimal weight: 3.9990 chunk 371 optimal weight: 4.9990 chunk 281 optimal weight: 8.9990 overall best weight: 3.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN D 160 GLN G 678 ASN ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 52132 Z= 0.191 Angle : 0.518 9.051 70557 Z= 0.269 Chirality : 0.039 0.199 8065 Planarity : 0.004 0.049 9000 Dihedral : 6.719 173.785 7088 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.11), residues: 6264 helix: 1.71 (0.10), residues: 2747 sheet: -0.63 (0.16), residues: 1086 loop : -0.10 (0.13), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 6 356 HIS 0.005 0.001 HIS 7 620 PHE 0.032 0.001 PHE 5 550 TYR 0.019 0.001 TYR G 922 ARG 0.009 0.000 ARG F 868 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 6.488 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: 2 276 MET cc_start: 0.9655 (mmp) cc_final: 0.9448 (mmp) REVERT: 2 783 MET cc_start: 0.8872 (mtp) cc_final: 0.8504 (mtp) REVERT: 2 823 MET cc_start: 0.9621 (ptp) cc_final: 0.9407 (ptp) REVERT: 3 261 MET cc_start: 0.8929 (tpt) cc_final: 0.8604 (tpp) REVERT: 3 383 LEU cc_start: 0.9764 (mt) cc_final: 0.9539 (mt) REVERT: 3 386 MET cc_start: 0.9226 (tpt) cc_final: 0.8657 (tpp) REVERT: 3 462 MET cc_start: 0.9628 (mmp) cc_final: 0.9394 (mmm) REVERT: 3 478 MET cc_start: 0.8821 (tpt) cc_final: 0.8360 (tpp) REVERT: 4 314 MET cc_start: 0.8439 (ppp) cc_final: 0.7727 (ppp) REVERT: 4 847 MET cc_start: 0.8386 (ppp) cc_final: 0.8054 (mmm) REVERT: 5 65 MET cc_start: 0.9567 (mmp) cc_final: 0.9191 (mmm) REVERT: 5 182 MET cc_start: 0.9603 (tpt) cc_final: 0.9340 (tpp) REVERT: 5 252 ASP cc_start: 0.9021 (m-30) cc_final: 0.8562 (p0) REVERT: 5 393 MET cc_start: 0.9228 (tpp) cc_final: 0.8401 (tpp) REVERT: 5 404 MET cc_start: 0.9217 (tmm) cc_final: 0.8840 (tmm) REVERT: 5 552 MET cc_start: 0.9820 (tpp) cc_final: 0.9400 (tpp) REVERT: 6 313 MET cc_start: 0.9623 (ptm) cc_final: 0.9286 (ptm) REVERT: 6 629 MET cc_start: 0.9706 (mmp) cc_final: 0.9283 (mmm) REVERT: 7 64 MET cc_start: 0.9441 (mmp) cc_final: 0.9008 (mmm) REVERT: 7 448 MET cc_start: 0.8936 (tpt) cc_final: 0.8620 (tpt) REVERT: 7 459 MET cc_start: 0.9435 (tpt) cc_final: 0.9119 (tpp) REVERT: 7 498 MET cc_start: 0.9397 (tpt) cc_final: 0.9187 (tpp) REVERT: 7 529 MET cc_start: 0.8568 (tmm) cc_final: 0.8220 (tmm) REVERT: 7 541 MET cc_start: 0.9100 (ptm) cc_final: 0.8897 (ptm) REVERT: 7 652 MET cc_start: 0.7277 (ppp) cc_final: 0.7033 (ppp) REVERT: A 100 MET cc_start: 0.9395 (mmt) cc_final: 0.8956 (mmm) REVERT: C 159 ASN cc_start: 0.8669 (t0) cc_final: 0.8133 (t0) REVERT: D 103 MET cc_start: 0.9557 (mmp) cc_final: 0.9342 (mmm) REVERT: D 129 MET cc_start: 0.9399 (mmm) cc_final: 0.9170 (mmm) REVERT: E 1 MET cc_start: 0.8467 (tmm) cc_final: 0.8010 (tmm) REVERT: E 44 MET cc_start: 0.9490 (mtp) cc_final: 0.9055 (mtp) REVERT: E 362 MET cc_start: 0.9683 (tmm) cc_final: 0.9151 (tmm) REVERT: E 366 MET cc_start: 0.9112 (mmp) cc_final: 0.8876 (mmm) REVERT: E 380 MET cc_start: 0.9017 (mmp) cc_final: 0.8572 (mmm) REVERT: F 477 MET cc_start: 0.9269 (mmm) cc_final: 0.8873 (mmm) REVERT: F 778 MET cc_start: 0.8472 (mmp) cc_final: 0.7930 (mmm) REVERT: H 477 MET cc_start: 0.8634 (mmm) cc_final: 0.8359 (mmm) REVERT: H 774 MET cc_start: 0.8808 (mpp) cc_final: 0.8564 (mpp) REVERT: H 778 MET cc_start: 0.8739 (mmp) cc_final: 0.8334 (mmm) REVERT: N 65 GLN cc_start: 0.9138 (tp40) cc_final: 0.8827 (tp-100) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.5694 time to fit residues: 172.0648 Evaluate side-chains 155 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 6.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 376 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 363 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 387 optimal weight: 5.9990 chunk 415 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 478 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 349 ASN ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 386 HIS ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 797 GLN 6 357 GLN 6 649 GLN 7 622 HIS 7 625 GLN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 GLN D 160 GLN E 18 ASN ** F 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 ASN G 678 ASN G 725 ASN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 GLN ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 52132 Z= 0.286 Angle : 0.589 10.172 70557 Z= 0.306 Chirality : 0.039 0.194 8065 Planarity : 0.004 0.048 9000 Dihedral : 6.869 179.071 7088 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 0.04 % Allowed : 0.94 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.11), residues: 6264 helix: 1.58 (0.10), residues: 2733 sheet: -0.69 (0.15), residues: 1090 loop : -0.17 (0.13), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 3 111 HIS 0.008 0.001 HIS 7 620 PHE 0.033 0.002 PHE 5 482 TYR 0.017 0.001 TYR N 22 ARG 0.010 0.001 ARG F 868 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 7.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 276 MET cc_start: 0.9689 (mmp) cc_final: 0.9449 (mmp) REVERT: 2 783 MET cc_start: 0.8849 (mtp) cc_final: 0.8479 (mtp) REVERT: 2 823 MET cc_start: 0.9593 (ptp) cc_final: 0.9355 (ptp) REVERT: 3 261 MET cc_start: 0.8983 (tpt) cc_final: 0.8622 (tpp) REVERT: 3 386 MET cc_start: 0.9270 (tpt) cc_final: 0.8695 (tpp) REVERT: 3 407 MET cc_start: 0.9391 (pmm) cc_final: 0.9122 (pmm) REVERT: 3 462 MET cc_start: 0.9669 (mmp) cc_final: 0.9450 (mmm) REVERT: 3 478 MET cc_start: 0.8683 (tpt) cc_final: 0.8383 (tpp) REVERT: 4 233 MET cc_start: 0.9526 (ttt) cc_final: 0.9172 (tmm) REVERT: 4 314 MET cc_start: 0.8535 (ppp) cc_final: 0.7847 (ppp) REVERT: 4 847 MET cc_start: 0.8438 (ppp) cc_final: 0.8096 (mmm) REVERT: 5 65 MET cc_start: 0.9581 (mmp) cc_final: 0.9125 (mmm) REVERT: 5 182 MET cc_start: 0.9623 (tpt) cc_final: 0.9273 (tpp) REVERT: 5 252 ASP cc_start: 0.9076 (m-30) cc_final: 0.8590 (p0) REVERT: 5 276 MET cc_start: 0.9141 (pmm) cc_final: 0.8831 (pmm) REVERT: 5 393 MET cc_start: 0.9232 (tpp) cc_final: 0.8381 (tpp) REVERT: 5 552 MET cc_start: 0.9857 (tpp) cc_final: 0.9459 (tpp) REVERT: 6 313 MET cc_start: 0.9676 (ptm) cc_final: 0.9378 (ptm) REVERT: 6 629 MET cc_start: 0.9692 (mmp) cc_final: 0.9305 (mmm) REVERT: 7 64 MET cc_start: 0.9491 (mmp) cc_final: 0.9065 (mmm) REVERT: 7 448 MET cc_start: 0.9044 (tpt) cc_final: 0.8709 (tpt) REVERT: 7 459 MET cc_start: 0.9433 (tpt) cc_final: 0.9121 (tpp) REVERT: A 100 MET cc_start: 0.9421 (mmt) cc_final: 0.9010 (mmm) REVERT: C 191 MET cc_start: 0.9404 (ppp) cc_final: 0.9197 (tmm) REVERT: D 129 MET cc_start: 0.9376 (mmm) cc_final: 0.9136 (mmm) REVERT: D 277 MET cc_start: 0.9688 (mmm) cc_final: 0.9243 (mmm) REVERT: E 1 MET cc_start: 0.8503 (tmm) cc_final: 0.8051 (tmm) REVERT: E 44 MET cc_start: 0.9486 (mtp) cc_final: 0.9067 (mtp) REVERT: E 362 MET cc_start: 0.9660 (tmm) cc_final: 0.9065 (tmm) REVERT: E 380 MET cc_start: 0.9045 (mmp) cc_final: 0.8651 (mmm) REVERT: F 477 MET cc_start: 0.9281 (mmm) cc_final: 0.8981 (mmm) REVERT: F 778 MET cc_start: 0.8314 (mmp) cc_final: 0.7786 (mmm) REVERT: H 774 MET cc_start: 0.8909 (mpp) cc_final: 0.8693 (mpp) REVERT: H 778 MET cc_start: 0.8579 (mmp) cc_final: 0.8174 (mmm) REVERT: H 821 MET cc_start: 0.8994 (ttt) cc_final: 0.8541 (tpp) REVERT: N 36 ASP cc_start: 0.9482 (p0) cc_final: 0.9084 (p0) REVERT: N 65 GLN cc_start: 0.9164 (tp-100) cc_final: 0.8879 (tp-100) REVERT: N 78 PHE cc_start: 0.9609 (m-10) cc_final: 0.9236 (m-10) outliers start: 2 outliers final: 0 residues processed: 164 average time/residue: 0.6028 time to fit residues: 176.4552 Evaluate side-chains 152 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 6.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 554 optimal weight: 3.9990 chunk 583 optimal weight: 6.9990 chunk 532 optimal weight: 5.9990 chunk 567 optimal weight: 9.9990 chunk 341 optimal weight: 3.9990 chunk 247 optimal weight: 0.0050 chunk 445 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 512 optimal weight: 0.8980 chunk 536 optimal weight: 20.0000 chunk 565 optimal weight: 6.9990 overall best weight: 2.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 349 ASN ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 493 GLN ** 3 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 357 GLN ** 7 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 555 GLN G 678 ASN ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 52132 Z= 0.169 Angle : 0.516 9.987 70557 Z= 0.268 Chirality : 0.039 0.176 8065 Planarity : 0.003 0.049 9000 Dihedral : 6.788 172.641 7088 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.11), residues: 6264 helix: 1.71 (0.10), residues: 2734 sheet: -0.58 (0.16), residues: 1089 loop : -0.12 (0.13), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 74 HIS 0.005 0.001 HIS 7 620 PHE 0.027 0.001 PHE 2 520 TYR 0.017 0.001 TYR H 862 ARG 0.005 0.000 ARG F 868 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 6.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8845 (mtp) cc_final: 0.8466 (mtp) REVERT: 2 823 MET cc_start: 0.9605 (ptp) cc_final: 0.9340 (ptp) REVERT: 3 261 MET cc_start: 0.8966 (tpt) cc_final: 0.8627 (tpp) REVERT: 3 383 LEU cc_start: 0.9793 (mt) cc_final: 0.9565 (mt) REVERT: 3 386 MET cc_start: 0.9217 (tpt) cc_final: 0.8633 (tpp) REVERT: 3 462 MET cc_start: 0.9636 (mmp) cc_final: 0.9411 (mmm) REVERT: 3 478 MET cc_start: 0.8708 (tpt) cc_final: 0.8330 (tpp) REVERT: 4 233 MET cc_start: 0.9522 (ttt) cc_final: 0.9172 (tmm) REVERT: 4 314 MET cc_start: 0.8378 (ppp) cc_final: 0.7661 (ppp) REVERT: 4 847 MET cc_start: 0.8415 (ppp) cc_final: 0.8074 (mmm) REVERT: 5 65 MET cc_start: 0.9574 (mmp) cc_final: 0.9202 (mmm) REVERT: 5 182 MET cc_start: 0.9526 (tpt) cc_final: 0.9310 (tpp) REVERT: 5 252 ASP cc_start: 0.9053 (m-30) cc_final: 0.8614 (p0) REVERT: 5 276 MET cc_start: 0.9117 (pmm) cc_final: 0.8845 (pmm) REVERT: 5 393 MET cc_start: 0.9183 (tpp) cc_final: 0.8301 (tpp) REVERT: 5 552 MET cc_start: 0.9854 (tpp) cc_final: 0.9475 (tpp) REVERT: 6 313 MET cc_start: 0.9632 (ptm) cc_final: 0.9135 (ptp) REVERT: 6 629 MET cc_start: 0.9707 (mmp) cc_final: 0.9282 (mmm) REVERT: 7 64 MET cc_start: 0.9499 (mmp) cc_final: 0.9062 (mmm) REVERT: 7 448 MET cc_start: 0.9091 (tpt) cc_final: 0.8739 (tpt) REVERT: 7 459 MET cc_start: 0.9386 (tpt) cc_final: 0.9093 (tpp) REVERT: 7 498 MET cc_start: 0.9417 (tpt) cc_final: 0.9184 (tpp) REVERT: 7 529 MET cc_start: 0.8693 (tmm) cc_final: 0.8368 (tmm) REVERT: 7 541 MET cc_start: 0.9272 (ptm) cc_final: 0.8849 (tmm) REVERT: 7 621 MET cc_start: 0.8799 (mmt) cc_final: 0.8576 (mmt) REVERT: 7 652 MET cc_start: 0.7197 (ppp) cc_final: 0.6948 (ppp) REVERT: A 79 MET cc_start: 0.9710 (mtm) cc_final: 0.9414 (ptp) REVERT: A 100 MET cc_start: 0.9371 (mmt) cc_final: 0.9017 (mmm) REVERT: C 113 MET cc_start: 0.9312 (mmm) cc_final: 0.8888 (mmm) REVERT: C 159 ASN cc_start: 0.8680 (t0) cc_final: 0.8151 (t0) REVERT: D 103 MET cc_start: 0.9564 (mmp) cc_final: 0.9329 (mmm) REVERT: D 129 MET cc_start: 0.9292 (mmm) cc_final: 0.8999 (mmm) REVERT: D 277 MET cc_start: 0.9684 (mmm) cc_final: 0.9194 (mmm) REVERT: E 1 MET cc_start: 0.8410 (tmm) cc_final: 0.7985 (tmm) REVERT: E 44 MET cc_start: 0.9469 (mtp) cc_final: 0.9019 (mtp) REVERT: E 362 MET cc_start: 0.9672 (tmm) cc_final: 0.9138 (tmm) REVERT: E 366 MET cc_start: 0.9167 (mmp) cc_final: 0.8930 (mmm) REVERT: E 380 MET cc_start: 0.9025 (mmp) cc_final: 0.8627 (mmm) REVERT: F 477 MET cc_start: 0.9305 (mmm) cc_final: 0.9008 (mmm) REVERT: F 774 MET cc_start: 0.8837 (mpp) cc_final: 0.8577 (mpp) REVERT: F 778 MET cc_start: 0.8269 (mmp) cc_final: 0.7724 (mmm) REVERT: H 477 MET cc_start: 0.8807 (mmm) cc_final: 0.8434 (mmm) REVERT: H 778 MET cc_start: 0.8541 (mmp) cc_final: 0.8141 (mmm) REVERT: H 821 MET cc_start: 0.8981 (ttt) cc_final: 0.8537 (tpp) REVERT: N 65 GLN cc_start: 0.9134 (tp-100) cc_final: 0.8856 (tp-100) REVERT: N 88 ILE cc_start: 0.7104 (mm) cc_final: 0.6892 (mm) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.5973 time to fit residues: 179.6835 Evaluate side-chains 156 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 6.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 372 optimal weight: 5.9990 chunk 600 optimal weight: 20.0000 chunk 366 optimal weight: 0.5980 chunk 284 optimal weight: 2.9990 chunk 417 optimal weight: 3.9990 chunk 629 optimal weight: 0.8980 chunk 579 optimal weight: 8.9990 chunk 501 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 387 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 726 ASN 6 357 GLN ** 7 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN G 678 ASN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 52132 Z= 0.173 Angle : 0.519 14.269 70557 Z= 0.268 Chirality : 0.039 0.214 8065 Planarity : 0.003 0.050 9000 Dihedral : 6.758 169.364 7088 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.11), residues: 6264 helix: 1.72 (0.10), residues: 2736 sheet: -0.50 (0.16), residues: 1090 loop : -0.10 (0.13), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 190 HIS 0.015 0.001 HIS 2 621 PHE 0.024 0.001 PHE 2 520 TYR 0.021 0.001 TYR G 862 ARG 0.006 0.000 ARG H 524 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 6.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8839 (mtp) cc_final: 0.8466 (mtp) REVERT: 2 823 MET cc_start: 0.9575 (ptp) cc_final: 0.9307 (ptp) REVERT: 3 261 MET cc_start: 0.8974 (tpt) cc_final: 0.8630 (tpp) REVERT: 3 386 MET cc_start: 0.9219 (tpt) cc_final: 0.8657 (tpp) REVERT: 3 462 MET cc_start: 0.9631 (mmp) cc_final: 0.9393 (mmm) REVERT: 3 478 MET cc_start: 0.8769 (tpt) cc_final: 0.8295 (tpp) REVERT: 4 233 MET cc_start: 0.9532 (ttt) cc_final: 0.9176 (tmm) REVERT: 4 314 MET cc_start: 0.8401 (ppp) cc_final: 0.7697 (ppp) REVERT: 4 847 MET cc_start: 0.8407 (ppp) cc_final: 0.8072 (mmm) REVERT: 5 65 MET cc_start: 0.9572 (mmp) cc_final: 0.9196 (mmm) REVERT: 5 182 MET cc_start: 0.9519 (tpt) cc_final: 0.9308 (tpp) REVERT: 5 252 ASP cc_start: 0.9070 (m-30) cc_final: 0.8576 (p0) REVERT: 5 276 MET cc_start: 0.9091 (pmm) cc_final: 0.8798 (pmm) REVERT: 5 393 MET cc_start: 0.9186 (tpp) cc_final: 0.8305 (tpp) REVERT: 5 404 MET cc_start: 0.9041 (tmm) cc_final: 0.8833 (tmm) REVERT: 5 552 MET cc_start: 0.9855 (tpp) cc_final: 0.9473 (tpp) REVERT: 6 313 MET cc_start: 0.9617 (ptm) cc_final: 0.9127 (ptp) REVERT: 6 629 MET cc_start: 0.9713 (mmp) cc_final: 0.9282 (mmm) REVERT: 7 64 MET cc_start: 0.9483 (mmp) cc_final: 0.9060 (mmm) REVERT: 7 448 MET cc_start: 0.9141 (tpt) cc_final: 0.8787 (tpt) REVERT: 7 459 MET cc_start: 0.9394 (tpt) cc_final: 0.9099 (tpp) REVERT: 7 498 MET cc_start: 0.9390 (tpt) cc_final: 0.9173 (tpp) REVERT: 7 529 MET cc_start: 0.8580 (tmm) cc_final: 0.8254 (tmm) REVERT: 7 541 MET cc_start: 0.9253 (ptm) cc_final: 0.8841 (tmm) REVERT: 7 621 MET cc_start: 0.8845 (mmt) cc_final: 0.8643 (mmt) REVERT: A 100 MET cc_start: 0.9349 (mmt) cc_final: 0.8943 (mmm) REVERT: C 79 MET cc_start: 0.8931 (ptm) cc_final: 0.8636 (ptm) REVERT: C 113 MET cc_start: 0.9333 (mmm) cc_final: 0.8902 (mmm) REVERT: C 159 ASN cc_start: 0.8707 (t0) cc_final: 0.8172 (t0) REVERT: D 103 MET cc_start: 0.9566 (mmp) cc_final: 0.9338 (mmm) REVERT: D 129 MET cc_start: 0.9320 (mmm) cc_final: 0.9026 (mmm) REVERT: D 277 MET cc_start: 0.9684 (mmm) cc_final: 0.9180 (mmm) REVERT: E 1 MET cc_start: 0.8242 (tmm) cc_final: 0.7756 (tmm) REVERT: E 44 MET cc_start: 0.9480 (mtp) cc_final: 0.9032 (mtp) REVERT: E 362 MET cc_start: 0.9669 (tmm) cc_final: 0.9170 (tmm) REVERT: E 366 MET cc_start: 0.9170 (mmp) cc_final: 0.8929 (mmm) REVERT: E 380 MET cc_start: 0.9047 (mmp) cc_final: 0.8648 (mmm) REVERT: F 477 MET cc_start: 0.9306 (mmm) cc_final: 0.9008 (mmm) REVERT: F 774 MET cc_start: 0.8856 (mpp) cc_final: 0.8553 (mpp) REVERT: F 778 MET cc_start: 0.8254 (mmp) cc_final: 0.7748 (mmm) REVERT: H 477 MET cc_start: 0.8825 (mmm) cc_final: 0.8444 (mmm) REVERT: H 774 MET cc_start: 0.8886 (mpp) cc_final: 0.8546 (mpp) REVERT: H 778 MET cc_start: 0.8537 (mmp) cc_final: 0.8132 (mmm) REVERT: H 821 MET cc_start: 0.8949 (ttt) cc_final: 0.8490 (tpp) REVERT: N 36 ASP cc_start: 0.9475 (p0) cc_final: 0.8998 (p0) REVERT: N 65 GLN cc_start: 0.9157 (tp-100) cc_final: 0.8885 (tp-100) REVERT: N 78 PHE cc_start: 0.9634 (m-10) cc_final: 0.9217 (m-10) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.5932 time to fit residues: 174.5262 Evaluate side-chains 155 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 6.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 398 optimal weight: 9.9990 chunk 534 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 462 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 139 optimal weight: 30.0000 chunk 502 optimal weight: 4.9990 chunk 210 optimal weight: 0.8980 chunk 515 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 349 ASN ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 726 ASN 6 357 GLN 7 468 GLN ** 7 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN G 678 ASN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.026558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.019711 restraints weight = 762956.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.020295 restraints weight = 468989.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.020693 restraints weight = 334425.406| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 52132 Z= 0.229 Angle : 0.549 13.513 70557 Z= 0.284 Chirality : 0.039 0.222 8065 Planarity : 0.004 0.049 9000 Dihedral : 6.820 164.444 7088 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.11), residues: 6264 helix: 1.66 (0.10), residues: 2744 sheet: -0.55 (0.16), residues: 1102 loop : -0.13 (0.13), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 190 HIS 0.018 0.001 HIS 2 621 PHE 0.022 0.001 PHE 2 520 TYR 0.023 0.001 TYR 4 580 ARG 0.005 0.000 ARG H 524 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7161.71 seconds wall clock time: 135 minutes 56.91 seconds (8156.91 seconds total)