Starting phenix.real_space_refine on Thu Mar 21 04:34:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/03_2024/8hir_34827_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/03_2024/8hir_34827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/03_2024/8hir_34827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/03_2024/8hir_34827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/03_2024/8hir_34827_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/03_2024/8hir_34827_updated.pdb" } resolution = 3.18 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= 0.007 sd= 0.133 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 K 4 8.98 5 Zn 4 6.06 5 S 208 5.16 5 Na 4 4.78 5 C 18908 2.51 5 N 4848 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A ASP 504": "OD1" <-> "OD2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A ASP 843": "OD1" <-> "OD2" Residue "A PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1014": "OE1" <-> "OE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B ASP 413": "OD1" <-> "OD2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "B ASP 504": "OD1" <-> "OD2" Residue "B TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 631": "OE1" <-> "OE2" Residue "B TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 860": "OE1" <-> "OE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C ASP 384": "OD1" <-> "OD2" Residue "C ASP 401": "OD1" <-> "OD2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C ASP 413": "OD1" <-> "OD2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C ASP 504": "OD1" <-> "OD2" Residue "C TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "C TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 830": "OE1" <-> "OE2" Residue "C ASP 839": "OD1" <-> "OD2" Residue "C GLU 860": "OE1" <-> "OE2" Residue "C PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1148": "OE1" <-> "OE2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 138": "OD1" <-> "OD2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 384": "OD1" <-> "OD2" Residue "D ASP 401": "OD1" <-> "OD2" Residue "D GLU 411": "OE1" <-> "OE2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "D ASP 504": "OD1" <-> "OD2" Residue "D TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 839": "OD1" <-> "OD2" Residue "D TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1014": "OE1" <-> "OE2" Residue "D GLU 1148": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29168 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "C" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "D" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 17 Unusual residues: {' K': 4, ' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4558 SG CYS A 777 82.687 95.289 12.517 1.00113.91 S ATOM 4564 SG CYS A 778 85.660 98.570 12.340 1.00115.70 S ATOM 4618 SG CYS A 785 86.098 95.282 10.992 1.00138.43 S ATOM 11836 SG CYS B 777 95.308 67.082 12.496 1.00113.48 S ATOM 11842 SG CYS B 778 98.582 64.093 12.329 1.00117.04 S ATOM 11896 SG CYS B 785 95.296 63.676 10.963 1.00136.80 S ATOM 19114 SG CYS C 777 67.051 54.450 12.490 1.00112.86 S ATOM 19120 SG CYS C 778 64.079 51.170 12.324 1.00115.83 S ATOM 19174 SG CYS C 785 63.629 54.465 10.977 1.00137.33 S ATOM 26392 SG CYS D 777 54.468 82.685 12.517 1.00116.50 S ATOM 26398 SG CYS D 778 51.170 85.650 12.341 1.00118.42 S ATOM 26452 SG CYS D 785 54.472 86.094 10.989 1.00137.08 S Time building chain proxies: 14.31, per 1000 atoms: 0.49 Number of scatterers: 29168 At special positions: 0 Unit cell: (150.8, 150.8, 139.36, 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 4 29.99 K 4 19.00 S 208 16.00 Na 4 11.00 O 5192 8.00 N 4848 7.00 C 18908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.34 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1307 " pdb="ZN ZN A1307 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1307 " - pdb=" SG CYS A 777 " pdb="ZN ZN A1307 " - pdb=" SG CYS A 785 " pdb="ZN ZN A1307 " - pdb=" SG CYS A 778 " pdb=" ZN B1303 " pdb="ZN ZN B1303 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 785 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 778 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 777 " pdb=" ZN C1303 " pdb="ZN ZN C1303 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 778 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 777 " pdb=" ZN D1303 " pdb="ZN ZN D1303 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 785 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 778 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 777 " Number of angles added : 12 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 24 sheets defined 44.7% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.44 Creating SS restraints... Processing helix chain 'A' and resid 91 through 94 No H-bonds generated for 'chain 'A' and resid 91 through 94' Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 109 through 135 removed outlier: 3.790A pdb=" N LEU A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 165 through 168 No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 175 through 197 Processing helix chain 'A' and resid 205 through 208 No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.600A pdb=" N GLU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 4.857A pdb=" N ILE A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 253 removed outlier: 3.533A pdb=" N GLU A 250 " --> pdb=" O HIS A 247 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 294 removed outlier: 4.118A pdb=" N ILE A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 325 through 357 Proline residue: A 343 - end of helix removed outlier: 4.242A pdb=" N GLU A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 357 " --> pdb=" O TRP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 368 No H-bonds generated for 'chain 'A' and resid 365 through 368' Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.516A pdb=" N ASN A 391 " --> pdb=" O MET A 387 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 414 through 419 removed outlier: 4.136A pdb=" N ARG A 418 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 419' Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.870A pdb=" N ARG A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 481 removed outlier: 4.010A pdb=" N THR A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 509 through 517 removed outlier: 3.590A pdb=" N ALA A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.601A pdb=" N THR A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 removed outlier: 3.540A pdb=" N GLY A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 630 through 632 No H-bonds generated for 'chain 'A' and resid 630 through 632' Processing helix chain 'A' and resid 776 through 779 No H-bonds generated for 'chain 'A' and resid 776 through 779' Processing helix chain 'A' and resid 793 through 796 No H-bonds generated for 'chain 'A' and resid 793 through 796' Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.614A pdb=" N ASN A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 817 " --> pdb=" O GLY A 813 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 819 " --> pdb=" O TYR A 815 " (cutoff:3.500A) Proline residue: A 820 - end of helix No H-bonds generated for 'chain 'A' and resid 812 through 822' Processing helix chain 'A' and resid 844 through 850 removed outlier: 3.837A pdb=" N ALA A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 872 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 894 through 897 No H-bonds generated for 'chain 'A' and resid 894 through 897' Processing helix chain 'A' and resid 899 through 911 removed outlier: 3.657A pdb=" N VAL A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 929 removed outlier: 4.100A pdb=" N ARG A 928 " --> pdb=" O SER A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 952 removed outlier: 3.512A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 965 No H-bonds generated for 'chain 'A' and resid 962 through 965' Processing helix chain 'A' and resid 972 through 974 No H-bonds generated for 'chain 'A' and resid 972 through 974' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.589A pdb=" N TYR A 980 " --> pdb=" O THR A 977 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 981 " --> pdb=" O LEU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 995 Processing helix chain 'A' and resid 1014 through 1016 No H-bonds generated for 'chain 'A' and resid 1014 through 1016' Processing helix chain 'A' and resid 1022 through 1032 Processing helix chain 'A' and resid 1133 through 1140 removed outlier: 3.625A pdb=" N LEU A1138 " --> pdb=" O SER A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1160 Processing helix chain 'B' and resid 91 through 94 No H-bonds generated for 'chain 'B' and resid 91 through 94' Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.541A pdb=" N LEU B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 135 removed outlier: 3.767A pdb=" N LEU B 113 " --> pdb=" O GLN B 109 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 165 through 168 No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 175 through 197 Processing helix chain 'B' and resid 205 through 208 No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 210 through 226 removed outlier: 3.616A pdb=" N GLU B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Proline residue: B 221 - end of helix removed outlier: 4.701A pdb=" N ILE B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 253 removed outlier: 3.552A pdb=" N GLU B 250 " --> pdb=" O HIS B 247 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 294 removed outlier: 4.040A pdb=" N ILE B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 325 through 357 Proline residue: B 343 - end of helix removed outlier: 4.236A pdb=" N GLU B 355 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B 357 " --> pdb=" O TRP B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 368 No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 383 through 393 removed outlier: 3.501A pdb=" N ASN B 391 " --> pdb=" O MET B 387 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU B 392 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 414 through 419 removed outlier: 4.121A pdb=" N ARG B 418 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 414 through 419' Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.896A pdb=" N ARG B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 481 removed outlier: 3.999A pdb=" N THR B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 497 Processing helix chain 'B' and resid 509 through 517 removed outlier: 3.591A pdb=" N ALA B 515 " --> pdb=" O GLU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 533 removed outlier: 3.601A pdb=" N THR B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 558 removed outlier: 3.529A pdb=" N GLY B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 590 Processing helix chain 'B' and resid 630 through 632 No H-bonds generated for 'chain 'B' and resid 630 through 632' Processing helix chain 'B' and resid 776 through 779 No H-bonds generated for 'chain 'B' and resid 776 through 779' Processing helix chain 'B' and resid 793 through 796 No H-bonds generated for 'chain 'B' and resid 793 through 796' Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.635A pdb=" N ASN B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 817 " --> pdb=" O GLY B 813 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 818 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 819 " --> pdb=" O TYR B 815 " (cutoff:3.500A) Proline residue: B 820 - end of helix No H-bonds generated for 'chain 'B' and resid 812 through 822' Processing helix chain 'B' and resid 844 through 850 removed outlier: 3.830A pdb=" N ALA B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 872 Processing helix chain 'B' and resid 874 through 876 No H-bonds generated for 'chain 'B' and resid 874 through 876' Processing helix chain 'B' and resid 888 through 890 No H-bonds generated for 'chain 'B' and resid 888 through 890' Processing helix chain 'B' and resid 894 through 897 No H-bonds generated for 'chain 'B' and resid 894 through 897' Processing helix chain 'B' and resid 899 through 911 removed outlier: 3.659A pdb=" N VAL B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 929 removed outlier: 4.112A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 952 removed outlier: 3.504A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 965 No H-bonds generated for 'chain 'B' and resid 962 through 965' Processing helix chain 'B' and resid 972 through 974 No H-bonds generated for 'chain 'B' and resid 972 through 974' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.566A pdb=" N TYR B 980 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN B 981 " --> pdb=" O LEU B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 995 Processing helix chain 'B' and resid 1014 through 1016 No H-bonds generated for 'chain 'B' and resid 1014 through 1016' Processing helix chain 'B' and resid 1022 through 1032 Processing helix chain 'B' and resid 1133 through 1140 removed outlier: 3.624A pdb=" N LEU B1138 " --> pdb=" O SER B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1160 Processing helix chain 'C' and resid 91 through 94 No H-bonds generated for 'chain 'C' and resid 91 through 94' Processing helix chain 'C' and resid 97 through 105 Processing helix chain 'C' and resid 109 through 135 removed outlier: 3.783A pdb=" N LEU C 113 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 165 through 168 No H-bonds generated for 'chain 'C' and resid 165 through 168' Processing helix chain 'C' and resid 175 through 197 Processing helix chain 'C' and resid 205 through 208 No H-bonds generated for 'chain 'C' and resid 205 through 208' Processing helix chain 'C' and resid 210 through 226 removed outlier: 3.620A pdb=" N GLU C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Proline residue: C 221 - end of helix removed outlier: 4.887A pdb=" N ILE C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 255 removed outlier: 3.556A pdb=" N GLU C 250 " --> pdb=" O HIS C 247 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN C 254 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 294 removed outlier: 3.981A pdb=" N ILE C 273 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 325 through 357 Proline residue: C 343 - end of helix removed outlier: 4.240A pdb=" N GLU C 355 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN C 357 " --> pdb=" O TRP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 368 No H-bonds generated for 'chain 'C' and resid 365 through 368' Processing helix chain 'C' and resid 383 through 393 removed outlier: 3.591A pdb=" N ASN C 391 " --> pdb=" O MET C 387 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 399 No H-bonds generated for 'chain 'C' and resid 397 through 399' Processing helix chain 'C' and resid 414 through 420 removed outlier: 4.104A pdb=" N ARG C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.888A pdb=" N ARG C 444 " --> pdb=" O GLN C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 481 removed outlier: 4.004A pdb=" N THR C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 497 No H-bonds generated for 'chain 'C' and resid 495 through 497' Processing helix chain 'C' and resid 509 through 517 removed outlier: 3.591A pdb=" N ALA C 515 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 533 removed outlier: 3.618A pdb=" N THR C 531 " --> pdb=" O SER C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 558 removed outlier: 3.535A pdb=" N GLY C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY C 558 " --> pdb=" O GLY C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 590 Processing helix chain 'C' and resid 630 through 632 No H-bonds generated for 'chain 'C' and resid 630 through 632' Processing helix chain 'C' and resid 776 through 779 No H-bonds generated for 'chain 'C' and resid 776 through 779' Processing helix chain 'C' and resid 793 through 796 No H-bonds generated for 'chain 'C' and resid 793 through 796' Processing helix chain 'C' and resid 812 through 822 removed outlier: 3.636A pdb=" N ASN C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE C 817 " --> pdb=" O GLY C 813 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 819 " --> pdb=" O TYR C 815 " (cutoff:3.500A) Proline residue: C 820 - end of helix No H-bonds generated for 'chain 'C' and resid 812 through 822' Processing helix chain 'C' and resid 844 through 850 removed outlier: 3.832A pdb=" N ALA C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 872 Processing helix chain 'C' and resid 874 through 876 No H-bonds generated for 'chain 'C' and resid 874 through 876' Processing helix chain 'C' and resid 888 through 890 No H-bonds generated for 'chain 'C' and resid 888 through 890' Processing helix chain 'C' and resid 894 through 897 No H-bonds generated for 'chain 'C' and resid 894 through 897' Processing helix chain 'C' and resid 899 through 911 removed outlier: 3.664A pdb=" N VAL C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 910 " --> pdb=" O GLN C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 929 removed outlier: 4.094A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 952 removed outlier: 3.513A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 965 No H-bonds generated for 'chain 'C' and resid 962 through 965' Processing helix chain 'C' and resid 972 through 974 No H-bonds generated for 'chain 'C' and resid 972 through 974' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.566A pdb=" N TYR C 980 " --> pdb=" O THR C 977 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN C 981 " --> pdb=" O LEU C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 995 Processing helix chain 'C' and resid 1014 through 1016 No H-bonds generated for 'chain 'C' and resid 1014 through 1016' Processing helix chain 'C' and resid 1022 through 1032 Processing helix chain 'C' and resid 1133 through 1140 removed outlier: 3.619A pdb=" N LEU C1138 " --> pdb=" O SER C1134 " (cutoff:3.500A) Processing helix chain 'C' and resid 1145 through 1160 Processing helix chain 'D' and resid 91 through 94 No H-bonds generated for 'chain 'D' and resid 91 through 94' Processing helix chain 'D' and resid 97 through 105 removed outlier: 3.517A pdb=" N LEU D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 135 removed outlier: 3.760A pdb=" N LEU D 113 " --> pdb=" O GLN D 109 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 114 " --> pdb=" O ARG D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 165 through 168 No H-bonds generated for 'chain 'D' and resid 165 through 168' Processing helix chain 'D' and resid 175 through 197 Processing helix chain 'D' and resid 205 through 208 No H-bonds generated for 'chain 'D' and resid 205 through 208' Processing helix chain 'D' and resid 210 through 226 removed outlier: 3.598A pdb=" N GLU D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 4.845A pdb=" N ILE D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 253 removed outlier: 3.643A pdb=" N GLU D 250 " --> pdb=" O HIS D 247 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 294 removed outlier: 4.119A pdb=" N ILE D 273 " --> pdb=" O ASN D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 312 Processing helix chain 'D' and resid 325 through 357 Proline residue: D 343 - end of helix removed outlier: 4.240A pdb=" N GLU D 355 " --> pdb=" O TYR D 351 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN D 357 " --> pdb=" O TRP D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 368 No H-bonds generated for 'chain 'D' and resid 365 through 368' Processing helix chain 'D' and resid 383 through 393 removed outlier: 3.520A pdb=" N ASN D 391 " --> pdb=" O MET D 387 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 399 No H-bonds generated for 'chain 'D' and resid 397 through 399' Processing helix chain 'D' and resid 414 through 420 removed outlier: 4.133A pdb=" N ARG D 418 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL D 419 " --> pdb=" O GLN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 removed outlier: 3.876A pdb=" N ARG D 444 " --> pdb=" O GLN D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 481 removed outlier: 4.008A pdb=" N THR D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'D' and resid 509 through 517 removed outlier: 3.589A pdb=" N ALA D 515 " --> pdb=" O GLU D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 533 removed outlier: 3.602A pdb=" N THR D 531 " --> pdb=" O SER D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 removed outlier: 3.567A pdb=" N GLY D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY D 558 " --> pdb=" O GLY D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 590 Processing helix chain 'D' and resid 630 through 632 No H-bonds generated for 'chain 'D' and resid 630 through 632' Processing helix chain 'D' and resid 776 through 779 No H-bonds generated for 'chain 'D' and resid 776 through 779' Processing helix chain 'D' and resid 793 through 796 No H-bonds generated for 'chain 'D' and resid 793 through 796' Processing helix chain 'D' and resid 812 through 822 removed outlier: 3.612A pdb=" N ASN D 816 " --> pdb=" O ASN D 812 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE D 817 " --> pdb=" O GLY D 813 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 818 " --> pdb=" O LEU D 814 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D 819 " --> pdb=" O TYR D 815 " (cutoff:3.500A) Proline residue: D 820 - end of helix No H-bonds generated for 'chain 'D' and resid 812 through 822' Processing helix chain 'D' and resid 844 through 850 removed outlier: 3.838A pdb=" N ALA D 849 " --> pdb=" O HIS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 872 Processing helix chain 'D' and resid 874 through 876 No H-bonds generated for 'chain 'D' and resid 874 through 876' Processing helix chain 'D' and resid 888 through 890 No H-bonds generated for 'chain 'D' and resid 888 through 890' Processing helix chain 'D' and resid 894 through 897 No H-bonds generated for 'chain 'D' and resid 894 through 897' Processing helix chain 'D' and resid 899 through 911 removed outlier: 3.686A pdb=" N VAL D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 910 " --> pdb=" O GLN D 906 " (cutoff:3.500A) Processing helix chain 'D' and resid 924 through 929 removed outlier: 4.108A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 952 removed outlier: 3.502A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 946 " --> pdb=" O LEU D 942 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 948 " --> pdb=" O LYS D 944 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 965 No H-bonds generated for 'chain 'D' and resid 962 through 965' Processing helix chain 'D' and resid 972 through 974 No H-bonds generated for 'chain 'D' and resid 972 through 974' Processing helix chain 'D' and resid 976 through 984 removed outlier: 3.586A pdb=" N TYR D 980 " --> pdb=" O THR D 977 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN D 981 " --> pdb=" O LEU D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 995 Processing helix chain 'D' and resid 1014 through 1016 No H-bonds generated for 'chain 'D' and resid 1014 through 1016' Processing helix chain 'D' and resid 1022 through 1032 Processing helix chain 'D' and resid 1133 through 1140 removed outlier: 3.617A pdb=" N LEU D1138 " --> pdb=" O SER D1134 " (cutoff:3.500A) Processing helix chain 'D' and resid 1145 through 1160 Processing sheet with id= A, first strand: chain 'A' and resid 505 through 508 removed outlier: 6.129A pdb=" N CYS A 453 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN A 490 " --> pdb=" O CYS A 453 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE A 455 " --> pdb=" O GLN A 490 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 375 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N LEU A 456 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N CYS A 377 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A 408 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.832A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 750 through 753 Processing sheet with id= D, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.297A pdb=" N ILE A 834 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N MET A 859 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU A 836 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE A 804 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 880 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER A 916 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL A 882 " --> pdb=" O SER A 916 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 918 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 4.094A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1039 through 1044 Processing sheet with id= G, first strand: chain 'B' and resid 505 through 508 removed outlier: 6.132A pdb=" N CYS B 453 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLN B 490 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE B 455 " --> pdb=" O GLN B 490 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 375 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N LEU B 456 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N CYS B 377 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS B 408 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.866A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 750 through 753 Processing sheet with id= J, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.275A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE B 804 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU B 880 " --> pdb=" O ILE B 804 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER B 916 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL B 882 " --> pdb=" O SER B 916 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B 918 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 4.129A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 1039 through 1044 Processing sheet with id= M, first strand: chain 'C' and resid 505 through 508 removed outlier: 6.151A pdb=" N CYS C 453 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN C 490 " --> pdb=" O CYS C 453 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE C 455 " --> pdb=" O GLN C 490 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL C 375 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LEU C 456 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N CYS C 377 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS C 408 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.861A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 750 through 753 Processing sheet with id= P, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.271A pdb=" N ILE C 834 " --> pdb=" O TYR C 857 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N MET C 859 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU C 836 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE C 804 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 880 " --> pdb=" O ILE C 804 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER C 916 " --> pdb=" O LEU C 880 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL C 882 " --> pdb=" O SER C 916 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR C 918 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 4.112A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1039 through 1044 Processing sheet with id= S, first strand: chain 'D' and resid 505 through 508 removed outlier: 6.136A pdb=" N CYS D 453 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN D 490 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE D 455 " --> pdb=" O GLN D 490 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL D 375 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU D 456 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N CYS D 377 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS D 408 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.840A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 750 through 753 Processing sheet with id= V, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.291A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE D 804 " --> pdb=" O ASP D 878 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU D 880 " --> pdb=" O ILE D 804 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER D 916 " --> pdb=" O LEU D 880 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL D 882 " --> pdb=" O SER D 916 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 918 " --> pdb=" O VAL D 882 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 4.104A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 1039 through 1044 983 hydrogen bonds defined for protein. 2667 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: 10.80 Time building geometry restraints manager: 12.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9201 1.34 - 1.46: 6777 1.46 - 1.58: 13562 1.58 - 1.70: 0 1.70 - 1.81: 304 Bond restraints: 29844 Sorted by residual: bond pdb=" CB PRO C 230 " pdb=" CG PRO C 230 " ideal model delta sigma weight residual 1.492 1.390 0.102 5.00e-02 4.00e+02 4.14e+00 bond pdb=" CA PRO C 229 " pdb=" C PRO C 229 " ideal model delta sigma weight residual 1.517 1.536 -0.019 9.30e-03 1.16e+04 4.13e+00 bond pdb=" CA ILE C 203 " pdb=" CB ILE C 203 " ideal model delta sigma weight residual 1.540 1.563 -0.023 1.36e-02 5.41e+03 2.88e+00 bond pdb=" CA ILE B 203 " pdb=" CB ILE B 203 " ideal model delta sigma weight residual 1.540 1.562 -0.022 1.36e-02 5.41e+03 2.61e+00 bond pdb=" CA ILE D 203 " pdb=" CB ILE D 203 " ideal model delta sigma weight residual 1.540 1.562 -0.022 1.36e-02 5.41e+03 2.61e+00 ... (remaining 29839 not shown) Histogram of bond angle deviations from ideal: 82.95 - 93.59: 8 93.59 - 104.23: 457 104.23 - 114.87: 18106 114.87 - 125.51: 21448 125.51 - 136.15: 481 Bond angle restraints: 40500 Sorted by residual: angle pdb=" N ARG D 172 " pdb=" CA ARG D 172 " pdb=" C ARG D 172 " ideal model delta sigma weight residual 109.79 82.95 26.84 1.56e+00 4.11e-01 2.96e+02 angle pdb=" N ARG A 172 " pdb=" CA ARG A 172 " pdb=" C ARG A 172 " ideal model delta sigma weight residual 109.79 83.15 26.64 1.56e+00 4.11e-01 2.92e+02 angle pdb=" N ARG B 172 " pdb=" CA ARG B 172 " pdb=" C ARG B 172 " ideal model delta sigma weight residual 109.79 83.30 26.49 1.56e+00 4.11e-01 2.88e+02 angle pdb=" N ARG C 172 " pdb=" CA ARG C 172 " pdb=" C ARG C 172 " ideal model delta sigma weight residual 109.79 83.31 26.48 1.56e+00 4.11e-01 2.88e+02 angle pdb=" N LYS C 173 " pdb=" CA LYS C 173 " pdb=" CB LYS C 173 " ideal model delta sigma weight residual 110.39 91.56 18.83 1.59e+00 3.96e-01 1.40e+02 ... (remaining 40495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15553 17.94 - 35.89: 1825 35.89 - 53.83: 393 53.83 - 71.77: 65 71.77 - 89.71: 16 Dihedral angle restraints: 17852 sinusoidal: 7008 harmonic: 10844 Sorted by residual: dihedral pdb=" C ARG A 172 " pdb=" N ARG A 172 " pdb=" CA ARG A 172 " pdb=" CB ARG A 172 " ideal model delta harmonic sigma weight residual -122.60 -106.79 -15.81 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" C ARG B 172 " pdb=" N ARG B 172 " pdb=" CA ARG B 172 " pdb=" CB ARG B 172 " ideal model delta harmonic sigma weight residual -122.60 -106.79 -15.81 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" C ARG C 172 " pdb=" N ARG C 172 " pdb=" CA ARG C 172 " pdb=" CB ARG C 172 " ideal model delta harmonic sigma weight residual -122.60 -106.87 -15.73 0 2.50e+00 1.60e-01 3.96e+01 ... (remaining 17849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 4522 0.115 - 0.229: 73 0.229 - 0.344: 5 0.344 - 0.458: 6 0.458 - 0.573: 6 Chirality restraints: 4612 Sorted by residual: chirality pdb=" CA ILE B 203 " pdb=" N ILE B 203 " pdb=" C ILE B 203 " pdb=" CB ILE B 203 " both_signs ideal model delta sigma weight residual False 2.43 3.01 -0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" CA ARG A 172 " pdb=" N ARG A 172 " pdb=" C ARG A 172 " pdb=" CB ARG A 172 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" CA ARG B 172 " pdb=" N ARG B 172 " pdb=" C ARG B 172 " pdb=" CB ARG B 172 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 4609 not shown) Planarity restraints: 5088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 228 " 0.076 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO C 229 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO C 229 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 229 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B1191 " 0.035 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO B1192 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B1192 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B1192 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C1191 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO C1192 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C1192 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C1192 " -0.029 5.00e-02 4.00e+02 ... (remaining 5085 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.63: 389 2.63 - 3.26: 30260 3.26 - 3.88: 56163 3.88 - 4.51: 77858 4.51 - 5.14: 123749 Nonbonded interactions: 288419 Sorted by model distance: nonbonded pdb=" N ARG D 172 " pdb=" O ARG D 172 " model vdw 2.000 2.496 nonbonded pdb=" N ARG A 172 " pdb=" O ARG A 172 " model vdw 2.005 2.496 nonbonded pdb=" N ARG C 172 " pdb=" O ARG C 172 " model vdw 2.006 2.496 nonbonded pdb=" N ARG B 172 " pdb=" O ARG B 172 " model vdw 2.008 2.496 nonbonded pdb=" OD2 ASP C 468 " pdb=" ND2 ASN C 496 " model vdw 2.055 2.520 ... (remaining 288414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 85 through 1205) selection = (chain 'B' and resid 85 through 1205) selection = (chain 'C' and resid 85 through 1205) selection = (chain 'D' and resid 85 through 1205) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.020 Extract box with map and model: 5.440 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 81.330 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 0.102 29844 Z= 0.187 Angle : 0.768 26.841 40500 Z= 0.427 Chirality : 0.049 0.573 4612 Planarity : 0.004 0.106 5088 Dihedral : 15.768 89.714 10828 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.09 % Allowed : 22.31 % Favored : 77.59 % Cbeta Deviations : 0.23 % 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: -1.87 (0.13), residues: 3632 helix: -1.67 (0.12), residues: 1636 sheet: -1.42 (0.26), residues: 396 loop : -0.45 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 177 HIS 0.004 0.001 HIS C 586 PHE 0.025 0.001 PHE D 932 TYR 0.025 0.001 TYR A 130 ARG 0.009 0.001 ARG A 828 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 560 time to evaluate : 3.407 Fit side-chains revert: symmetry clash REVERT: A 163 ASN cc_start: 0.8099 (m110) cc_final: 0.7328 (p0) REVERT: A 232 ARG cc_start: 0.6242 (mtt90) cc_final: 0.5994 (mmt90) REVERT: A 426 SER cc_start: 0.8059 (t) cc_final: 0.7592 (m) REVERT: A 576 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7714 (tp30) REVERT: A 876 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.5526 (p90) REVERT: A 909 PHE cc_start: 0.8291 (t80) cc_final: 0.7337 (m-80) REVERT: A 1020 ARG cc_start: 0.7803 (mtm110) cc_final: 0.7218 (ptp-170) REVERT: B 388 ASP cc_start: 0.7727 (m-30) cc_final: 0.7445 (m-30) REVERT: B 909 PHE cc_start: 0.8233 (t80) cc_final: 0.7294 (m-80) REVERT: B 1020 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7512 (mtm110) REVERT: C 163 ASN cc_start: 0.7807 (m-40) cc_final: 0.7182 (p0) REVERT: C 176 LEU cc_start: 0.8163 (mt) cc_final: 0.7960 (mm) REVERT: C 426 SER cc_start: 0.8031 (t) cc_final: 0.7560 (m) REVERT: C 576 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7730 (tp30) REVERT: C 792 ASP cc_start: 0.7633 (p0) cc_final: 0.7214 (p0) REVERT: C 909 PHE cc_start: 0.8238 (t80) cc_final: 0.7332 (m-10) REVERT: C 1020 ARG cc_start: 0.7806 (mtm110) cc_final: 0.7481 (mtm110) REVERT: D 174 MET cc_start: 0.7954 (pmm) cc_final: 0.6515 (mpp) REVERT: D 177 TRP cc_start: 0.8388 (t60) cc_final: 0.8081 (t60) REVERT: D 426 SER cc_start: 0.8076 (t) cc_final: 0.7610 (m) REVERT: D 794 LYS cc_start: 0.7652 (tptt) cc_final: 0.7450 (tptt) REVERT: D 909 PHE cc_start: 0.8040 (t80) cc_final: 0.7490 (m-80) REVERT: D 1020 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7484 (mtm110) outliers start: 3 outliers final: 1 residues processed: 561 average time/residue: 0.4443 time to fit residues: 385.7553 Evaluate side-chains 525 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 523 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 1045 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 285 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 330 optimal weight: 0.3980 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 119 ASN A 151 GLN A 241 ASN A 291 HIS A 369 GLN A 490 GLN A 499 HIS A 505 HIS A 844 HIS A 871 GLN A 879 ASN A 923 HIS A 955 ASN A1147 GLN B 108 ASN B 119 ASN B 151 GLN B 241 ASN B 291 HIS B 369 GLN B 490 GLN B 499 HIS B 505 HIS B 844 HIS B 871 GLN B 879 ASN B 955 ASN B1147 GLN C 108 ASN C 119 ASN C 151 GLN C 241 ASN C 369 GLN C 490 GLN C 499 HIS C 505 HIS C 844 HIS C 871 GLN C 879 ASN C 955 ASN C1147 GLN D 108 ASN D 119 ASN D 151 GLN D 241 ASN D 291 HIS D 369 GLN D 490 GLN D 499 HIS D 505 HIS D 844 HIS D 871 GLN D 879 ASN D 955 ASN D1147 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 29844 Z= 0.395 Angle : 0.647 13.300 40500 Z= 0.326 Chirality : 0.046 0.247 4612 Planarity : 0.004 0.041 5088 Dihedral : 4.886 40.451 4023 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.45 % Allowed : 22.22 % Favored : 74.34 % 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: -1.39 (0.14), residues: 3632 helix: -1.01 (0.12), residues: 1628 sheet: -1.39 (0.25), residues: 416 loop : -0.45 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 177 HIS 0.005 0.001 HIS D 563 PHE 0.029 0.002 PHE D 932 TYR 0.017 0.002 TYR A 130 ARG 0.004 0.000 ARG A1020 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 556 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.6572 (OUTLIER) cc_final: 0.4696 (m-10) REVERT: A 163 ASN cc_start: 0.8106 (m110) cc_final: 0.7285 (p0) REVERT: A 195 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8160 (mm) REVERT: A 222 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7500 (t80) REVERT: A 354 MET cc_start: 0.7018 (ppp) cc_final: 0.6129 (mtt) REVERT: A 388 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7138 (m-30) REVERT: A 426 SER cc_start: 0.8033 (t) cc_final: 0.7528 (m) REVERT: A 576 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7852 (tp30) REVERT: A 631 GLU cc_start: 0.7440 (mp0) cc_final: 0.7188 (mp0) REVERT: A 908 MET cc_start: 0.8654 (mmp) cc_final: 0.8185 (mmt) REVERT: A 909 PHE cc_start: 0.8279 (t80) cc_final: 0.7432 (m-80) REVERT: B 153 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.4917 (m-10) REVERT: B 163 ASN cc_start: 0.7487 (p0) cc_final: 0.7019 (p0) REVERT: B 177 TRP cc_start: 0.8344 (t60) cc_final: 0.8030 (t60) REVERT: B 570 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8554 (mtmt) REVERT: B 876 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.5756 (p90) REVERT: B 908 MET cc_start: 0.8678 (mmp) cc_final: 0.8222 (mmt) REVERT: B 909 PHE cc_start: 0.8225 (t80) cc_final: 0.7368 (m-80) REVERT: C 153 TYR cc_start: 0.6624 (OUTLIER) cc_final: 0.5953 (m-10) REVERT: C 163 ASN cc_start: 0.7914 (m-40) cc_final: 0.7311 (t0) REVERT: C 576 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7847 (tp30) REVERT: C 792 ASP cc_start: 0.7619 (p0) cc_final: 0.7181 (p0) REVERT: C 908 MET cc_start: 0.8657 (mmp) cc_final: 0.8185 (mmt) REVERT: C 909 PHE cc_start: 0.8229 (t80) cc_final: 0.7384 (m-10) REVERT: C 927 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8527 (mtm) REVERT: D 153 TYR cc_start: 0.6589 (OUTLIER) cc_final: 0.4690 (m-10) REVERT: D 163 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.6967 (p0) REVERT: D 222 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7363 (t80) REVERT: D 388 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.7119 (m-30) REVERT: D 576 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7837 (tp30) REVERT: D 843 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: D 876 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.5780 (p90) REVERT: D 908 MET cc_start: 0.8649 (mmp) cc_final: 0.8178 (mmt) REVERT: D 909 PHE cc_start: 0.8154 (t80) cc_final: 0.7322 (m-80) outliers start: 109 outliers final: 70 residues processed: 635 average time/residue: 0.4203 time to fit residues: 418.0670 Evaluate side-chains 601 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 517 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 829 LYS Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 898 ASP Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 1000 THR Chi-restraints excluded: chain C residue 1045 SER Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 527 SER Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 809 THR Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 898 ASP Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 1000 THR Chi-restraints excluded: chain D residue 1001 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 331 optimal weight: 0.6980 chunk 357 optimal weight: 9.9990 chunk 294 optimal weight: 0.8980 chunk 328 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 265 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 400 GLN B 400 GLN B 550 GLN B 923 HIS C 108 ASN C 923 HIS D 108 ASN D 400 GLN D 923 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29844 Z= 0.148 Angle : 0.545 13.442 40500 Z= 0.270 Chirality : 0.041 0.210 4612 Planarity : 0.004 0.043 5088 Dihedral : 4.418 34.657 4020 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.63 % Allowed : 22.88 % Favored : 74.49 % 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: -0.96 (0.14), residues: 3632 helix: -0.57 (0.13), residues: 1636 sheet: -1.06 (0.26), residues: 404 loop : -0.36 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 177 HIS 0.005 0.001 HIS D 586 PHE 0.035 0.001 PHE C 97 TYR 0.014 0.001 TYR A 130 ARG 0.005 0.000 ARG B1020 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 590 time to evaluate : 4.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.4618 (m-10) REVERT: A 163 ASN cc_start: 0.8119 (m110) cc_final: 0.7290 (p0) REVERT: A 222 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7532 (t80) REVERT: A 275 PHE cc_start: 0.7550 (t80) cc_final: 0.7211 (t80) REVERT: A 354 MET cc_start: 0.6910 (ppp) cc_final: 0.5900 (mtt) REVERT: A 388 ASP cc_start: 0.7221 (m-30) cc_final: 0.6955 (m-30) REVERT: A 392 GLU cc_start: 0.8681 (tp30) cc_final: 0.8461 (tp30) REVERT: A 426 SER cc_start: 0.7947 (t) cc_final: 0.7490 (m) REVERT: A 576 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7802 (tp30) REVERT: A 780 ARG cc_start: 0.7834 (ttp80) cc_final: 0.7431 (ttt-90) REVERT: A 860 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8035 (mt-10) REVERT: A 908 MET cc_start: 0.8598 (mmp) cc_final: 0.8109 (mmt) REVERT: A 909 PHE cc_start: 0.8144 (t80) cc_final: 0.7259 (m-80) REVERT: A 920 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: B 163 ASN cc_start: 0.7447 (p0) cc_final: 0.6996 (p0) REVERT: B 177 TRP cc_start: 0.8316 (t60) cc_final: 0.8057 (t60) REVERT: B 180 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8166 (mm-40) REVERT: B 275 PHE cc_start: 0.7566 (t80) cc_final: 0.7315 (t80) REVERT: B 388 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: B 392 GLU cc_start: 0.8653 (tp30) cc_final: 0.8064 (tp30) REVERT: B 426 SER cc_start: 0.8011 (t) cc_final: 0.7560 (m) REVERT: B 491 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8180 (tp) REVERT: B 570 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8515 (mtmt) REVERT: B 575 TYR cc_start: 0.8185 (m-80) cc_final: 0.7938 (m-80) REVERT: B 576 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7814 (tp30) REVERT: B 908 MET cc_start: 0.8585 (mmp) cc_final: 0.8107 (mmt) REVERT: B 909 PHE cc_start: 0.8177 (t80) cc_final: 0.7216 (m-80) REVERT: B 920 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: B 1020 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7476 (mtm110) REVERT: C 153 TYR cc_start: 0.6464 (OUTLIER) cc_final: 0.4675 (m-10) REVERT: C 163 ASN cc_start: 0.7851 (m-40) cc_final: 0.7119 (p0) REVERT: C 275 PHE cc_start: 0.7557 (t80) cc_final: 0.7309 (t80) REVERT: C 388 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6933 (m-30) REVERT: C 392 GLU cc_start: 0.8669 (tp30) cc_final: 0.8081 (tp30) REVERT: C 426 SER cc_start: 0.7956 (t) cc_final: 0.7489 (m) REVERT: C 491 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8188 (tp) REVERT: C 570 LYS cc_start: 0.8824 (mmmm) cc_final: 0.8530 (mtmt) REVERT: C 576 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7844 (tp30) REVERT: C 631 GLU cc_start: 0.7962 (mp0) cc_final: 0.7724 (mp0) REVERT: C 780 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7309 (ttt-90) REVERT: C 792 ASP cc_start: 0.7616 (p0) cc_final: 0.7169 (p0) REVERT: C 860 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7980 (mt-10) REVERT: C 908 MET cc_start: 0.8578 (mmp) cc_final: 0.8083 (mmt) REVERT: C 909 PHE cc_start: 0.8161 (t80) cc_final: 0.7227 (m-80) REVERT: C 920 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: D 153 TYR cc_start: 0.6574 (OUTLIER) cc_final: 0.4626 (m-10) REVERT: D 163 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7025 (p0) REVERT: D 174 MET cc_start: 0.7774 (pmm) cc_final: 0.6444 (mpp) REVERT: D 222 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7440 (t80) REVERT: D 354 MET cc_start: 0.6961 (ppp) cc_final: 0.5960 (mtt) REVERT: D 388 ASP cc_start: 0.7213 (m-30) cc_final: 0.6944 (m-30) REVERT: D 392 GLU cc_start: 0.8686 (tp30) cc_final: 0.8472 (tp30) REVERT: D 426 SER cc_start: 0.7904 (t) cc_final: 0.7448 (m) REVERT: D 491 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8199 (tp) REVERT: D 576 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7820 (tp30) REVERT: D 631 GLU cc_start: 0.7588 (mp0) cc_final: 0.7309 (mp0) REVERT: D 843 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: D 878 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: D 908 MET cc_start: 0.8585 (mmp) cc_final: 0.8094 (mmt) REVERT: D 909 PHE cc_start: 0.8105 (t80) cc_final: 0.7217 (m-80) REVERT: D 920 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7812 (tt0) outliers start: 83 outliers final: 34 residues processed: 642 average time/residue: 0.4202 time to fit residues: 422.7568 Evaluate side-chains 586 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 535 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 1045 SER Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 222 optimal weight: 3.9990 chunk 332 optimal weight: 0.8980 chunk 351 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 chunk 314 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 844 HIS B 844 HIS B1046 HIS C 108 ASN C 844 HIS D 108 ASN D 844 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29844 Z= 0.270 Angle : 0.568 13.740 40500 Z= 0.281 Chirality : 0.044 0.220 4612 Planarity : 0.004 0.049 5088 Dihedral : 4.425 35.621 4020 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.27 % Allowed : 21.80 % Favored : 73.92 % 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 (0.14), residues: 3632 helix: -0.49 (0.13), residues: 1616 sheet: -1.11 (0.26), residues: 412 loop : -0.29 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 177 HIS 0.005 0.001 HIS D 586 PHE 0.029 0.001 PHE C 97 TYR 0.015 0.001 TYR C1167 ARG 0.005 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 574 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.4749 (m-10) REVERT: A 163 ASN cc_start: 0.8164 (m110) cc_final: 0.7106 (p0) REVERT: A 222 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7658 (t80) REVERT: A 367 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6181 (mtt180) REVERT: A 388 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7158 (m-30) REVERT: A 426 SER cc_start: 0.7978 (t) cc_final: 0.7510 (m) REVERT: A 576 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7847 (tp30) REVERT: A 631 GLU cc_start: 0.7605 (mp0) cc_final: 0.7360 (mp0) REVERT: A 908 MET cc_start: 0.8602 (mmp) cc_final: 0.8132 (mmt) REVERT: A 909 PHE cc_start: 0.8153 (t80) cc_final: 0.7300 (m-10) REVERT: A 920 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: B 153 TYR cc_start: 0.6572 (OUTLIER) cc_final: 0.5090 (m-10) REVERT: B 163 ASN cc_start: 0.7634 (p0) cc_final: 0.7157 (p0) REVERT: B 177 TRP cc_start: 0.8332 (t60) cc_final: 0.8006 (t60) REVERT: B 180 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8219 (mm-40) REVERT: B 275 PHE cc_start: 0.7633 (t80) cc_final: 0.7412 (t80) REVERT: B 367 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6257 (mtt180) REVERT: B 388 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: B 426 SER cc_start: 0.7994 (t) cc_final: 0.7528 (m) REVERT: B 570 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8355 (pttp) REVERT: B 575 TYR cc_start: 0.8188 (m-80) cc_final: 0.7897 (m-80) REVERT: B 576 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7846 (tp30) REVERT: B 792 ASP cc_start: 0.7678 (p0) cc_final: 0.7287 (p0) REVERT: B 876 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.5743 (p90) REVERT: B 908 MET cc_start: 0.8599 (mmp) cc_final: 0.8131 (mmt) REVERT: B 909 PHE cc_start: 0.8112 (t80) cc_final: 0.7285 (m-10) REVERT: B 920 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: C 153 TYR cc_start: 0.6547 (OUTLIER) cc_final: 0.4740 (m-10) REVERT: C 163 ASN cc_start: 0.7877 (m-40) cc_final: 0.7127 (p0) REVERT: C 275 PHE cc_start: 0.7635 (t80) cc_final: 0.7392 (t80) REVERT: C 367 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6255 (mtt180) REVERT: C 388 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: C 426 SER cc_start: 0.7939 (t) cc_final: 0.7466 (m) REVERT: C 566 MET cc_start: 0.7768 (ttp) cc_final: 0.7250 (tmm) REVERT: C 570 LYS cc_start: 0.8809 (mmmm) cc_final: 0.8523 (mtmt) REVERT: C 576 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7807 (tp30) REVERT: C 780 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7216 (ttp80) REVERT: C 792 ASP cc_start: 0.7583 (p0) cc_final: 0.7169 (p0) REVERT: C 908 MET cc_start: 0.8624 (mmp) cc_final: 0.8162 (mmt) REVERT: C 909 PHE cc_start: 0.8121 (t80) cc_final: 0.7275 (m-10) REVERT: C 920 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: D 153 TYR cc_start: 0.6626 (OUTLIER) cc_final: 0.4732 (m-10) REVERT: D 163 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.6874 (p0) REVERT: D 180 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8328 (mm-40) REVERT: D 222 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7487 (t80) REVERT: D 367 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6181 (mtt180) REVERT: D 388 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.7096 (m-30) REVERT: D 426 SER cc_start: 0.7938 (t) cc_final: 0.7474 (m) REVERT: D 566 MET cc_start: 0.7719 (ttp) cc_final: 0.7208 (tmm) REVERT: D 576 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7802 (tp30) REVERT: D 631 GLU cc_start: 0.7666 (mp0) cc_final: 0.7427 (mp0) REVERT: D 843 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7878 (m-30) REVERT: D 876 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.5727 (p90) REVERT: D 908 MET cc_start: 0.8605 (mmp) cc_final: 0.8146 (mmt) REVERT: D 909 PHE cc_start: 0.8090 (t80) cc_final: 0.7195 (m-80) REVERT: D 920 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7724 (tt0) outliers start: 135 outliers final: 89 residues processed: 662 average time/residue: 0.4405 time to fit residues: 458.7883 Evaluate side-chains 646 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 535 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1136 GLN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 898 ASP Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1045 SER Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 809 THR Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1136 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 300 optimal weight: 3.9990 chunk 243 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 179 optimal weight: 0.0370 chunk 315 optimal weight: 0.2980 chunk 88 optimal weight: 6.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 152 ASN C 108 ASN D 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29844 Z= 0.166 Angle : 0.548 14.433 40500 Z= 0.268 Chirality : 0.042 0.232 4612 Planarity : 0.004 0.051 5088 Dihedral : 4.255 31.855 4020 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.64 % Allowed : 22.91 % Favored : 73.45 % 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: -0.64 (0.14), residues: 3632 helix: -0.27 (0.13), residues: 1620 sheet: -0.93 (0.26), residues: 404 loop : -0.24 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 353 HIS 0.005 0.001 HIS D 586 PHE 0.030 0.001 PHE C 97 TYR 0.016 0.001 TYR A1167 ARG 0.007 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 578 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.6602 (OUTLIER) cc_final: 0.4740 (m-10) REVERT: A 163 ASN cc_start: 0.8149 (m110) cc_final: 0.7113 (p0) REVERT: A 222 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7607 (t80) REVERT: A 275 PHE cc_start: 0.7454 (t80) cc_final: 0.7159 (t80) REVERT: A 354 MET cc_start: 0.6787 (ppp) cc_final: 0.5879 (mtt) REVERT: A 388 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7112 (m-30) REVERT: A 426 SER cc_start: 0.7927 (t) cc_final: 0.7477 (m) REVERT: A 575 TYR cc_start: 0.8150 (m-80) cc_final: 0.7851 (m-80) REVERT: A 576 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7864 (tp30) REVERT: A 780 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7255 (ttp80) REVERT: A 792 ASP cc_start: 0.7815 (p0) cc_final: 0.7267 (p0) REVERT: A 908 MET cc_start: 0.8586 (mmp) cc_final: 0.8144 (mmt) REVERT: A 909 PHE cc_start: 0.8159 (t80) cc_final: 0.7233 (m-10) REVERT: A 920 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: B 153 TYR cc_start: 0.6550 (OUTLIER) cc_final: 0.5082 (m-10) REVERT: B 163 ASN cc_start: 0.7630 (p0) cc_final: 0.7120 (p0) REVERT: B 177 TRP cc_start: 0.8294 (t60) cc_final: 0.8035 (t60) REVERT: B 180 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8174 (mm-40) REVERT: B 275 PHE cc_start: 0.7660 (t80) cc_final: 0.7402 (t80) REVERT: B 367 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6227 (mtt180) REVERT: B 388 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: B 426 SER cc_start: 0.7939 (t) cc_final: 0.7493 (m) REVERT: B 570 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8343 (pttp) REVERT: B 575 TYR cc_start: 0.8162 (m-80) cc_final: 0.7888 (m-80) REVERT: B 576 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7833 (tp30) REVERT: B 792 ASP cc_start: 0.7667 (p0) cc_final: 0.7256 (p0) REVERT: B 876 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.5685 (p90) REVERT: B 908 MET cc_start: 0.8552 (mmp) cc_final: 0.8113 (mmt) REVERT: B 909 PHE cc_start: 0.8143 (t80) cc_final: 0.7243 (m-10) REVERT: B 920 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: B 951 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6823 (pp20) REVERT: B 1020 ARG cc_start: 0.7769 (mtm110) cc_final: 0.7421 (mtm110) REVERT: C 153 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.4794 (m-10) REVERT: C 163 ASN cc_start: 0.7851 (m-40) cc_final: 0.6886 (p0) REVERT: C 177 TRP cc_start: 0.8274 (t60) cc_final: 0.7994 (t60) REVERT: C 275 PHE cc_start: 0.7668 (t80) cc_final: 0.7390 (t80) REVERT: C 426 SER cc_start: 0.7872 (t) cc_final: 0.7418 (m) REVERT: C 566 MET cc_start: 0.7785 (ttp) cc_final: 0.7233 (tmm) REVERT: C 570 LYS cc_start: 0.8789 (mmmm) cc_final: 0.8514 (mtmt) REVERT: C 575 TYR cc_start: 0.8170 (m-80) cc_final: 0.7878 (m-80) REVERT: C 576 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7813 (tp30) REVERT: C 792 ASP cc_start: 0.7554 (p0) cc_final: 0.7113 (p0) REVERT: C 876 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.5662 (p90) REVERT: C 908 MET cc_start: 0.8556 (mmp) cc_final: 0.8135 (mmt) REVERT: C 909 PHE cc_start: 0.8132 (t80) cc_final: 0.7245 (m-10) REVERT: C 920 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: D 153 TYR cc_start: 0.6625 (OUTLIER) cc_final: 0.4669 (m-10) REVERT: D 163 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7022 (p0) REVERT: D 180 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8372 (mm-40) REVERT: D 222 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7628 (t80) REVERT: D 388 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.7101 (m-30) REVERT: D 426 SER cc_start: 0.7882 (t) cc_final: 0.7436 (m) REVERT: D 566 MET cc_start: 0.7758 (ttp) cc_final: 0.7213 (tmm) REVERT: D 575 TYR cc_start: 0.8150 (m-80) cc_final: 0.7837 (m-80) REVERT: D 576 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7775 (tp30) REVERT: D 631 GLU cc_start: 0.7657 (mp0) cc_final: 0.7406 (mp0) REVERT: D 843 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7893 (m-30) REVERT: D 876 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.5841 (p90) REVERT: D 908 MET cc_start: 0.8557 (mmp) cc_final: 0.8137 (mmt) REVERT: D 909 PHE cc_start: 0.8021 (t80) cc_final: 0.7118 (m-80) REVERT: D 920 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7762 (tt0) outliers start: 115 outliers final: 66 residues processed: 653 average time/residue: 0.4324 time to fit residues: 441.6407 Evaluate side-chains 629 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 543 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1136 GLN Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1045 SER Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 1136 GLN Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 10.0000 chunk 316 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 352 optimal weight: 0.9990 chunk 292 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 184 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 586 HIS A 844 HIS A1046 HIS B 586 HIS C 108 ASN C 586 HIS D 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29844 Z= 0.227 Angle : 0.568 14.706 40500 Z= 0.278 Chirality : 0.043 0.241 4612 Planarity : 0.004 0.050 5088 Dihedral : 4.260 31.587 4020 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.27 % Allowed : 22.63 % Favored : 73.10 % 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: -0.53 (0.14), residues: 3632 helix: -0.20 (0.13), residues: 1600 sheet: -1.02 (0.26), residues: 412 loop : -0.10 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.005 0.001 HIS A 586 PHE 0.026 0.001 PHE C 97 TYR 0.024 0.001 TYR B 582 ARG 0.007 0.000 ARG C1020 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 562 time to evaluate : 3.930 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: A 153 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.4796 (m-10) REVERT: A 163 ASN cc_start: 0.8103 (m110) cc_final: 0.7082 (p0) REVERT: A 222 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7611 (t80) REVERT: A 275 PHE cc_start: 0.7523 (t80) cc_final: 0.7221 (t80) REVERT: A 354 MET cc_start: 0.6868 (ppp) cc_final: 0.5991 (mtt) REVERT: A 367 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6171 (mtt180) REVERT: A 426 SER cc_start: 0.7935 (t) cc_final: 0.7480 (m) REVERT: A 566 MET cc_start: 0.7131 (ppp) cc_final: 0.6848 (tmm) REVERT: A 575 TYR cc_start: 0.8182 (m-80) cc_final: 0.7842 (m-80) REVERT: A 576 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7813 (tp30) REVERT: A 631 GLU cc_start: 0.7707 (mp0) cc_final: 0.7329 (mp0) REVERT: A 780 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7183 (ttp80) REVERT: A 792 ASP cc_start: 0.7750 (p0) cc_final: 0.7214 (p0) REVERT: A 908 MET cc_start: 0.8580 (mmp) cc_final: 0.8160 (mmt) REVERT: A 909 PHE cc_start: 0.8094 (t80) cc_final: 0.7250 (m-10) REVERT: A 920 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: A 951 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6827 (pp20) REVERT: B 153 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.5190 (m-10) REVERT: B 163 ASN cc_start: 0.7768 (p0) cc_final: 0.7304 (p0) REVERT: B 177 TRP cc_start: 0.8319 (t60) cc_final: 0.8072 (t60) REVERT: B 180 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8233 (mm-40) REVERT: B 275 PHE cc_start: 0.7706 (t80) cc_final: 0.7457 (t80) REVERT: B 367 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6254 (mtt180) REVERT: B 388 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7155 (m-30) REVERT: B 426 SER cc_start: 0.7955 (t) cc_final: 0.7500 (m) REVERT: B 566 MET cc_start: 0.7146 (ppp) cc_final: 0.6859 (tmm) REVERT: B 570 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8340 (pttp) REVERT: B 575 TYR cc_start: 0.8183 (m-80) cc_final: 0.7798 (m-80) REVERT: B 576 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7834 (tp30) REVERT: B 792 ASP cc_start: 0.7641 (p0) cc_final: 0.7212 (p0) REVERT: B 876 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.5918 (p90) REVERT: B 908 MET cc_start: 0.8573 (mmp) cc_final: 0.8151 (mmt) REVERT: B 909 PHE cc_start: 0.8154 (t80) cc_final: 0.7260 (m-10) REVERT: B 920 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: B 951 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6861 (pp20) REVERT: C 153 TYR cc_start: 0.6664 (OUTLIER) cc_final: 0.4941 (m-10) REVERT: C 163 ASN cc_start: 0.7867 (m-40) cc_final: 0.6893 (p0) REVERT: C 177 TRP cc_start: 0.8276 (t60) cc_final: 0.7965 (t60) REVERT: C 199 TYR cc_start: 0.8040 (t80) cc_final: 0.7719 (t80) REVERT: C 275 PHE cc_start: 0.7711 (t80) cc_final: 0.7402 (t80) REVERT: C 367 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6195 (mtt180) REVERT: C 388 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7227 (m-30) REVERT: C 426 SER cc_start: 0.7883 (t) cc_final: 0.7425 (m) REVERT: C 566 MET cc_start: 0.7889 (ttp) cc_final: 0.7263 (tmm) REVERT: C 570 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8516 (mtmt) REVERT: C 575 TYR cc_start: 0.8203 (m-80) cc_final: 0.7876 (m-80) REVERT: C 576 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7823 (tp30) REVERT: C 780 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7167 (ttp80) REVERT: C 792 ASP cc_start: 0.7532 (p0) cc_final: 0.7141 (p0) REVERT: C 876 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.5786 (p90) REVERT: C 908 MET cc_start: 0.8594 (mmp) cc_final: 0.8142 (mmt) REVERT: C 909 PHE cc_start: 0.8142 (t80) cc_final: 0.7258 (m-10) REVERT: C 920 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: C 1020 ARG cc_start: 0.7775 (mtm110) cc_final: 0.7417 (mtm110) REVERT: D 153 TYR cc_start: 0.6666 (OUTLIER) cc_final: 0.4708 (m-10) REVERT: D 163 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.6867 (p0) REVERT: D 180 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8385 (mm-40) REVERT: D 195 ILE cc_start: 0.8538 (mm) cc_final: 0.8272 (mt) REVERT: D 222 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7598 (t80) REVERT: D 354 MET cc_start: 0.6859 (ppp) cc_final: 0.5977 (mtt) REVERT: D 367 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6152 (mtt180) REVERT: D 388 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7105 (m-30) REVERT: D 426 SER cc_start: 0.7895 (t) cc_final: 0.7444 (m) REVERT: D 566 MET cc_start: 0.7855 (ttp) cc_final: 0.7244 (tmm) REVERT: D 575 TYR cc_start: 0.8172 (m-80) cc_final: 0.7835 (m-80) REVERT: D 576 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7824 (tp30) REVERT: D 631 GLU cc_start: 0.7641 (mp0) cc_final: 0.7372 (mp0) REVERT: D 876 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.5879 (p90) REVERT: D 908 MET cc_start: 0.8552 (mmp) cc_final: 0.8141 (mmt) REVERT: D 909 PHE cc_start: 0.8042 (t80) cc_final: 0.7169 (m-10) REVERT: D 920 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: D 951 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6800 (pp20) outliers start: 135 outliers final: 85 residues processed: 653 average time/residue: 0.4269 time to fit residues: 436.6765 Evaluate side-chains 652 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 543 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 498 PHE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 898 ASP Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1045 SER Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 809 THR Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 955 ASN Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 1136 GLN Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 4.9990 chunk 39 optimal weight: 0.0370 chunk 200 optimal weight: 4.9990 chunk 257 optimal weight: 0.0770 chunk 199 optimal weight: 0.1980 chunk 296 optimal weight: 0.0670 chunk 196 optimal weight: 40.0000 chunk 350 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 108 ASN C1046 HIS D 108 ASN D 586 HIS D1046 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29844 Z= 0.138 Angle : 0.545 14.053 40500 Z= 0.266 Chirality : 0.041 0.257 4612 Planarity : 0.003 0.050 5088 Dihedral : 4.016 24.587 4020 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.94 % Allowed : 23.51 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3632 helix: -0.01 (0.13), residues: 1660 sheet: -0.82 (0.26), residues: 404 loop : -0.07 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 353 HIS 0.004 0.000 HIS D 586 PHE 0.020 0.001 PHE C 97 TYR 0.024 0.001 TYR C 582 ARG 0.008 0.000 ARG B1020 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 585 time to evaluate : 3.522 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: A 163 ASN cc_start: 0.8173 (m110) cc_final: 0.7147 (p0) REVERT: A 195 ILE cc_start: 0.8462 (mm) cc_final: 0.8231 (mt) REVERT: A 199 TYR cc_start: 0.7661 (t80) cc_final: 0.7046 (t80) REVERT: A 222 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7587 (t80) REVERT: A 275 PHE cc_start: 0.7607 (t80) cc_final: 0.7304 (t80) REVERT: A 354 MET cc_start: 0.6729 (ppp) cc_final: 0.5958 (mtt) REVERT: A 367 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6270 (mtt180) REVERT: A 388 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7137 (m-30) REVERT: A 426 SER cc_start: 0.7848 (t) cc_final: 0.7430 (m) REVERT: A 566 MET cc_start: 0.7362 (ppp) cc_final: 0.7059 (tmm) REVERT: A 570 LYS cc_start: 0.8835 (mmmm) cc_final: 0.8507 (mtmt) REVERT: A 575 TYR cc_start: 0.8131 (m-80) cc_final: 0.7906 (m-80) REVERT: A 576 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7760 (tp30) REVERT: A 780 ARG cc_start: 0.7857 (ttp80) cc_final: 0.7261 (ttp80) REVERT: A 792 ASP cc_start: 0.7712 (p0) cc_final: 0.7219 (p0) REVERT: A 876 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.6066 (p90) REVERT: A 908 MET cc_start: 0.8511 (mmp) cc_final: 0.8110 (mmt) REVERT: A 909 PHE cc_start: 0.8051 (t80) cc_final: 0.7178 (m-10) REVERT: A 920 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: A 951 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6811 (pp20) REVERT: A 958 PHE cc_start: 0.8377 (p90) cc_final: 0.8094 (p90) REVERT: A 1020 ARG cc_start: 0.7759 (mtm110) cc_final: 0.7197 (ptp-170) REVERT: B 163 ASN cc_start: 0.7707 (p0) cc_final: 0.7437 (p0) REVERT: B 177 TRP cc_start: 0.8269 (t60) cc_final: 0.8026 (t60) REVERT: B 180 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8183 (mm-40) REVERT: B 199 TYR cc_start: 0.7843 (t80) cc_final: 0.7404 (t80) REVERT: B 275 PHE cc_start: 0.7621 (t80) cc_final: 0.7335 (t80) REVERT: B 388 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: B 426 SER cc_start: 0.7863 (t) cc_final: 0.7439 (m) REVERT: B 566 MET cc_start: 0.7344 (ppp) cc_final: 0.7018 (tmm) REVERT: B 570 LYS cc_start: 0.8823 (mmmm) cc_final: 0.8405 (pttp) REVERT: B 575 TYR cc_start: 0.8077 (m-80) cc_final: 0.7849 (m-80) REVERT: B 576 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7754 (tp30) REVERT: B 792 ASP cc_start: 0.7613 (p0) cc_final: 0.7188 (p0) REVERT: B 876 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.5967 (p90) REVERT: B 909 PHE cc_start: 0.8035 (t80) cc_final: 0.7178 (m-10) REVERT: B 920 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: B 951 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6938 (pp20) REVERT: B 958 PHE cc_start: 0.8392 (p90) cc_final: 0.8116 (p90) REVERT: B 1020 ARG cc_start: 0.7768 (mtm110) cc_final: 0.7452 (mtm110) REVERT: C 163 ASN cc_start: 0.7824 (m-40) cc_final: 0.6911 (p0) REVERT: C 177 TRP cc_start: 0.8236 (t60) cc_final: 0.7903 (t60) REVERT: C 192 MET cc_start: 0.8109 (mmt) cc_final: 0.7691 (mmm) REVERT: C 199 TYR cc_start: 0.7804 (t80) cc_final: 0.7150 (t80) REVERT: C 275 PHE cc_start: 0.7586 (t80) cc_final: 0.7281 (t80) REVERT: C 367 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6198 (mtt180) REVERT: C 388 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7150 (m-30) REVERT: C 418 ARG cc_start: 0.7212 (ptp-110) cc_final: 0.6617 (ptp90) REVERT: C 426 SER cc_start: 0.7794 (t) cc_final: 0.7372 (m) REVERT: C 566 MET cc_start: 0.7832 (ttp) cc_final: 0.7217 (tmm) REVERT: C 570 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8423 (pttp) REVERT: C 576 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7780 (tp30) REVERT: C 631 GLU cc_start: 0.7969 (mp0) cc_final: 0.7450 (tt0) REVERT: C 780 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7221 (ttp80) REVERT: C 792 ASP cc_start: 0.7571 (p0) cc_final: 0.7161 (p0) REVERT: C 876 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.5892 (p90) REVERT: C 909 PHE cc_start: 0.8025 (t80) cc_final: 0.7180 (m-10) REVERT: C 920 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: C 958 PHE cc_start: 0.8380 (p90) cc_final: 0.8123 (p90) REVERT: C 1020 ARG cc_start: 0.7764 (mtm110) cc_final: 0.7438 (mtm110) REVERT: D 98 LYS cc_start: 0.5089 (tttt) cc_final: 0.4628 (ttpt) REVERT: D 163 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.6950 (p0) REVERT: D 180 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8327 (mm-40) REVERT: D 195 ILE cc_start: 0.8473 (mm) cc_final: 0.8237 (mt) REVERT: D 199 TYR cc_start: 0.7766 (t80) cc_final: 0.7520 (t80) REVERT: D 222 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7548 (t80) REVERT: D 354 MET cc_start: 0.6764 (ppp) cc_final: 0.5941 (mtt) REVERT: D 388 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: D 426 SER cc_start: 0.7815 (t) cc_final: 0.7407 (m) REVERT: D 566 MET cc_start: 0.7782 (ttp) cc_final: 0.7277 (tmm) REVERT: D 575 TYR cc_start: 0.8124 (m-80) cc_final: 0.7903 (m-80) REVERT: D 576 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7780 (tp30) REVERT: D 631 GLU cc_start: 0.7831 (mp0) cc_final: 0.7562 (mp0) REVERT: D 780 ARG cc_start: 0.8098 (ttt-90) cc_final: 0.7479 (ttt-90) REVERT: D 792 ASP cc_start: 0.7749 (p0) cc_final: 0.7269 (p0) REVERT: D 843 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: D 876 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.5937 (p90) REVERT: D 878 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8025 (m-30) REVERT: D 908 MET cc_start: 0.8511 (mmp) cc_final: 0.8122 (mmt) REVERT: D 909 PHE cc_start: 0.7889 (t80) cc_final: 0.7095 (m-10) REVERT: D 920 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: D 951 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6822 (pp20) REVERT: D 958 PHE cc_start: 0.8402 (p90) cc_final: 0.8134 (p90) REVERT: D 1020 ARG cc_start: 0.7770 (mtm110) cc_final: 0.7449 (mtm110) outliers start: 93 outliers final: 43 residues processed: 643 average time/residue: 0.4367 time to fit residues: 434.0942 Evaluate side-chains 612 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 547 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1136 GLN Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 1045 SER Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 1136 GLN Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 0.0470 chunk 140 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 68 optimal weight: 0.0570 chunk 67 optimal weight: 0.7980 chunk 223 optimal weight: 0.5980 chunk 239 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 275 optimal weight: 9.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 108 ASN B 206 GLN D 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29844 Z= 0.148 Angle : 0.556 15.485 40500 Z= 0.268 Chirality : 0.041 0.261 4612 Planarity : 0.003 0.049 5088 Dihedral : 3.937 23.079 4020 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.47 % Allowed : 23.96 % Favored : 73.58 % 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: -0.26 (0.14), residues: 3632 helix: 0.07 (0.13), residues: 1660 sheet: -0.91 (0.25), residues: 428 loop : 0.02 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 353 HIS 0.003 0.000 HIS C 291 PHE 0.025 0.001 PHE C 97 TYR 0.016 0.001 TYR D1167 ARG 0.006 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 565 time to evaluate : 3.364 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: A 163 ASN cc_start: 0.8161 (m110) cc_final: 0.7148 (p0) REVERT: A 195 ILE cc_start: 0.8473 (mm) cc_final: 0.8251 (mt) REVERT: A 222 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7542 (t80) REVERT: A 275 PHE cc_start: 0.7630 (t80) cc_final: 0.7315 (t80) REVERT: A 354 MET cc_start: 0.6738 (ppp) cc_final: 0.5963 (mtt) REVERT: A 367 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6293 (mtt180) REVERT: A 388 ASP cc_start: 0.7403 (m-30) cc_final: 0.7142 (m-30) REVERT: A 426 SER cc_start: 0.7922 (t) cc_final: 0.7504 (m) REVERT: A 566 MET cc_start: 0.7403 (ppp) cc_final: 0.7049 (tmm) REVERT: A 570 LYS cc_start: 0.8820 (mmmm) cc_final: 0.8407 (pttp) REVERT: A 575 TYR cc_start: 0.8036 (m-80) cc_final: 0.7791 (m-80) REVERT: A 576 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7749 (tp30) REVERT: A 780 ARG cc_start: 0.7814 (ttp80) cc_final: 0.7191 (ttp80) REVERT: A 792 ASP cc_start: 0.7599 (p0) cc_final: 0.7085 (p0) REVERT: A 909 PHE cc_start: 0.8013 (t80) cc_final: 0.7136 (m-10) REVERT: A 920 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: A 951 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6896 (pp20) REVERT: A 958 PHE cc_start: 0.8353 (p90) cc_final: 0.8066 (p90) REVERT: A 1020 ARG cc_start: 0.7773 (mtm110) cc_final: 0.7172 (ptp-170) REVERT: B 177 TRP cc_start: 0.8266 (t60) cc_final: 0.8031 (t60) REVERT: B 180 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8237 (mm-40) REVERT: B 199 TYR cc_start: 0.7728 (t80) cc_final: 0.7165 (t80) REVERT: B 275 PHE cc_start: 0.7619 (t80) cc_final: 0.7293 (t80) REVERT: B 367 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6237 (mtt180) REVERT: B 388 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7155 (m-30) REVERT: B 426 SER cc_start: 0.7900 (t) cc_final: 0.7469 (m) REVERT: B 566 MET cc_start: 0.7384 (ppp) cc_final: 0.7036 (tmm) REVERT: B 570 LYS cc_start: 0.8806 (mmmm) cc_final: 0.8404 (pttp) REVERT: B 575 TYR cc_start: 0.8069 (m-80) cc_final: 0.7860 (m-80) REVERT: B 576 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7771 (tp30) REVERT: B 792 ASP cc_start: 0.7649 (p0) cc_final: 0.7220 (p0) REVERT: B 876 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.6029 (p90) REVERT: B 908 MET cc_start: 0.8450 (mmp) cc_final: 0.8040 (mmt) REVERT: B 909 PHE cc_start: 0.7996 (t80) cc_final: 0.7129 (m-10) REVERT: B 920 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: B 951 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6929 (pp20) REVERT: B 958 PHE cc_start: 0.8362 (p90) cc_final: 0.8102 (p90) REVERT: B 1020 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7437 (mtm110) REVERT: C 163 ASN cc_start: 0.7791 (m-40) cc_final: 0.6864 (p0) REVERT: C 177 TRP cc_start: 0.8205 (t60) cc_final: 0.7858 (t60) REVERT: C 199 TYR cc_start: 0.7723 (t80) cc_final: 0.6960 (t80) REVERT: C 275 PHE cc_start: 0.7651 (t80) cc_final: 0.7378 (t80) REVERT: C 367 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6265 (mtt180) REVERT: C 388 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7197 (m-30) REVERT: C 418 ARG cc_start: 0.7256 (ptp-110) cc_final: 0.6698 (ptp-170) REVERT: C 426 SER cc_start: 0.7821 (t) cc_final: 0.7415 (m) REVERT: C 566 MET cc_start: 0.7784 (ttp) cc_final: 0.7325 (tmm) REVERT: C 570 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8437 (pttp) REVERT: C 576 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7815 (tp30) REVERT: C 631 GLU cc_start: 0.8158 (mp0) cc_final: 0.7497 (tt0) REVERT: C 780 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7235 (ttp80) REVERT: C 792 ASP cc_start: 0.7538 (p0) cc_final: 0.7112 (p0) REVERT: C 876 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.5953 (p90) REVERT: C 878 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: C 908 MET cc_start: 0.8462 (mmp) cc_final: 0.8075 (mmt) REVERT: C 909 PHE cc_start: 0.7992 (t80) cc_final: 0.7132 (m-10) REVERT: C 920 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: C 958 PHE cc_start: 0.8342 (p90) cc_final: 0.8094 (p90) REVERT: C 1020 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7466 (mtm110) REVERT: D 98 LYS cc_start: 0.5061 (tttt) cc_final: 0.4613 (ttpt) REVERT: D 153 TYR cc_start: 0.6613 (OUTLIER) cc_final: 0.4671 (m-10) REVERT: D 163 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.6813 (p0) REVERT: D 180 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8331 (mm-40) REVERT: D 195 ILE cc_start: 0.8477 (mm) cc_final: 0.8255 (mt) REVERT: D 199 TYR cc_start: 0.7783 (t80) cc_final: 0.7283 (t80) REVERT: D 222 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7541 (t80) REVERT: D 354 MET cc_start: 0.6735 (ppp) cc_final: 0.5916 (mtt) REVERT: D 367 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6168 (mtt180) REVERT: D 388 ASP cc_start: 0.7362 (m-30) cc_final: 0.7098 (m-30) REVERT: D 426 SER cc_start: 0.7835 (t) cc_final: 0.7440 (m) REVERT: D 443 MET cc_start: 0.7417 (mtm) cc_final: 0.7198 (mtp) REVERT: D 566 MET cc_start: 0.7755 (ttp) cc_final: 0.7273 (tmm) REVERT: D 575 TYR cc_start: 0.8092 (m-80) cc_final: 0.7884 (m-80) REVERT: D 576 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7794 (tp30) REVERT: D 631 GLU cc_start: 0.7836 (mp0) cc_final: 0.7434 (mp0) REVERT: D 780 ARG cc_start: 0.8080 (ttt-90) cc_final: 0.7466 (ttt-90) REVERT: D 783 LYS cc_start: 0.7972 (tttt) cc_final: 0.7688 (tptm) REVERT: D 792 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7241 (p0) REVERT: D 843 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7953 (m-30) REVERT: D 876 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.5950 (p90) REVERT: D 878 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8044 (m-30) REVERT: D 909 PHE cc_start: 0.7889 (t80) cc_final: 0.7107 (m-80) REVERT: D 920 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: D 951 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6906 (pp20) REVERT: D 958 PHE cc_start: 0.8346 (p90) cc_final: 0.8076 (p90) REVERT: D 1020 ARG cc_start: 0.7780 (mtm110) cc_final: 0.7449 (mtm110) outliers start: 78 outliers final: 47 residues processed: 615 average time/residue: 0.4424 time to fit residues: 424.0483 Evaluate side-chains 620 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 549 time to evaluate : 3.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 1136 GLN Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 792 ASP Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 1136 GLN Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 chunk 306 optimal weight: 5.9990 chunk 326 optimal weight: 0.9980 chunk 196 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 295 optimal weight: 2.9990 chunk 309 optimal weight: 3.9990 chunk 325 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN C 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 29844 Z= 0.301 Angle : 0.608 15.388 40500 Z= 0.297 Chirality : 0.045 0.253 4612 Planarity : 0.004 0.048 5088 Dihedral : 4.237 30.121 4020 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.29 % Allowed : 23.48 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3632 helix: -0.03 (0.13), residues: 1612 sheet: -0.94 (0.26), residues: 412 loop : -0.00 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 353 HIS 0.004 0.001 HIS D 586 PHE 0.026 0.002 PHE D 932 TYR 0.021 0.001 TYR D 582 ARG 0.007 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 558 time to evaluate : 3.300 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: A 153 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.4727 (m-10) REVERT: A 163 ASN cc_start: 0.8215 (m110) cc_final: 0.7141 (p0) REVERT: A 222 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7597 (t80) REVERT: A 250 GLU cc_start: 0.7894 (pt0) cc_final: 0.7672 (pt0) REVERT: A 275 PHE cc_start: 0.7743 (t80) cc_final: 0.7473 (t80) REVERT: A 354 MET cc_start: 0.6715 (ppp) cc_final: 0.5970 (mtt) REVERT: A 367 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6308 (mtt180) REVERT: A 426 SER cc_start: 0.7975 (t) cc_final: 0.7546 (m) REVERT: A 566 MET cc_start: 0.7604 (ppp) cc_final: 0.6834 (ttp) REVERT: A 570 LYS cc_start: 0.8819 (mmmm) cc_final: 0.8514 (mtmt) REVERT: A 575 TYR cc_start: 0.8131 (m-80) cc_final: 0.7710 (m-80) REVERT: A 576 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7871 (tp30) REVERT: A 792 ASP cc_start: 0.7642 (p0) cc_final: 0.7148 (p0) REVERT: A 876 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.6045 (p90) REVERT: A 908 MET cc_start: 0.8573 (mmp) cc_final: 0.8190 (mmt) REVERT: A 909 PHE cc_start: 0.8151 (t80) cc_final: 0.7139 (m-10) REVERT: A 920 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: A 951 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6574 (pp20) REVERT: B 153 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.5363 (m-80) REVERT: B 177 TRP cc_start: 0.8314 (t60) cc_final: 0.8073 (t60) REVERT: B 199 TYR cc_start: 0.7875 (t80) cc_final: 0.7326 (t80) REVERT: B 203 ILE cc_start: 0.7766 (tp) cc_final: 0.7504 (tp) REVERT: B 367 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6315 (mtt180) REVERT: B 388 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: B 426 SER cc_start: 0.7930 (t) cc_final: 0.7493 (m) REVERT: B 566 MET cc_start: 0.7624 (ppp) cc_final: 0.7338 (tmm) REVERT: B 570 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8407 (pttp) REVERT: B 575 TYR cc_start: 0.8161 (m-80) cc_final: 0.7765 (m-80) REVERT: B 576 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7805 (tp30) REVERT: B 792 ASP cc_start: 0.7565 (p0) cc_final: 0.7179 (p0) REVERT: B 876 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6127 (p90) REVERT: B 908 MET cc_start: 0.8558 (mmp) cc_final: 0.8154 (mmt) REVERT: B 909 PHE cc_start: 0.8120 (t80) cc_final: 0.7215 (m-10) REVERT: B 920 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: B 951 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6609 (pp20) REVERT: C 153 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.4912 (m-10) REVERT: C 163 ASN cc_start: 0.7900 (m-40) cc_final: 0.6970 (p0) REVERT: C 177 TRP cc_start: 0.8311 (t60) cc_final: 0.7939 (t60) REVERT: C 222 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7288 (t80) REVERT: C 275 PHE cc_start: 0.7749 (t80) cc_final: 0.7487 (t80) REVERT: C 367 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6218 (mtt180) REVERT: C 426 SER cc_start: 0.7897 (t) cc_final: 0.7458 (m) REVERT: C 566 MET cc_start: 0.8006 (ttp) cc_final: 0.7451 (tmm) REVERT: C 570 LYS cc_start: 0.8776 (mmmm) cc_final: 0.8389 (pttp) REVERT: C 576 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7857 (tp30) REVERT: C 631 GLU cc_start: 0.8063 (mp0) cc_final: 0.7464 (tt0) REVERT: C 792 ASP cc_start: 0.7567 (p0) cc_final: 0.7173 (p0) REVERT: C 876 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.6912 (p90) REVERT: C 908 MET cc_start: 0.8558 (mmp) cc_final: 0.8172 (mmt) REVERT: C 909 PHE cc_start: 0.8106 (t80) cc_final: 0.7205 (m-10) REVERT: C 920 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: D 98 LYS cc_start: 0.5095 (tttt) cc_final: 0.4635 (ttpt) REVERT: D 153 TYR cc_start: 0.6724 (OUTLIER) cc_final: 0.4694 (m-10) REVERT: D 163 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.6994 (p0) REVERT: D 180 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8313 (mm-40) REVERT: D 222 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7609 (t80) REVERT: D 354 MET cc_start: 0.6754 (ppp) cc_final: 0.5961 (mtt) REVERT: D 367 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6193 (mtt180) REVERT: D 426 SER cc_start: 0.7921 (t) cc_final: 0.7504 (m) REVERT: D 443 MET cc_start: 0.7476 (mtm) cc_final: 0.7257 (mtp) REVERT: D 566 MET cc_start: 0.7990 (ttp) cc_final: 0.7436 (tmm) REVERT: D 575 TYR cc_start: 0.8140 (m-80) cc_final: 0.7734 (m-80) REVERT: D 576 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7884 (tp30) REVERT: D 631 GLU cc_start: 0.7867 (mp0) cc_final: 0.7615 (mp0) REVERT: D 792 ASP cc_start: 0.7765 (p0) cc_final: 0.7256 (p0) REVERT: D 843 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7970 (m-30) REVERT: D 876 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.6951 (p90) REVERT: D 908 MET cc_start: 0.8570 (mmp) cc_final: 0.8195 (mmt) REVERT: D 909 PHE cc_start: 0.7982 (t80) cc_final: 0.7107 (m-80) REVERT: D 920 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: D 951 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6909 (pp20) outliers start: 104 outliers final: 61 residues processed: 635 average time/residue: 0.4540 time to fit residues: 454.4142 Evaluate side-chains 629 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 543 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 1136 GLN Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1136 GLN Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 0.0020 chunk 345 optimal weight: 0.0470 chunk 211 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 240 optimal weight: 5.9990 chunk 362 optimal weight: 2.9990 chunk 333 optimal weight: 0.8980 chunk 288 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 overall best weight: 0.5286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29844 Z= 0.154 Angle : 0.571 15.477 40500 Z= 0.278 Chirality : 0.042 0.270 4612 Planarity : 0.003 0.041 5088 Dihedral : 4.054 24.392 4020 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.50 % Allowed : 24.24 % Favored : 73.26 % 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: -0.24 (0.14), residues: 3632 helix: 0.07 (0.13), residues: 1664 sheet: -0.78 (0.26), residues: 404 loop : -0.01 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 353 HIS 0.003 0.000 HIS D 291 PHE 0.026 0.001 PHE B 275 TYR 0.023 0.001 TYR D 582 ARG 0.009 0.000 ARG C1020 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 555 time to evaluate : 3.320 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: A 163 ASN cc_start: 0.8249 (m110) cc_final: 0.7209 (p0) REVERT: A 177 TRP cc_start: 0.8228 (t60) cc_final: 0.7718 (t60) REVERT: A 222 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7570 (t80) REVERT: A 250 GLU cc_start: 0.7901 (pt0) cc_final: 0.7661 (pt0) REVERT: A 275 PHE cc_start: 0.7773 (t80) cc_final: 0.7516 (t80) REVERT: A 354 MET cc_start: 0.6871 (ppp) cc_final: 0.6043 (mtt) REVERT: A 367 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6272 (mtt180) REVERT: A 388 ASP cc_start: 0.7422 (m-30) cc_final: 0.7147 (m-30) REVERT: A 426 SER cc_start: 0.7897 (t) cc_final: 0.7487 (m) REVERT: A 570 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8350 (pttp) REVERT: A 575 TYR cc_start: 0.8073 (m-80) cc_final: 0.7787 (m-80) REVERT: A 576 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7798 (tp30) REVERT: A 780 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7224 (ttp80) REVERT: A 792 ASP cc_start: 0.7616 (p0) cc_final: 0.7114 (p0) REVERT: A 876 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.6048 (p90) REVERT: A 908 MET cc_start: 0.8506 (mmp) cc_final: 0.8071 (mmt) REVERT: A 909 PHE cc_start: 0.8054 (t80) cc_final: 0.7148 (m-10) REVERT: A 920 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: A 951 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6549 (pp20) REVERT: A 1020 ARG cc_start: 0.7756 (mtm110) cc_final: 0.7205 (ptp-170) REVERT: B 177 TRP cc_start: 0.8255 (t60) cc_final: 0.8001 (t60) REVERT: B 199 TYR cc_start: 0.7804 (t80) cc_final: 0.7216 (t80) REVERT: B 367 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6244 (mtt180) REVERT: B 388 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7192 (m-30) REVERT: B 426 SER cc_start: 0.7911 (t) cc_final: 0.7469 (m) REVERT: B 566 MET cc_start: 0.7615 (ppp) cc_final: 0.7214 (tmm) REVERT: B 570 LYS cc_start: 0.8807 (mmmm) cc_final: 0.8399 (pttp) REVERT: B 575 TYR cc_start: 0.8030 (m-80) cc_final: 0.7739 (m-80) REVERT: B 576 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7770 (tp30) REVERT: B 792 ASP cc_start: 0.7628 (p0) cc_final: 0.7213 (p0) REVERT: B 876 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.5999 (p90) REVERT: B 908 MET cc_start: 0.8508 (mmp) cc_final: 0.8067 (mmt) REVERT: B 909 PHE cc_start: 0.8044 (t80) cc_final: 0.7167 (m-10) REVERT: B 920 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: B 951 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6615 (pp20) REVERT: B 958 PHE cc_start: 0.8411 (p90) cc_final: 0.8134 (p90) REVERT: B 1020 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7498 (mtm110) REVERT: C 163 ASN cc_start: 0.7862 (m-40) cc_final: 0.6955 (p0) REVERT: C 222 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7219 (t80) REVERT: C 228 TRP cc_start: 0.5881 (m-90) cc_final: 0.5497 (m-90) REVERT: C 275 PHE cc_start: 0.7697 (t80) cc_final: 0.7459 (t80) REVERT: C 367 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6236 (mtt180) REVERT: C 418 ARG cc_start: 0.7254 (ptp-110) cc_final: 0.6615 (ptp90) REVERT: C 426 SER cc_start: 0.7820 (t) cc_final: 0.7420 (m) REVERT: C 566 MET cc_start: 0.7842 (ttp) cc_final: 0.7296 (tmm) REVERT: C 570 LYS cc_start: 0.8763 (mmmm) cc_final: 0.8409 (pttp) REVERT: C 576 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7801 (tp30) REVERT: C 631 GLU cc_start: 0.8215 (mp0) cc_final: 0.7603 (tt0) REVERT: C 780 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7211 (ttp80) REVERT: C 792 ASP cc_start: 0.7500 (p0) cc_final: 0.7086 (p0) REVERT: C 876 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.6852 (p90) REVERT: C 878 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: C 908 MET cc_start: 0.8511 (mmp) cc_final: 0.8098 (mmt) REVERT: C 909 PHE cc_start: 0.8024 (t80) cc_final: 0.7153 (m-10) REVERT: C 920 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: C 958 PHE cc_start: 0.8366 (p90) cc_final: 0.8152 (p90) REVERT: C 1020 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7458 (mtm110) REVERT: D 98 LYS cc_start: 0.5167 (tttt) cc_final: 0.4717 (ttpt) REVERT: D 153 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.4592 (m-10) REVERT: D 163 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7149 (p0) REVERT: D 180 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8323 (mm-40) REVERT: D 222 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7607 (t80) REVERT: D 354 MET cc_start: 0.6895 (ppp) cc_final: 0.6029 (mtt) REVERT: D 367 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6214 (mtt180) REVERT: D 388 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: D 426 SER cc_start: 0.7843 (t) cc_final: 0.7447 (m) REVERT: D 443 MET cc_start: 0.7460 (mtm) cc_final: 0.7229 (mtp) REVERT: D 566 MET cc_start: 0.7828 (ttp) cc_final: 0.7286 (tmm) REVERT: D 575 TYR cc_start: 0.8056 (m-80) cc_final: 0.7748 (m-80) REVERT: D 576 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7794 (tp30) REVERT: D 631 GLU cc_start: 0.7852 (mp0) cc_final: 0.7585 (mp0) REVERT: D 792 ASP cc_start: 0.7700 (p0) cc_final: 0.7199 (p0) REVERT: D 843 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: D 876 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.6826 (p90) REVERT: D 878 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: D 908 MET cc_start: 0.8495 (mmp) cc_final: 0.8090 (mmt) REVERT: D 909 PHE cc_start: 0.7906 (t80) cc_final: 0.7112 (m-80) REVERT: D 920 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: D 930 MET cc_start: 0.9189 (mmm) cc_final: 0.8958 (mmm) REVERT: D 951 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6589 (pp20) REVERT: D 1020 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7234 (ptp-170) outliers start: 79 outliers final: 48 residues processed: 611 average time/residue: 0.4339 time to fit residues: 416.3733 Evaluate side-chains 622 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 549 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 1136 GLN Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain B residue 1193 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 809 THR Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 1136 GLN Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 4.9990 chunk 307 optimal weight: 0.2980 chunk 88 optimal weight: 0.6980 chunk 266 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 289 optimal weight: 2.9990 chunk 121 optimal weight: 0.0060 chunk 296 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 108 ASN C 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.165905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121884 restraints weight = 35827.578| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.55 r_work: 0.3270 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29844 Z= 0.145 Angle : 0.563 15.372 40500 Z= 0.272 Chirality : 0.042 0.265 4612 Planarity : 0.003 0.040 5088 Dihedral : 3.917 20.581 4020 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.41 % Allowed : 24.75 % Favored : 72.85 % 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: -0.15 (0.14), residues: 3632 helix: 0.18 (0.13), residues: 1660 sheet: -0.83 (0.25), residues: 428 loop : 0.05 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 177 HIS 0.003 0.000 HIS D 291 PHE 0.036 0.001 PHE A 97 TYR 0.017 0.001 TYR A1167 ARG 0.008 0.000 ARG A1020 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8140.95 seconds wall clock time: 146 minutes 7.03 seconds (8767.03 seconds total)