Starting phenix.real_space_refine on Fri Mar 22 02:11:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghf_40044/03_2024/8ghf_40044_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghf_40044/03_2024/8ghf_40044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghf_40044/03_2024/8ghf_40044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghf_40044/03_2024/8ghf_40044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghf_40044/03_2024/8ghf_40044_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghf_40044/03_2024/8ghf_40044_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 P 72 5.49 5 Mg 4 5.21 5 S 184 5.16 5 Na 4 4.78 5 C 21072 2.51 5 N 4764 2.21 5 O 5812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 601": "OD1" <-> "OD2" Residue "A PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A ASP 726": "OD1" <-> "OD2" Residue "A ASP 798": "OD1" <-> "OD2" Residue "A ASP 895": "OD1" <-> "OD2" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 989": "OD1" <-> "OD2" Residue "A TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 370": "OD1" <-> "OD2" Residue "B ASP 601": "OD1" <-> "OD2" Residue "B PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 726": "OD1" <-> "OD2" Residue "B ASP 798": "OD1" <-> "OD2" Residue "B ASP 895": "OD1" <-> "OD2" Residue "B PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "C PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 601": "OD1" <-> "OD2" Residue "C PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C ASP 726": "OD1" <-> "OD2" Residue "C ASP 798": "OD1" <-> "OD2" Residue "C ASP 895": "OD1" <-> "OD2" Residue "C PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 601": "OD1" <-> "OD2" Residue "D PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 699": "OE1" <-> "OE2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "D ASP 726": "OD1" <-> "OD2" Residue "D ASP 798": "OD1" <-> "OD2" Residue "D ASP 895": "OD1" <-> "OD2" Residue "D PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 989": "OD1" <-> "OD2" Residue "D TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31920 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7209 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 910, 7201 Classifications: {'peptide': 910} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 18} Link IDs: {'PTRANS': 27, 'TRANS': 882} Chain breaks: 5 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 910, 7201 Classifications: {'peptide': 910} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 18} Link IDs: {'PTRANS': 27, 'TRANS': 882} Chain breaks: 5 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 7357 Chain: "B" Number of atoms: 7209 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 910, 7201 Classifications: {'peptide': 910} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 18} Link IDs: {'PTRANS': 27, 'TRANS': 882} Chain breaks: 5 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 910, 7201 Classifications: {'peptide': 910} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 18} Link IDs: {'PTRANS': 27, 'TRANS': 882} Chain breaks: 5 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 7357 Chain: "C" Number of atoms: 7209 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 910, 7201 Classifications: {'peptide': 910} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 18} Link IDs: {'PTRANS': 27, 'TRANS': 882} Chain breaks: 5 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 910, 7201 Classifications: {'peptide': 910} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 18} Link IDs: {'PTRANS': 27, 'TRANS': 882} Chain breaks: 5 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 7357 Chain: "D" Number of atoms: 7209 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 910, 7201 Classifications: {'peptide': 910} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 18} Link IDs: {'PTRANS': 27, 'TRANS': 882} Chain breaks: 5 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 910, 7201 Classifications: {'peptide': 910} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 18} Link IDs: {'PTRANS': 27, 'TRANS': 882} Chain breaks: 5 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 7357 Chain: "A" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 804 Unusual residues: {' CA': 2, ' MG': 1, ' NA': 1, 'CLR': 6, 'POV': 23} Classifications: {'undetermined': 33} Link IDs: {None: 32} Unresolved non-hydrogen bonds: 568 Unresolved non-hydrogen angles: 626 Unresolved non-hydrogen dihedrals: 540 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 6, 'POV:plan-1': 17} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 738 Unusual residues: {' CA': 2, ' MG': 1, ' NA': 1, 'CLR': 6, 'POV': 21} Classifications: {'undetermined': 31} Link IDs: {None: 30} Unresolved non-hydrogen bonds: 530 Unresolved non-hydrogen angles: 576 Unresolved non-hydrogen dihedrals: 510 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 6, 'POV:plan-1': 17} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 771 Unusual residues: {' CA': 2, ' MG': 1, ' NA': 1, 'CLR': 6, 'POV': 22} Classifications: {'undetermined': 32} Link IDs: {None: 31} Unresolved non-hydrogen bonds: 549 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 525 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 6, 'POV:plan-1': 17} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 771 Unusual residues: {' CA': 2, ' MG': 1, ' NA': 1, 'CLR': 6, 'POV': 22} Classifications: {'undetermined': 32} Link IDs: {None: 31} Unresolved non-hydrogen bonds: 549 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 525 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 6, 'POV:plan-1': 17} Unresolved non-hydrogen planarities: 95 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AASN A 826 " occ=0.61 ... (14 atoms not shown) pdb=" ND2BASN A 826 " occ=0.39 residue: pdb=" N AASN B 826 " occ=0.66 ... (14 atoms not shown) pdb=" ND2BASN B 826 " occ=0.34 residue: pdb=" N AASN C 826 " occ=0.66 ... (14 atoms not shown) pdb=" ND2BASN C 826 " occ=0.34 residue: pdb=" N AASN D 826 " occ=0.68 ... (14 atoms not shown) pdb=" ND2BASN D 826 " occ=0.32 Time building chain proxies: 28.18, per 1000 atoms: 0.88 Number of scatterers: 31920 At special positions: 0 Unit cell: (150.829, 150.829, 129.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 8 19.99 S 184 16.00 P 72 15.00 Mg 4 11.99 Na 4 11.00 O 5812 8.00 N 4764 7.00 C 21072 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.06 Conformation dependent library (CDL) restraints added in 9.7 seconds 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6904 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 159 helices and 16 sheets defined 46.7% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.53 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 removed outlier: 3.779A pdb=" N SER A 28 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 29 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL A 31 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 34 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 47 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 105 removed outlier: 3.517A pdb=" N VAL A 97 " --> pdb=" O TRP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 135 removed outlier: 3.797A pdb=" N ILE A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 169 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 181 through 199 Proline residue: A 191 - end of helix removed outlier: 3.583A pdb=" N PHE A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 223 removed outlier: 3.728A pdb=" N LEU A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 215 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 216 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 217 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 218 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 259 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 298 through 326 removed outlier: 3.635A pdb=" N PHE A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.588A pdb=" N ASP A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 433 through 450 Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.782A pdb=" N ALA A 467 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS A 468 " --> pdb=" O HIS A 464 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 497 Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.633A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 561 Processing helix chain 'A' and resid 604 through 608 removed outlier: 3.564A pdb=" N ARG A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'A' and resid 734 through 742 removed outlier: 4.991A pdb=" N MET A 739 " --> pdb=" O ASN A 736 " (cutoff:3.500A) Proline residue: A 740 - end of helix Processing helix chain 'A' and resid 748 through 750 No H-bonds generated for 'chain 'A' and resid 748 through 750' Processing helix chain 'A' and resid 760 through 764 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 786 through 791 Processing helix chain 'A' and resid 794 through 796 No H-bonds generated for 'chain 'A' and resid 794 through 796' Processing helix chain 'A' and resid 818 through 829 removed outlier: 3.591A pdb=" N SER A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 875 No H-bonds generated for 'chain 'A' and resid 873 through 875' Processing helix chain 'A' and resid 885 through 890 removed outlier: 3.685A pdb=" N VAL A 888 " --> pdb=" O ASP A 885 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 907 through 911 Processing helix chain 'A' and resid 917 through 929 removed outlier: 3.638A pdb=" N ASP A 921 " --> pdb=" O SER A 918 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER A 922 " --> pdb=" O VAL A 919 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A 924 " --> pdb=" O ASP A 921 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 927 " --> pdb=" O MET A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 Processing helix chain 'A' and resid 947 through 956 Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 996 through 1007 Processing helix chain 'B' and resid 21 through 48 removed outlier: 3.769A pdb=" N SER B 28 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER B 29 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL B 31 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 34 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 47 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 105 removed outlier: 3.518A pdb=" N VAL B 97 " --> pdb=" O TRP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 135 removed outlier: 3.783A pdb=" N ILE B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 169 Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 181 through 199 Proline residue: B 191 - end of helix removed outlier: 3.582A pdb=" N PHE B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 223 removed outlier: 3.732A pdb=" N LEU B 214 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 215 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 216 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 217 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 218 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 259 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 298 through 326 removed outlier: 3.638A pdb=" N PHE B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 312 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.612A pdb=" N ASP B 362 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 433 through 450 Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.785A pdb=" N ALA B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS B 468 " --> pdb=" O HIS B 464 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 497 Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 524 through 532 removed outlier: 3.634A pdb=" N GLY B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 561 Processing helix chain 'B' and resid 604 through 608 removed outlier: 3.558A pdb=" N ARG B 607 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 702 No H-bonds generated for 'chain 'B' and resid 700 through 702' Processing helix chain 'B' and resid 707 through 712 Processing helix chain 'B' and resid 734 through 742 removed outlier: 4.992A pdb=" N MET B 739 " --> pdb=" O ASN B 736 " (cutoff:3.500A) Proline residue: B 740 - end of helix Processing helix chain 'B' and resid 748 through 750 No H-bonds generated for 'chain 'B' and resid 748 through 750' Processing helix chain 'B' and resid 760 through 764 Processing helix chain 'B' and resid 767 through 769 No H-bonds generated for 'chain 'B' and resid 767 through 769' Processing helix chain 'B' and resid 786 through 791 Processing helix chain 'B' and resid 794 through 796 No H-bonds generated for 'chain 'B' and resid 794 through 796' Processing helix chain 'B' and resid 818 through 829 removed outlier: 3.500A pdb=" N LYS B 828 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 875 No H-bonds generated for 'chain 'B' and resid 873 through 875' Processing helix chain 'B' and resid 885 through 890 removed outlier: 3.686A pdb=" N VAL B 888 " --> pdb=" O ASP B 885 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 905 No H-bonds generated for 'chain 'B' and resid 903 through 905' Processing helix chain 'B' and resid 907 through 911 Processing helix chain 'B' and resid 917 through 929 removed outlier: 3.636A pdb=" N ASP B 921 " --> pdb=" O SER B 918 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER B 922 " --> pdb=" O VAL B 919 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET B 924 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR B 927 " --> pdb=" O MET B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 941 removed outlier: 4.345A pdb=" N LEU B 934 " --> pdb=" O ASP B 931 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 941 " --> pdb=" O ARG B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 956 Processing helix chain 'B' and resid 970 through 972 No H-bonds generated for 'chain 'B' and resid 970 through 972' Processing helix chain 'B' and resid 996 through 1007 Processing helix chain 'C' and resid 21 through 46 removed outlier: 3.766A pdb=" N SER C 28 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER C 29 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL C 31 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 34 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 105 removed outlier: 3.520A pdb=" N VAL C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 135 removed outlier: 3.797A pdb=" N ILE C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 169 Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 181 through 199 Proline residue: C 191 - end of helix removed outlier: 3.578A pdb=" N PHE C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 223 removed outlier: 3.728A pdb=" N LEU C 214 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE C 215 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 216 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 217 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 218 " --> pdb=" O ILE C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 259 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 298 through 326 removed outlier: 3.643A pdb=" N PHE C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.615A pdb=" N ASP C 362 " --> pdb=" O ASN C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 393 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 433 through 450 Processing helix chain 'C' and resid 463 through 471 removed outlier: 3.781A pdb=" N ALA C 467 " --> pdb=" O TYR C 463 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS C 468 " --> pdb=" O HIS C 464 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 497 Processing helix chain 'C' and resid 503 through 510 Processing helix chain 'C' and resid 524 through 532 removed outlier: 3.634A pdb=" N GLY C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 561 Processing helix chain 'C' and resid 604 through 608 removed outlier: 3.559A pdb=" N ARG C 607 " --> pdb=" O GLU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 702 No H-bonds generated for 'chain 'C' and resid 700 through 702' Processing helix chain 'C' and resid 707 through 712 Processing helix chain 'C' and resid 734 through 742 removed outlier: 4.989A pdb=" N MET C 739 " --> pdb=" O ASN C 736 " (cutoff:3.500A) Proline residue: C 740 - end of helix Processing helix chain 'C' and resid 748 through 750 No H-bonds generated for 'chain 'C' and resid 748 through 750' Processing helix chain 'C' and resid 760 through 764 Processing helix chain 'C' and resid 767 through 769 No H-bonds generated for 'chain 'C' and resid 767 through 769' Processing helix chain 'C' and resid 786 through 791 Processing helix chain 'C' and resid 794 through 796 No H-bonds generated for 'chain 'C' and resid 794 through 796' Processing helix chain 'C' and resid 818 through 829 removed outlier: 3.512A pdb=" N LYS C 828 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 829 " --> pdb=" O LEU C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 875 No H-bonds generated for 'chain 'C' and resid 873 through 875' Processing helix chain 'C' and resid 885 through 890 removed outlier: 3.684A pdb=" N VAL C 888 " --> pdb=" O ASP C 885 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 905 No H-bonds generated for 'chain 'C' and resid 903 through 905' Processing helix chain 'C' and resid 907 through 911 Processing helix chain 'C' and resid 917 through 929 removed outlier: 3.634A pdb=" N ASP C 921 " --> pdb=" O SER C 918 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER C 922 " --> pdb=" O VAL C 919 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR C 927 " --> pdb=" O MET C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 941 removed outlier: 4.340A pdb=" N LEU C 934 " --> pdb=" O ASP C 931 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 941 " --> pdb=" O ARG C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 956 Processing helix chain 'C' and resid 970 through 972 No H-bonds generated for 'chain 'C' and resid 970 through 972' Processing helix chain 'C' and resid 996 through 1007 Processing helix chain 'D' and resid 21 through 48 removed outlier: 3.755A pdb=" N SER D 28 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER D 29 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL D 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE D 34 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS D 47 " --> pdb=" O ARG D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 105 removed outlier: 3.515A pdb=" N VAL D 97 " --> pdb=" O TRP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 135 removed outlier: 3.798A pdb=" N ILE D 124 " --> pdb=" O PHE D 120 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 169 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 181 through 199 Proline residue: D 191 - end of helix removed outlier: 3.581A pdb=" N PHE D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 223 removed outlier: 3.730A pdb=" N LEU D 214 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE D 215 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN D 216 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D 217 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER D 218 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 259 Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 298 through 326 removed outlier: 3.636A pdb=" N PHE D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU D 312 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.617A pdb=" N ASP D 362 " --> pdb=" O ASN D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 393 Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 433 through 450 Processing helix chain 'D' and resid 463 through 471 removed outlier: 3.784A pdb=" N ALA D 467 " --> pdb=" O TYR D 463 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS D 468 " --> pdb=" O HIS D 464 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 497 Processing helix chain 'D' and resid 503 through 510 Processing helix chain 'D' and resid 524 through 532 removed outlier: 3.633A pdb=" N GLY D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 561 Processing helix chain 'D' and resid 604 through 608 removed outlier: 3.557A pdb=" N ARG D 607 " --> pdb=" O GLU D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 702 No H-bonds generated for 'chain 'D' and resid 700 through 702' Processing helix chain 'D' and resid 707 through 712 Processing helix chain 'D' and resid 734 through 742 removed outlier: 4.986A pdb=" N MET D 739 " --> pdb=" O ASN D 736 " (cutoff:3.500A) Proline residue: D 740 - end of helix Processing helix chain 'D' and resid 760 through 764 Processing helix chain 'D' and resid 767 through 769 No H-bonds generated for 'chain 'D' and resid 767 through 769' Processing helix chain 'D' and resid 786 through 791 Processing helix chain 'D' and resid 794 through 796 No H-bonds generated for 'chain 'D' and resid 794 through 796' Processing helix chain 'D' and resid 818 through 829 removed outlier: 3.514A pdb=" N LYS D 828 " --> pdb=" O SER D 824 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 875 No H-bonds generated for 'chain 'D' and resid 873 through 875' Processing helix chain 'D' and resid 885 through 890 removed outlier: 3.695A pdb=" N VAL D 888 " --> pdb=" O ASP D 885 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 905 No H-bonds generated for 'chain 'D' and resid 903 through 905' Processing helix chain 'D' and resid 907 through 911 Processing helix chain 'D' and resid 917 through 929 removed outlier: 3.635A pdb=" N ASP D 921 " --> pdb=" O SER D 918 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER D 922 " --> pdb=" O VAL D 919 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR D 927 " --> pdb=" O MET D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 941 removed outlier: 4.346A pdb=" N LEU D 934 " --> pdb=" O ASP D 931 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 941 " --> pdb=" O ARG D 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 956 Processing helix chain 'D' and resid 970 through 972 No H-bonds generated for 'chain 'D' and resid 970 through 972' Processing helix chain 'D' and resid 996 through 1007 Processing sheet with id= A, first strand: chain 'A' and resid 481 through 485 removed outlier: 6.357A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN A 459 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU A 374 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL A 347 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 376 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N GLY A 349 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU A 378 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS A 379 " --> pdb=" O TYR A 401 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 535 through 539 removed outlier: 4.017A pdb=" N ALA A 567 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 580 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 914 through 916 removed outlier: 7.965A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 720 " --> pdb=" O MET A 799 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 758 " --> pdb=" O LEU A 779 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 976 through 981 removed outlier: 3.967A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 481 through 485 removed outlier: 6.357A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN B 459 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU B 374 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL B 347 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL B 376 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N GLY B 349 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU B 378 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS B 379 " --> pdb=" O TYR B 401 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 535 through 539 removed outlier: 3.933A pdb=" N ALA B 567 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE B 598 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N MET B 565 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 914 through 916 removed outlier: 7.968A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 720 " --> pdb=" O MET B 799 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 758 " --> pdb=" O LEU B 779 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 976 through 981 removed outlier: 3.973A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU B1052 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N CYS B1011 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 481 through 485 removed outlier: 6.363A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 459 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU C 374 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL C 347 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL C 376 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N GLY C 349 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N LEU C 378 " --> pdb=" O GLY C 349 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS C 379 " --> pdb=" O TYR C 401 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 535 through 539 removed outlier: 3.943A pdb=" N ALA C 567 " --> pdb=" O PHE C 596 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 914 through 916 removed outlier: 7.963A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 720 " --> pdb=" O MET C 799 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 758 " --> pdb=" O LEU C 779 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 976 through 981 removed outlier: 3.980A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 481 through 485 removed outlier: 6.358A pdb=" N ILE D 456 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE D 484 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR D 458 " --> pdb=" O ILE D 484 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN D 459 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N HIS D 344 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N LEU D 423 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU D 374 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL D 347 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL D 376 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N GLY D 349 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LEU D 378 " --> pdb=" O GLY D 349 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS D 379 " --> pdb=" O TYR D 401 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 535 through 539 removed outlier: 3.949A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 914 through 916 removed outlier: 7.968A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL D 720 " --> pdb=" O MET D 799 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY D 758 " --> pdb=" O LEU D 779 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 976 through 981 removed outlier: 3.978A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) 1084 hydrogen bonds defined for protein. 2695 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: 10.72 Time building geometry restraints manager: 12.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5139 1.33 - 1.45: 8343 1.45 - 1.57: 18634 1.57 - 1.69: 144 1.69 - 1.82: 276 Bond restraints: 32536 Sorted by residual: bond pdb=" N PRO D 191 " pdb=" CA PRO D 191 " ideal model delta sigma weight residual 1.465 1.495 -0.031 2.03e-02 2.43e+03 2.27e+00 bond pdb=" N PRO A 191 " pdb=" CA PRO A 191 " ideal model delta sigma weight residual 1.465 1.495 -0.031 2.03e-02 2.43e+03 2.27e+00 bond pdb=" N PRO C 191 " pdb=" CA PRO C 191 " ideal model delta sigma weight residual 1.465 1.495 -0.030 2.03e-02 2.43e+03 2.23e+00 bond pdb=" N PRO B 191 " pdb=" CA PRO B 191 " ideal model delta sigma weight residual 1.465 1.495 -0.030 2.03e-02 2.43e+03 2.16e+00 bond pdb=" C PRO C 191 " pdb=" N PRO C 192 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.28e-02 6.10e+03 1.91e+00 ... (remaining 32531 not shown) Histogram of bond angle deviations from ideal: 96.96 - 104.37: 515 104.37 - 111.78: 15293 111.78 - 119.20: 12012 119.20 - 126.61: 15693 126.61 - 134.02: 479 Bond angle restraints: 43992 Sorted by residual: angle pdb=" N GLY D 205 " pdb=" CA GLY D 205 " pdb=" C GLY D 205 " ideal model delta sigma weight residual 111.36 116.04 -4.68 1.17e+00 7.31e-01 1.60e+01 angle pdb=" N GLY A 205 " pdb=" CA GLY A 205 " pdb=" C GLY A 205 " ideal model delta sigma weight residual 111.36 116.02 -4.66 1.17e+00 7.31e-01 1.59e+01 angle pdb=" N GLY B 205 " pdb=" CA GLY B 205 " pdb=" C GLY B 205 " ideal model delta sigma weight residual 111.36 116.01 -4.65 1.17e+00 7.31e-01 1.58e+01 angle pdb=" N GLY C 205 " pdb=" CA GLY C 205 " pdb=" C GLY C 205 " ideal model delta sigma weight residual 111.36 115.98 -4.62 1.17e+00 7.31e-01 1.56e+01 angle pdb=" N PRO D 191 " pdb=" CA PRO D 191 " pdb=" C PRO D 191 " ideal model delta sigma weight residual 110.70 115.33 -4.63 1.22e+00 6.72e-01 1.44e+01 ... (remaining 43987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.34: 18104 22.34 - 44.69: 1939 44.69 - 67.03: 519 67.03 - 89.37: 64 89.37 - 111.72: 25 Dihedral angle restraints: 20651 sinusoidal: 9991 harmonic: 10660 Sorted by residual: dihedral pdb=" C1 CLR A1517 " pdb=" C2 CLR A1517 " pdb=" C3 CLR A1517 " pdb=" C4 CLR A1517 " ideal model delta sinusoidal sigma weight residual 57.41 -54.31 111.72 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C1 CLR C1520 " pdb=" C2 CLR C1520 " pdb=" C3 CLR C1520 " pdb=" C4 CLR C1520 " ideal model delta sinusoidal sigma weight residual 57.41 -54.12 111.53 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C1 CLR D1520 " pdb=" C2 CLR D1520 " pdb=" C3 CLR D1520 " pdb=" C4 CLR D1520 " ideal model delta sinusoidal sigma weight residual 57.41 -53.95 111.36 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 20648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3103 0.033 - 0.066: 1175 0.066 - 0.100: 380 0.100 - 0.133: 185 0.133 - 0.166: 13 Chirality restraints: 4856 Sorted by residual: chirality pdb=" CA THR B 968 " pdb=" N THR B 968 " pdb=" C THR B 968 " pdb=" CB THR B 968 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA THR A 968 " pdb=" N THR A 968 " pdb=" C THR A 968 " pdb=" CB THR A 968 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA THR D 968 " pdb=" N THR D 968 " pdb=" C THR D 968 " pdb=" CB THR D 968 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 4853 not shown) Planarity restraints: 5180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 985 " -0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO A 986 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 965 " 0.052 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO C 966 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO C 966 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 966 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 965 " 0.052 5.00e-02 4.00e+02 7.87e-02 9.92e+00 pdb=" N PRO A 966 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 966 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 966 " 0.044 5.00e-02 4.00e+02 ... (remaining 5177 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 9585 2.84 - 3.35: 26214 3.35 - 3.87: 49830 3.87 - 4.38: 58522 4.38 - 4.90: 103903 Nonbonded interactions: 248054 Sorted by model distance: nonbonded pdb=" O LYS C1002 " pdb=" OG1 THR C1006 " model vdw 2.321 2.440 nonbonded pdb=" O LYS D1002 " pdb=" OG1 THR D1006 " model vdw 2.322 2.440 nonbonded pdb=" O LYS A1002 " pdb=" OG1 THR A1006 " model vdw 2.327 2.440 nonbonded pdb=" O LYS B1002 " pdb=" OG1 THR B1006 " model vdw 2.331 2.440 nonbonded pdb=" O GLY D 102 " pdb=" OG SER D 106 " model vdw 2.343 2.440 ... (remaining 248049 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 19 through 825 or resid 827 through 1418 or (resid 1512 an \ d (name C1 or name C2 or name O11 or name O12 or name O13 or name O14)) or (resi \ d 1514 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C2 or name C3 or name O11 or name O12 or name O13 or name O14 \ or name O21 or name O31 or name P )) or (resid 1518 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name O11 or name O1 \ 2 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or nam \ e P )) or (resid 1521 and (name N or name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or na \ me C31 or name C32 or name O11 or name O12 or name O13 or name O14 or name O21 o \ r name O22 or name O31 or name O32 or name P )) or (resid 1522 and (name N or na \ me C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or \ name C21 or name C22 or name C23 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or n \ ame P )) or (resid 1530 and (name C31 or name C32 or name C33 or name C34)) or ( \ resid 1531 and (name C1 or name C2 or name C21 or name C22 or name C3 or name O2 \ 1 or name O22 or name O31)))) selection = (chain 'B' and (resid 19 through 825 or resid 827 through 1418 or (resid 1512 an \ d (name C1 or name C2 or name O11 or name O12 or name O13 or name O14)) or (resi \ d 1514 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C2 or name C3 or name O11 or name O12 or name O13 or name O14 \ or name O21 or name O31 or name P )) or (resid 1518 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name O11 or name O1 \ 2 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or nam \ e P )) or (resid 1521 and (name N or name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or na \ me C31 or name C32 or name O11 or name O12 or name O13 or name O14 or name O21 o \ r name O22 or name O31 or name O32 or name P )) or (resid 1522 and (name N or na \ me C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or \ name C21 or name C22 or name C23 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or n \ ame P )) or (resid 1530 and (name C31 or name C32 or name C33 or name C34)) or ( \ resid 1531 and (name C1 or name C2 or name C21 or name C22 or name C3 or name O2 \ 1 or name O22 or name O31)))) selection = (chain 'C' and (resid 19 through 825 or resid 827 through 1418 or (resid 1512 an \ d (name C1 or name C2 or name O11 or name O12 or name O13 or name O14)) or resid \ 1514 or (resid 1518 and (name N or name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C \ 24 or name C25 or name C26 or name O11 or name O12 or name O13 or name O14 or na \ me O21 or name O22 or name O31 or name O32 or name P )) or (resid 1521 and (name \ N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or nam \ e C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )) or (resid 1522 and (name N or name C1 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C2 \ 3 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P )) or (resid 1530 and (na \ me C31 or name C32 or name C33 or name C34)) or (resid 1531 and (name C1 or name \ C2 or name C21 or name C22 or name C3 or name O21 or name O22 or name O31)))) selection = (chain 'D' and (resid 19 through 825 or resid 827 through 1418 or (resid 1512 an \ d (name C1 or name C2 or name O11 or name O12 or name O13 or name O14)) or resid \ 1514 or (resid 1518 and (name N or name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C \ 24 or name C25 or name C26 or name O11 or name O12 or name O13 or name O14 or na \ me O21 or name O22 or name O31 or name O32 or name P )) or (resid 1521 and (name \ N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or nam \ e C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )) or (resid 1522 and (name N or name C1 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C2 \ 3 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P )) or (resid 1530 and (na \ me C31 or name C32 or name C33 or name C34)) or (resid 1531 and (name C1 or name \ C2 or name C21 or name C22 or name C3 or name O21 or name O22 or name O31)))) } 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=0.32 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: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 16.530 Check model and map are aligned: 0.450 Set scattering table: 0.330 Process input model: 96.950 Find NCS groups from input model: 2.630 Set up NCS constraints: 0.240 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:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 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 : 0.002 0.040 32536 Z= 0.158 Angle : 0.604 9.594 43992 Z= 0.311 Chirality : 0.042 0.166 4856 Planarity : 0.005 0.080 5180 Dihedral : 18.869 111.716 13747 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.45 % Allowed : 23.63 % Favored : 72.92 % 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: -0.85 (0.13), residues: 3540 helix: -0.27 (0.11), residues: 1724 sheet: 0.75 (0.28), residues: 380 loop : -1.18 (0.14), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 93 HIS 0.016 0.001 HIS D 586 PHE 0.017 0.001 PHE A 144 TYR 0.032 0.001 TYR B1007 ARG 0.002 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 299 time to evaluate : 4.320 Fit side-chains REVERT: A 587 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8258 (mm) REVERT: B 43 TRP cc_start: 0.6798 (OUTLIER) cc_final: 0.6066 (t60) REVERT: B 587 LEU cc_start: 0.8707 (tt) cc_final: 0.8210 (mm) REVERT: C 587 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8226 (mm) REVERT: C 983 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7758 (mp) REVERT: D 587 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8209 (mm) outliers start: 104 outliers final: 89 residues processed: 388 average time/residue: 0.9612 time to fit residues: 472.2776 Evaluate side-chains 384 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 290 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 871 THR Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 922 SER Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 974 ARG Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 871 THR Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 974 ARG Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 3.9990 chunk 275 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 chunk 212 optimal weight: 0.7980 chunk 330 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 449 ASN A 471 ASN A 496 GLN A 586 HIS A 590 GLN A 771 HIS A 807 GLN A 893 GLN A 907 GLN A 967 GLN A1027 GLN B 142 GLN B 449 ASN B 471 ASN B 496 GLN B 586 HIS B 590 GLN B 893 GLN B 907 GLN B 932 ASN B 967 GLN B1027 GLN ** B1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 GLN C 200 ASN C 449 ASN C 471 ASN C 496 GLN C 586 HIS C 590 GLN C 771 HIS C 893 GLN C 907 GLN C 932 ASN C 967 GLN C1027 GLN D 142 GLN D 449 ASN D 471 ASN D 496 GLN D 586 HIS D 590 GLN D 893 GLN D 907 GLN D 932 ASN D 967 GLN D1027 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32536 Z= 0.283 Angle : 0.553 6.613 43992 Z= 0.277 Chirality : 0.043 0.152 4856 Planarity : 0.005 0.064 5180 Dihedral : 15.439 89.719 7325 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.05 % Allowed : 20.82 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3540 helix: -0.04 (0.12), residues: 1736 sheet: 0.64 (0.28), residues: 384 loop : -1.08 (0.14), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 100 HIS 0.007 0.002 HIS B 586 PHE 0.015 0.002 PHE B 120 TYR 0.012 0.001 TYR A 928 ARG 0.004 0.001 ARG D 368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 293 time to evaluate : 3.229 Fit side-chains REVERT: A 957 ASN cc_start: 0.7216 (OUTLIER) cc_final: 0.6857 (m110) REVERT: A 982 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8234 (mt) REVERT: A 983 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7851 (mp) REVERT: A 1005 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7344 (tppt) REVERT: B 43 TRP cc_start: 0.6581 (OUTLIER) cc_final: 0.5301 (t60) REVERT: B 957 ASN cc_start: 0.7178 (OUTLIER) cc_final: 0.6834 (m110) REVERT: B 983 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7830 (mp) REVERT: B 1005 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7336 (tppt) REVERT: C 957 ASN cc_start: 0.7207 (OUTLIER) cc_final: 0.6846 (m110) REVERT: C 1005 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7340 (tppt) REVERT: D 957 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.6822 (m110) REVERT: D 983 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7855 (mp) REVERT: D 1005 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7333 (tppt) outliers start: 154 outliers final: 61 residues processed: 384 average time/residue: 1.1399 time to fit residues: 538.1945 Evaluate side-chains 357 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 283 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain A residue 1005 LYS Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 745 ASN Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 1005 LYS Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 974 ARG Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 989 ASP Chi-restraints excluded: chain C residue 1005 LYS Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 745 ASN Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 974 ARG Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 989 ASP Chi-restraints excluded: chain D residue 1005 LYS Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 225 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 chunk 357 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 328 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS B 693 HIS B 771 HIS C 586 HIS D 200 ASN D 586 HIS D 771 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32536 Z= 0.233 Angle : 0.500 6.913 43992 Z= 0.252 Chirality : 0.042 0.142 4856 Planarity : 0.004 0.061 5180 Dihedral : 15.053 89.626 7263 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.74 % Allowed : 22.48 % Favored : 73.78 % 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: -0.51 (0.13), residues: 3540 helix: 0.03 (0.12), residues: 1736 sheet: 0.78 (0.27), residues: 384 loop : -1.01 (0.14), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 43 HIS 0.007 0.001 HIS D 586 PHE 0.013 0.001 PHE C 315 TYR 0.010 0.001 TYR C 198 ARG 0.002 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 292 time to evaluate : 3.582 Fit side-chains REVERT: A 43 TRP cc_start: 0.6579 (OUTLIER) cc_final: 0.5431 (t60) REVERT: A 199 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7553 (mp) REVERT: A 957 ASN cc_start: 0.7282 (OUTLIER) cc_final: 0.6910 (m110) REVERT: A 983 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7864 (mp) REVERT: A 1002 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7937 (tmtm) REVERT: B 43 TRP cc_start: 0.6578 (OUTLIER) cc_final: 0.5495 (t60) REVERT: B 199 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7568 (mp) REVERT: B 957 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.6893 (m110) REVERT: B 983 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7839 (mp) REVERT: B 1002 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7936 (tmtm) REVERT: C 43 TRP cc_start: 0.6626 (OUTLIER) cc_final: 0.5518 (t60) REVERT: C 199 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7563 (mp) REVERT: C 957 ASN cc_start: 0.7273 (OUTLIER) cc_final: 0.6896 (m110) REVERT: C 1002 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7926 (tmtm) REVERT: D 43 TRP cc_start: 0.6633 (OUTLIER) cc_final: 0.5483 (t60) REVERT: D 199 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7548 (mp) REVERT: D 957 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.6885 (m110) REVERT: D 974 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7904 (ptt180) REVERT: D 982 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8298 (mt) REVERT: D 983 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7884 (mp) REVERT: D 1002 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7927 (tmtm) outliers start: 113 outliers final: 51 residues processed: 360 average time/residue: 1.1479 time to fit residues: 508.4861 Evaluate side-chains 365 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 293 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 43 TRP Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 1002 LYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 43 TRP Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 974 ARG Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 989 ASP Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 974 ARG Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 989 ASP Chi-restraints excluded: chain D residue 990 LEU Chi-restraints excluded: chain D residue 1002 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 332 optimal weight: 8.9990 chunk 351 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 314 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 586 HIS A 693 HIS A 932 ASN B 200 ASN B 459 GLN B 586 HIS C 459 GLN C 586 HIS C 693 HIS C 807 GLN D 459 GLN D 586 HIS D 693 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 32536 Z= 0.396 Angle : 0.611 6.991 43992 Z= 0.304 Chirality : 0.046 0.172 4856 Planarity : 0.005 0.061 5180 Dihedral : 15.661 89.388 7242 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.81 % Allowed : 20.34 % Favored : 73.84 % 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: -0.75 (0.13), residues: 3540 helix: -0.20 (0.12), residues: 1724 sheet: 0.81 (0.27), residues: 384 loop : -1.11 (0.14), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 43 HIS 0.007 0.002 HIS C 254 PHE 0.016 0.002 PHE B 120 TYR 0.015 0.002 TYR D 928 ARG 0.003 0.001 ARG B 368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 298 time to evaluate : 3.341 Fit side-chains REVERT: A 43 TRP cc_start: 0.6636 (OUTLIER) cc_final: 0.5713 (t60) REVERT: A 94 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7133 (mpp) REVERT: A 199 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7652 (mp) REVERT: A 957 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.6930 (m110) REVERT: A 983 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7999 (mp) REVERT: A 1002 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8007 (tmtm) REVERT: B 43 TRP cc_start: 0.6623 (OUTLIER) cc_final: 0.5864 (t60) REVERT: B 94 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7184 (mpp) REVERT: B 199 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7676 (mp) REVERT: B 699 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: B 957 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.6920 (m110) REVERT: B 983 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.7977 (mp) REVERT: B 1002 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8005 (tmtm) REVERT: C 43 TRP cc_start: 0.6611 (OUTLIER) cc_final: 0.5681 (t60) REVERT: C 48 TYR cc_start: 0.5744 (OUTLIER) cc_final: 0.5517 (m-80) REVERT: C 94 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7185 (mpp) REVERT: C 199 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7665 (mp) REVERT: C 957 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.6926 (m110) REVERT: C 983 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8016 (mp) REVERT: C 1002 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7973 (tmtm) REVERT: D 43 TRP cc_start: 0.6625 (OUTLIER) cc_final: 0.5699 (t60) REVERT: D 94 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7184 (mpp) REVERT: D 199 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7644 (mp) REVERT: D 957 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.6907 (m110) REVERT: D 983 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7951 (mp) REVERT: D 1002 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7983 (tmtm) outliers start: 178 outliers final: 68 residues processed: 398 average time/residue: 1.0967 time to fit residues: 540.1392 Evaluate side-chains 386 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 292 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 TRP Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 1002 LYS Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain C residue 43 TRP Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 974 ARG Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 989 ASP Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 974 ARG Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 989 ASP Chi-restraints excluded: chain D residue 1002 LYS Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 2.9990 chunk 199 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 261 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 300 optimal weight: 0.2980 chunk 243 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 0.1980 chunk 315 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS C 586 HIS C 807 GLN D 586 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 32536 Z= 0.130 Angle : 0.459 7.549 43992 Z= 0.231 Chirality : 0.039 0.138 4856 Planarity : 0.004 0.059 5180 Dihedral : 14.602 89.941 7238 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.97 % Allowed : 23.09 % Favored : 73.94 % 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: -0.27 (0.14), residues: 3540 helix: 0.21 (0.13), residues: 1736 sheet: 0.95 (0.28), residues: 380 loop : -0.88 (0.14), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 43 HIS 0.007 0.001 HIS D 586 PHE 0.014 0.001 PHE C 315 TYR 0.007 0.001 TYR C 198 ARG 0.001 0.000 ARG D 974 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 305 time to evaluate : 2.830 Fit side-chains REVERT: A 43 TRP cc_start: 0.6449 (OUTLIER) cc_final: 0.5563 (t60) REVERT: A 199 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7541 (mp) REVERT: A 957 ASN cc_start: 0.7267 (OUTLIER) cc_final: 0.6854 (m110) REVERT: A 983 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.7991 (mp) REVERT: B 43 TRP cc_start: 0.6554 (OUTLIER) cc_final: 0.5878 (t60) REVERT: B 199 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7564 (mp) REVERT: B 957 ASN cc_start: 0.7237 (OUTLIER) cc_final: 0.6869 (m110) REVERT: B 983 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7966 (mp) REVERT: C 43 TRP cc_start: 0.6457 (OUTLIER) cc_final: 0.5629 (t60) REVERT: C 199 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7559 (mp) REVERT: C 957 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.6844 (m110) REVERT: D 43 TRP cc_start: 0.6450 (OUTLIER) cc_final: 0.5570 (t60) REVERT: D 199 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7513 (mp) REVERT: D 957 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.6859 (m110) REVERT: D 983 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7939 (mp) outliers start: 89 outliers final: 43 residues processed: 364 average time/residue: 1.0997 time to fit residues: 495.4549 Evaluate side-chains 347 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 289 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 TRP Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 43 TRP Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 983 LEU 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: 0.8980 chunk 206 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 352 optimal weight: 6.9990 chunk 292 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 29 optimal weight: 0.0980 chunk 116 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS C 586 HIS D 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32536 Z= 0.190 Angle : 0.473 7.303 43992 Z= 0.238 Chirality : 0.040 0.139 4856 Planarity : 0.004 0.059 5180 Dihedral : 14.439 89.723 7226 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.16 % Allowed : 23.06 % Favored : 73.78 % 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: -0.22 (0.14), residues: 3540 helix: 0.25 (0.13), residues: 1736 sheet: 0.97 (0.28), residues: 380 loop : -0.84 (0.14), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 43 HIS 0.016 0.001 HIS A 586 PHE 0.015 0.001 PHE C 315 TYR 0.010 0.001 TYR A 928 ARG 0.002 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 291 time to evaluate : 3.263 Fit side-chains REVERT: A 43 TRP cc_start: 0.6436 (OUTLIER) cc_final: 0.5578 (t60) REVERT: A 199 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7570 (mp) REVERT: A 957 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.6857 (m110) REVERT: A 983 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.7986 (mp) REVERT: B 43 TRP cc_start: 0.6532 (OUTLIER) cc_final: 0.5897 (t60) REVERT: B 199 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7624 (mp) REVERT: B 957 ASN cc_start: 0.7287 (OUTLIER) cc_final: 0.6872 (m110) REVERT: B 983 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7950 (mp) REVERT: B 990 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8283 (tt) REVERT: C 43 TRP cc_start: 0.6460 (OUTLIER) cc_final: 0.5665 (t60) REVERT: C 199 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7621 (mp) REVERT: C 957 ASN cc_start: 0.7310 (OUTLIER) cc_final: 0.6846 (m110) REVERT: C 983 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7984 (mp) REVERT: D 43 TRP cc_start: 0.6477 (OUTLIER) cc_final: 0.5620 (t60) REVERT: D 199 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7585 (mp) REVERT: D 957 ASN cc_start: 0.7289 (OUTLIER) cc_final: 0.6826 (m110) REVERT: D 983 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7954 (mp) outliers start: 95 outliers final: 52 residues processed: 355 average time/residue: 1.0544 time to fit residues: 466.6498 Evaluate side-chains 361 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 292 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 TRP Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 745 ASN Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain C residue 43 TRP Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 296 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 350 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS C 586 HIS D 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32536 Z= 0.181 Angle : 0.471 7.162 43992 Z= 0.236 Chirality : 0.040 0.139 4856 Planarity : 0.004 0.060 5180 Dihedral : 14.176 89.392 7226 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.26 % Allowed : 23.09 % Favored : 73.65 % 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: 3540 helix: 0.30 (0.13), residues: 1736 sheet: 1.00 (0.28), residues: 380 loop : -0.79 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 43 HIS 0.008 0.001 HIS A 586 PHE 0.016 0.001 PHE C 315 TYR 0.010 0.001 TYR D 928 ARG 0.001 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 293 time to evaluate : 3.285 Fit side-chains REVERT: A 43 TRP cc_start: 0.6437 (OUTLIER) cc_final: 0.5585 (t60) REVERT: A 94 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7110 (mpp) REVERT: A 199 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7569 (mp) REVERT: A 957 ASN cc_start: 0.7324 (OUTLIER) cc_final: 0.6865 (m110) REVERT: A 983 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7990 (mp) REVERT: B 43 TRP cc_start: 0.6503 (OUTLIER) cc_final: 0.5793 (t60) REVERT: B 199 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7597 (mp) REVERT: B 957 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.6885 (m110) REVERT: B 983 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7953 (mp) REVERT: B 990 LEU cc_start: 0.8612 (mt) cc_final: 0.8318 (tt) REVERT: C 43 TRP cc_start: 0.6456 (OUTLIER) cc_final: 0.5669 (t60) REVERT: C 199 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7571 (mp) REVERT: C 957 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.6844 (m110) REVERT: C 983 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.7999 (mp) REVERT: D 43 TRP cc_start: 0.6462 (OUTLIER) cc_final: 0.5615 (t60) REVERT: D 199 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7544 (mp) REVERT: D 957 ASN cc_start: 0.7285 (OUTLIER) cc_final: 0.6817 (m110) REVERT: D 983 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7967 (mp) outliers start: 98 outliers final: 64 residues processed: 354 average time/residue: 1.1120 time to fit residues: 491.2385 Evaluate side-chains 377 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 296 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 TRP Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 745 ASN Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 43 TRP Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 989 ASP Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 989 ASP Chi-restraints excluded: chain D residue 990 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 4.9990 chunk 140 optimal weight: 0.0370 chunk 209 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 223 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 275 optimal weight: 5.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS C 586 HIS D 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32536 Z= 0.150 Angle : 0.449 7.062 43992 Z= 0.225 Chirality : 0.039 0.137 4856 Planarity : 0.004 0.059 5180 Dihedral : 13.816 89.402 7226 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.19 % Allowed : 23.12 % Favored : 73.68 % 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: -0.06 (0.14), residues: 3540 helix: 0.38 (0.13), residues: 1740 sheet: 1.12 (0.29), residues: 360 loop : -0.76 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 43 HIS 0.007 0.001 HIS A 586 PHE 0.015 0.001 PHE B 315 TYR 0.008 0.001 TYR A 928 ARG 0.001 0.000 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 299 time to evaluate : 3.237 Fit side-chains REVERT: A 43 TRP cc_start: 0.6378 (OUTLIER) cc_final: 0.5552 (t60) REVERT: A 199 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7554 (mp) REVERT: A 957 ASN cc_start: 0.7291 (OUTLIER) cc_final: 0.6847 (m110) REVERT: A 983 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8003 (mp) REVERT: B 199 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7563 (mp) REVERT: B 983 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7938 (mp) REVERT: B 990 LEU cc_start: 0.8603 (mt) cc_final: 0.8278 (tt) REVERT: C 43 TRP cc_start: 0.6392 (OUTLIER) cc_final: 0.5625 (t60) REVERT: C 199 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7554 (mp) REVERT: C 957 ASN cc_start: 0.7274 (OUTLIER) cc_final: 0.6860 (m110) REVERT: C 983 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7994 (mp) REVERT: D 43 TRP cc_start: 0.6416 (OUTLIER) cc_final: 0.5597 (t60) REVERT: D 199 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7530 (mp) REVERT: D 957 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.6817 (m110) REVERT: D 983 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7964 (mp) outliers start: 96 outliers final: 64 residues processed: 357 average time/residue: 1.0529 time to fit residues: 467.8111 Evaluate side-chains 374 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 296 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 43 TRP Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 745 ASN Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 43 TRP Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 990 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 2.9990 chunk 336 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 326 optimal weight: 0.0570 chunk 196 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 256 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 295 optimal weight: 2.9990 chunk 309 optimal weight: 6.9990 chunk 325 optimal weight: 3.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS C 586 HIS D 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32536 Z= 0.204 Angle : 0.483 7.587 43992 Z= 0.242 Chirality : 0.041 0.139 4856 Planarity : 0.004 0.059 5180 Dihedral : 13.899 89.183 7226 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.26 % Allowed : 23.00 % Favored : 73.75 % 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: -0.14 (0.14), residues: 3540 helix: 0.30 (0.13), residues: 1736 sheet: 1.01 (0.28), residues: 380 loop : -0.79 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 43 HIS 0.009 0.001 HIS A 586 PHE 0.014 0.001 PHE B 315 TYR 0.011 0.001 TYR C 928 ARG 0.001 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 300 time to evaluate : 3.625 Fit side-chains REVERT: A 43 TRP cc_start: 0.6400 (OUTLIER) cc_final: 0.5636 (t60) REVERT: A 94 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7145 (mpp) REVERT: A 199 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7605 (mp) REVERT: A 957 ASN cc_start: 0.7331 (OUTLIER) cc_final: 0.6865 (m110) REVERT: A 983 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8033 (mp) REVERT: B 199 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7612 (mp) REVERT: B 983 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7989 (mp) REVERT: B 990 LEU cc_start: 0.8597 (mt) cc_final: 0.8235 (tt) REVERT: C 43 TRP cc_start: 0.6422 (OUTLIER) cc_final: 0.5728 (t60) REVERT: C 199 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7628 (mp) REVERT: C 957 ASN cc_start: 0.7326 (OUTLIER) cc_final: 0.6855 (m110) REVERT: C 983 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.7978 (mp) REVERT: D 43 TRP cc_start: 0.6402 (OUTLIER) cc_final: 0.5637 (t60) REVERT: D 199 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7599 (mp) REVERT: D 957 ASN cc_start: 0.7310 (OUTLIER) cc_final: 0.6839 (m110) REVERT: D 983 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8002 (mp) outliers start: 98 outliers final: 66 residues processed: 363 average time/residue: 1.0744 time to fit residues: 489.5330 Evaluate side-chains 383 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 302 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 TRP Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 745 ASN Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 43 TRP Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 989 ASP Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 989 ASP Chi-restraints excluded: chain D residue 990 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 0.0770 chunk 345 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 chunk 362 optimal weight: 0.0870 chunk 333 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 223 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS C 586 HIS D 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32536 Z= 0.144 Angle : 0.452 6.984 43992 Z= 0.226 Chirality : 0.039 0.138 4856 Planarity : 0.004 0.059 5180 Dihedral : 13.626 87.133 7226 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.94 % Allowed : 23.28 % Favored : 73.78 % 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: -0.03 (0.14), residues: 3540 helix: 0.39 (0.13), residues: 1740 sheet: 1.12 (0.29), residues: 360 loop : -0.72 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 43 HIS 0.009 0.001 HIS A 586 PHE 0.015 0.001 PHE B 315 TYR 0.008 0.001 TYR B 928 ARG 0.001 0.000 ARG B 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 300 time to evaluate : 3.151 Fit side-chains REVERT: A 43 TRP cc_start: 0.6405 (OUTLIER) cc_final: 0.5717 (t60) REVERT: A 94 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7136 (mpp) REVERT: A 199 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7559 (mp) REVERT: A 957 ASN cc_start: 0.7301 (OUTLIER) cc_final: 0.6856 (m110) REVERT: A 983 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8007 (mp) REVERT: B 199 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7553 (mp) REVERT: B 957 ASN cc_start: 0.7201 (OUTLIER) cc_final: 0.6827 (m110) REVERT: B 983 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7940 (mp) REVERT: B 990 LEU cc_start: 0.8594 (mt) cc_final: 0.8214 (tt) REVERT: C 43 TRP cc_start: 0.6407 (OUTLIER) cc_final: 0.5746 (t60) REVERT: C 199 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7537 (mp) REVERT: C 586 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6944 (p90) REVERT: C 587 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8233 (mm) REVERT: C 957 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.6847 (m110) REVERT: C 983 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7958 (mp) REVERT: D 43 TRP cc_start: 0.6395 (OUTLIER) cc_final: 0.5711 (t60) REVERT: D 199 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7532 (mp) REVERT: D 586 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.6934 (p90) REVERT: D 587 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8235 (mm) REVERT: D 957 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.6814 (m110) REVERT: D 983 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7963 (mp) outliers start: 88 outliers final: 55 residues processed: 354 average time/residue: 1.0929 time to fit residues: 483.2979 Evaluate side-chains 375 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 300 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 TRP Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 745 ASN Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 43 TRP Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 586 HIS Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 989 ASP Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 989 ASP Chi-restraints excluded: chain D residue 990 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 0.8980 chunk 307 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 266 optimal weight: 9.9990 chunk 42 optimal weight: 0.0970 chunk 80 optimal weight: 0.9990 chunk 289 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 296 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS C 586 HIS D 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.100049 restraints weight = 72910.788| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.03 r_work: 0.3014 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32536 Z= 0.124 Angle : 0.441 7.915 43992 Z= 0.221 Chirality : 0.039 0.137 4856 Planarity : 0.004 0.059 5180 Dihedral : 13.439 85.188 7226 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.62 % Allowed : 23.51 % Favored : 73.87 % 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: 0.05 (0.14), residues: 3540 helix: 0.46 (0.13), residues: 1740 sheet: 1.13 (0.29), residues: 360 loop : -0.67 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 43 HIS 0.011 0.001 HIS C 586 PHE 0.014 0.001 PHE A 315 TYR 0.008 0.001 TYR A 928 ARG 0.001 0.000 ARG B 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9406.21 seconds wall clock time: 167 minutes 42.93 seconds (10062.93 seconds total)