Starting phenix.real_space_refine on Sat Dec 28 10:39:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpq_34940/12_2024/8hpq_34940.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpq_34940/12_2024/8hpq_34940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hpq_34940/12_2024/8hpq_34940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpq_34940/12_2024/8hpq_34940.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpq_34940/12_2024/8hpq_34940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpq_34940/12_2024/8hpq_34940.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9426 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 189 5.16 5 C 28131 2.51 5 N 7410 2.21 5 O 8625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 44355 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8059 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1029, 8051 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 55, 'TRANS': 973} Chain breaks: 9 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 1029, 8051 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 55, 'TRANS': 973} Chain breaks: 9 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 8228 Chain: "H" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "M" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1656 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "N" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "B" Number of atoms: 8059 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1029, 8051 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 55, 'TRANS': 973} Chain breaks: 9 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 1029, 8051 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 55, 'TRANS': 973} Chain breaks: 9 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 8228 Chain: "P" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "Q" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "E" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1656 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "F" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "C" Number of atoms: 8059 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1029, 8051 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 55, 'TRANS': 973} Chain breaks: 9 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 1029, 8051 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 55, 'TRANS': 973} Chain breaks: 9 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 8228 Chain: "I" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "J" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "R" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1656 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "S" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 27.75, per 1000 atoms: 0.63 Number of scatterers: 44355 At special positions: 0 Unit cell: (215.04, 232.68, 245.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 189 16.00 O 8625 8.00 N 7410 7.00 C 28131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 375 " distance=2.03 Simple disulfide: pdb=" SG CYS A 393 " - pdb=" SG CYS A 446 " distance=2.04 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 539 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 631 " - pdb=" SG CYS A 663 " distance=2.03 Simple disulfide: pdb=" SG CYS A 676 " - pdb=" SG CYS A 685 " distance=2.03 Simple disulfide: pdb=" SG CYS A 752 " - pdb=" SG CYS A 774 " distance=2.03 Simple disulfide: pdb=" SG CYS A 757 " - pdb=" SG CYS A 763 " distance=2.03 Simple disulfide: pdb=" SG CYS A1046 " - pdb=" SG CYS A1057 " distance=2.03 Simple disulfide: pdb=" SG CYS A1096 " - pdb=" SG CYS A1140 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.04 Simple disulfide: pdb=" SG CYS H 231 " - pdb=" SG CYS L 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.03 Simple disulfide: pdb=" SG CYS M 149 " - pdb=" SG CYS M 205 " distance=2.04 Simple disulfide: pdb=" SG CYS M 225 " - pdb=" SG CYS N 216 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 136 " - pdb=" SG CYS N 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 375 " distance=2.03 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 446 " distance=2.03 Simple disulfide: pdb=" SG CYS B 405 " - pdb=" SG CYS B 539 " distance=2.03 Simple disulfide: pdb=" SG CYS B 494 " - pdb=" SG CYS B 502 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 631 " - pdb=" SG CYS B 663 " distance=2.03 Simple disulfide: pdb=" SG CYS B 676 " - pdb=" SG CYS B 685 " distance=2.03 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 774 " distance=2.03 Simple disulfide: pdb=" SG CYS B 757 " - pdb=" SG CYS B 763 " distance=2.03 Simple disulfide: pdb=" SG CYS B1046 " - pdb=" SG CYS B1057 " distance=2.03 Simple disulfide: pdb=" SG CYS B1096 " - pdb=" SG CYS B1140 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS P 155 " - pdb=" SG CYS P 211 " distance=2.04 Simple disulfide: pdb=" SG CYS P 231 " - pdb=" SG CYS Q 215 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 135 " - pdb=" SG CYS Q 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 149 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 180 " distance=2.03 Simple disulfide: pdb=" SG CYS C 305 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 375 " distance=2.03 Simple disulfide: pdb=" SG CYS C 393 " - pdb=" SG CYS C 446 " distance=2.04 Simple disulfide: pdb=" SG CYS C 405 " - pdb=" SG CYS C 539 " distance=2.03 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 502 " distance=2.03 Simple disulfide: pdb=" SG CYS C 552 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 631 " - pdb=" SG CYS C 663 " distance=2.03 Simple disulfide: pdb=" SG CYS C 676 " - pdb=" SG CYS C 685 " distance=2.03 Simple disulfide: pdb=" SG CYS C 752 " - pdb=" SG CYS C 774 " distance=2.03 Simple disulfide: pdb=" SG CYS C 757 " - pdb=" SG CYS C 763 " distance=2.03 Simple disulfide: pdb=" SG CYS C1046 " - pdb=" SG CYS C1057 " distance=2.03 Simple disulfide: pdb=" SG CYS C1096 " - pdb=" SG CYS C1140 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.04 Simple disulfide: pdb=" SG CYS I 231 " - pdb=" SG CYS J 215 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.04 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 195 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 95 " distance=2.03 Simple disulfide: pdb=" SG CYS R 149 " - pdb=" SG CYS R 205 " distance=2.04 Simple disulfide: pdb=" SG CYS R 225 " - pdb=" SG CYS S 216 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.04 Simple disulfide: pdb=" SG CYS S 136 " - pdb=" SG CYS S 196 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=4, symmetry=0 Links applied NAG-ASN " NAG A1201 " - " ASN A 357 " " NAG B1201 " - " ASN B 357 " " NAG C1201 " - " ASN C 357 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.34 Conformation dependent library (CDL) restraints added in 7.0 seconds 11312 Ramachandran restraints generated. 5656 Oldfield, 0 Emsley, 5656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10698 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 104 sheets defined 16.4% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.51 Creating SS restraints... Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.583A pdb=" N VAL A 355 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.564A pdb=" N TRP A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 385 Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.868A pdb=" N LEU A 401 " --> pdb=" O PRO A 398 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN A 402 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 404 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.855A pdb=" N VAL A 634 " --> pdb=" O CYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 758 Processing helix chain 'A' and resid 760 through 768 Processing helix chain 'A' and resid 769 through 771 No H-bonds generated for 'chain 'A' and resid 769 through 771' Processing helix chain 'A' and resid 772 through 797 removed outlier: 3.521A pdb=" N ASP A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 840 Processing helix chain 'A' and resid 880 through 898 Processing helix chain 'A' and resid 911 through 923 Processing helix chain 'A' and resid 926 through 933 removed outlier: 3.969A pdb=" N LEU A 930 " --> pdb=" O THR A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 955 Processing helix chain 'A' and resid 959 through 979 Processing helix chain 'A' and resid 980 through 982 No H-bonds generated for 'chain 'A' and resid 980 through 982' Processing helix chain 'A' and resid 990 through 998 Processing helix chain 'A' and resid 999 through 1046 removed outlier: 4.126A pdb=" N VAL A1005 " --> pdb=" O PRO A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1161 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.644A pdb=" N THR H 92 " --> pdb=" O PRO H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 200 through 204 removed outlier: 3.795A pdb=" N LEU H 204 " --> pdb=" O SER H 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'M' and resid 165 through 167 No H-bonds generated for 'chain 'M' and resid 165 through 167' Processing helix chain 'M' and resid 196 through 201 removed outlier: 4.488A pdb=" N THR M 200 " --> pdb=" O SER M 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 128 Processing helix chain 'N' and resid 185 through 190 removed outlier: 3.867A pdb=" N LYS N 190 " --> pdb=" O ALA N 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 351 through 358 removed outlier: 3.583A pdb=" N VAL B 355 " --> pdb=" O PRO B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.564A pdb=" N TRP B 367 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 385 Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.868A pdb=" N LEU B 401 " --> pdb=" O PRO B 398 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN B 402 " --> pdb=" O THR B 399 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 404 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 630 through 634 removed outlier: 3.855A pdb=" N VAL B 634 " --> pdb=" O CYS B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 758 Processing helix chain 'B' and resid 760 through 768 Processing helix chain 'B' and resid 769 through 771 No H-bonds generated for 'chain 'B' and resid 769 through 771' Processing helix chain 'B' and resid 772 through 797 removed outlier: 3.521A pdb=" N ASP B 789 " --> pdb=" O ALA B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 840 Processing helix chain 'B' and resid 880 through 898 Processing helix chain 'B' and resid 911 through 923 Processing helix chain 'B' and resid 926 through 933 removed outlier: 3.970A pdb=" N LEU B 930 " --> pdb=" O THR B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 955 Processing helix chain 'B' and resid 959 through 979 Processing helix chain 'B' and resid 980 through 982 No H-bonds generated for 'chain 'B' and resid 980 through 982' Processing helix chain 'B' and resid 990 through 998 Processing helix chain 'B' and resid 999 through 1046 removed outlier: 4.126A pdb=" N VAL B1005 " --> pdb=" O PRO B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1161 Processing helix chain 'P' and resid 88 through 92 removed outlier: 3.644A pdb=" N THR P 92 " --> pdb=" O PRO P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 173 No H-bonds generated for 'chain 'P' and resid 171 through 173' Processing helix chain 'P' and resid 200 through 204 removed outlier: 3.795A pdb=" N LEU P 204 " --> pdb=" O SER P 201 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 32 No H-bonds generated for 'chain 'Q' and resid 30 through 32' Processing helix chain 'Q' and resid 183 through 188 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 196 through 201 removed outlier: 4.488A pdb=" N THR E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 128 Processing helix chain 'F' and resid 185 through 190 removed outlier: 3.867A pdb=" N LYS F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 318 Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.583A pdb=" N VAL C 355 " --> pdb=" O PRO C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.564A pdb=" N TRP C 367 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 385 Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.869A pdb=" N LEU C 401 " --> pdb=" O PRO C 398 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASN C 402 " --> pdb=" O THR C 399 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 404 " --> pdb=" O LEU C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 424 Processing helix chain 'C' and resid 431 through 436 Processing helix chain 'C' and resid 630 through 634 removed outlier: 3.856A pdb=" N VAL C 634 " --> pdb=" O CYS C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 758 Processing helix chain 'C' and resid 760 through 768 Processing helix chain 'C' and resid 769 through 771 No H-bonds generated for 'chain 'C' and resid 769 through 771' Processing helix chain 'C' and resid 772 through 797 removed outlier: 3.521A pdb=" N ASP C 789 " --> pdb=" O ALA C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 840 Processing helix chain 'C' and resid 880 through 898 Processing helix chain 'C' and resid 911 through 923 Processing helix chain 'C' and resid 926 through 933 removed outlier: 3.970A pdb=" N LEU C 930 " --> pdb=" O THR C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 955 Processing helix chain 'C' and resid 959 through 979 Processing helix chain 'C' and resid 980 through 982 No H-bonds generated for 'chain 'C' and resid 980 through 982' Processing helix chain 'C' and resid 990 through 998 Processing helix chain 'C' and resid 999 through 1046 removed outlier: 4.126A pdb=" N VAL C1005 " --> pdb=" O PRO C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1155 through 1161 Processing helix chain 'I' and resid 88 through 92 removed outlier: 3.644A pdb=" N THR I 92 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing helix chain 'I' and resid 200 through 204 removed outlier: 3.794A pdb=" N LEU I 204 " --> pdb=" O SER I 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 183 through 188 Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 86 through 90 Processing helix chain 'R' and resid 165 through 167 No H-bonds generated for 'chain 'R' and resid 165 through 167' Processing helix chain 'R' and resid 196 through 201 removed outlier: 4.488A pdb=" N THR R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 128 Processing helix chain 'S' and resid 185 through 190 removed outlier: 3.867A pdb=" N LYS S 190 " --> pdb=" O ALA S 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 8.098A pdb=" N ASN A 77 " --> pdb=" O TYR A 283 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR A 283 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE A 215 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP A 242 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE A 217 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 59 removed outlier: 3.705A pdb=" N ARG B 581 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B 589 " --> pdb=" O GLY B 580 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP B 588 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 71 removed outlier: 4.052A pdb=" N ASP A 301 " --> pdb=" O LYS A 292 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 99 removed outlier: 3.919A pdb=" N GLY A 117 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 140 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 182 " --> pdb=" O VAL A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 147 through 155 removed outlier: 6.470A pdb=" N GLN A 148 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS A 150 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL A 173 " --> pdb=" O CYS A 150 " (cutoff:3.500A) removed outlier: 12.143A pdb=" N ASP A 152 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N PHE A 171 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 330 removed outlier: 5.170A pdb=" N ILE A 326 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR A 613 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN A 328 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 611 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 330 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 339 through 342 removed outlier: 5.209A pdb=" N ASP A 588 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 589 " --> pdb=" O GLY A 580 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N PHE A 579 " --> pdb=" O PHE C 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 372 Processing sheet with id=AA9, first strand: chain 'A' and resid 466 through 468 Processing sheet with id=AB1, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AB2, first strand: chain 'A' and resid 668 through 669 removed outlier: 5.868A pdb=" N GLU A 668 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N THR A 710 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE A 684 " --> pdb=" O ILE A 680 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 715 through 716 removed outlier: 6.219A pdb=" N ALA A 715 " --> pdb=" O ILE C 802 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 725 through 742 removed outlier: 6.451A pdb=" N SER A 725 " --> pdb=" O THR A1090 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A1090 " --> pdb=" O SER A 725 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 727 " --> pdb=" O ASN A1088 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN A1088 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A1086 " --> pdb=" O PRO A 729 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLY A1073 " --> pdb=" O SER A1069 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER A1069 " --> pdb=" O GLY A1073 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A1075 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A1077 " --> pdb=" O SER A1065 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER A1065 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A1079 " --> pdb=" O LEU A1063 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 725 through 742 removed outlier: 6.451A pdb=" N SER A 725 " --> pdb=" O THR A1090 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A1090 " --> pdb=" O SER A 725 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 727 " --> pdb=" O ASN A1088 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN A1088 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A1086 " --> pdb=" O PRO A 729 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A1092 " --> pdb=" O PHE A1109 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE A1109 " --> pdb=" O ALA A1092 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 747 through 750 removed outlier: 4.322A pdb=" N LYS A 747 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.194A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.351A pdb=" N PHE H 101 " --> pdb=" O PHE H 115 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N PHE H 115 " --> pdb=" O PHE H 101 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.212A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.212A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 166 through 169 removed outlier: 4.179A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.747A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.954A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 145 through 151 Processing sheet with id=AC9, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.826A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.389A pdb=" N TYR M 33 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.732A pdb=" N CYS M 95 " --> pdb=" O TRP M 112 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP M 112 " --> pdb=" O CYS M 95 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG M 97 " --> pdb=" O ASP M 110 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA M 108 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.953A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.953A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 160 through 163 removed outlier: 3.585A pdb=" N TYR M 203 " --> pdb=" O VAL M 220 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.630A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.619A pdb=" N GLU N 107 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 116 through 120 removed outlier: 5.744A pdb=" N TYR N 175 " --> pdb=" O ASN N 140 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER N 176 " --> pdb=" O THR N 166 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 155 through 157 removed outlier: 4.155A pdb=" N TRP N 150 " --> pdb=" O GLN N 157 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 45 through 46 removed outlier: 8.097A pdb=" N ASN B 77 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR B 283 " --> pdb=" O ASN B 77 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE B 215 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP B 242 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 217 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 58 through 59 removed outlier: 3.755A pdb=" N ARG C 581 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA C 589 " --> pdb=" O GLY C 580 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASP C 588 " --> pdb=" O ILE C 601 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 64 through 71 removed outlier: 4.053A pdb=" N ASP B 301 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 97 through 99 removed outlier: 3.920A pdb=" N GLY B 117 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 140 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE B 182 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 147 through 155 removed outlier: 6.470A pdb=" N GLN B 148 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS B 150 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL B 173 " --> pdb=" O CYS B 150 " (cutoff:3.500A) removed outlier: 12.144A pdb=" N ASP B 152 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N PHE B 171 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 325 through 333 removed outlier: 5.170A pdb=" N ILE B 326 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR B 613 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLN B 328 " --> pdb=" O VAL B 611 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 611 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER B 330 " --> pdb=" O VAL B 609 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 609 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY B 608 " --> pdb=" O GLN B 627 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 368 through 372 Processing sheet with id=AE8, first strand: chain 'B' and resid 466 through 468 Processing sheet with id=AE9, first strand: chain 'B' and resid 487 through 488 Processing sheet with id=AF1, first strand: chain 'B' and resid 668 through 669 removed outlier: 5.869A pdb=" N GLU B 668 " --> pdb=" O ALA B 708 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR B 710 " --> pdb=" O GLU B 668 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE B 684 " --> pdb=" O ILE B 680 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 725 through 742 removed outlier: 6.451A pdb=" N SER B 725 " --> pdb=" O THR B1090 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR B1090 " --> pdb=" O SER B 725 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 727 " --> pdb=" O ASN B1088 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN B1088 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU B1086 " --> pdb=" O PRO B 729 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLY B1073 " --> pdb=" O SER B1069 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER B1069 " --> pdb=" O GLY B1073 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B1075 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU B1077 " --> pdb=" O SER B1065 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER B1065 " --> pdb=" O LEU B1077 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B1079 " --> pdb=" O LEU B1063 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 725 through 742 removed outlier: 6.451A pdb=" N SER B 725 " --> pdb=" O THR B1090 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR B1090 " --> pdb=" O SER B 725 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 727 " --> pdb=" O ASN B1088 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN B1088 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU B1086 " --> pdb=" O PRO B 729 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B1092 " --> pdb=" O PHE B1109 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE B1109 " --> pdb=" O ALA B1092 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 747 through 750 removed outlier: 4.323A pdb=" N LYS B 747 " --> pdb=" O LEU B 875 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 801 through 802 Processing sheet with id=AF6, first strand: chain 'B' and resid 1134 through 1136 Processing sheet with id=AF7, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'P' and resid 11 through 12 removed outlier: 6.193A pdb=" N ARG P 40 " --> pdb=" O TRP P 49 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TRP P 49 " --> pdb=" O ARG P 40 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 11 through 12 removed outlier: 7.351A pdb=" N PHE P 101 " --> pdb=" O PHE P 115 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N PHE P 115 " --> pdb=" O PHE P 101 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 135 through 139 removed outlier: 6.211A pdb=" N TYR P 191 " --> pdb=" O ASP P 159 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 135 through 139 removed outlier: 6.211A pdb=" N TYR P 191 " --> pdb=" O ASP P 159 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 166 through 169 removed outlier: 4.179A pdb=" N TYR P 209 " --> pdb=" O VAL P 226 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.747A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 106 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TYR Q 50 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 115 through 119 removed outlier: 5.955A pdb=" N TYR Q 174 " --> pdb=" O ASN Q 139 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 145 through 151 Processing sheet with id=AG8, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.826A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.388A pdb=" N TYR E 33 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.731A pdb=" N CYS E 95 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TRP E 112 " --> pdb=" O CYS E 95 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG E 97 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA E 108 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 129 through 133 removed outlier: 5.953A pdb=" N TYR E 185 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 129 through 133 removed outlier: 5.953A pdb=" N TYR E 185 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 160 through 163 removed outlier: 3.585A pdb=" N TYR E 203 " --> pdb=" O VAL E 220 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.630A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.620A pdb=" N GLU F 107 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 116 through 120 removed outlier: 5.743A pdb=" N TYR F 175 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER F 176 " --> pdb=" O THR F 166 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 155 through 157 removed outlier: 4.155A pdb=" N TRP F 150 " --> pdb=" O GLN F 157 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 45 through 46 removed outlier: 8.098A pdb=" N ASN C 77 " --> pdb=" O TYR C 283 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR C 283 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE C 215 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP C 242 " --> pdb=" O PHE C 215 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE C 217 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 64 through 71 removed outlier: 4.052A pdb=" N ASP C 301 " --> pdb=" O LYS C 292 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 97 through 99 removed outlier: 3.920A pdb=" N GLY C 117 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 140 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 182 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 147 through 155 removed outlier: 6.471A pdb=" N GLN C 148 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS C 150 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL C 173 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 12.143A pdb=" N ASP C 152 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N PHE C 171 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 325 through 333 removed outlier: 5.169A pdb=" N ILE C 326 " --> pdb=" O THR C 613 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR C 613 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLN C 328 " --> pdb=" O VAL C 611 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C 611 " --> pdb=" O GLN C 328 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER C 330 " --> pdb=" O VAL C 609 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY C 608 " --> pdb=" O GLN C 627 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 368 through 372 Processing sheet with id=AI6, first strand: chain 'C' and resid 466 through 468 Processing sheet with id=AI7, first strand: chain 'C' and resid 487 through 488 Processing sheet with id=AI8, first strand: chain 'C' and resid 668 through 669 removed outlier: 5.868A pdb=" N GLU C 668 " --> pdb=" O ALA C 708 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N THR C 710 " --> pdb=" O GLU C 668 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 684 " --> pdb=" O ILE C 680 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'C' and resid 725 through 742 removed outlier: 6.451A pdb=" N SER C 725 " --> pdb=" O THR C1090 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C1090 " --> pdb=" O SER C 725 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA C 727 " --> pdb=" O ASN C1088 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN C1088 " --> pdb=" O ALA C 727 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C1086 " --> pdb=" O PRO C 729 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY C1073 " --> pdb=" O SER C1069 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER C1069 " --> pdb=" O GLY C1073 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C1075 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU C1077 " --> pdb=" O SER C1065 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER C1065 " --> pdb=" O LEU C1077 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C1079 " --> pdb=" O LEU C1063 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'C' and resid 725 through 742 removed outlier: 6.451A pdb=" N SER C 725 " --> pdb=" O THR C1090 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C1090 " --> pdb=" O SER C 725 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA C 727 " --> pdb=" O ASN C1088 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN C1088 " --> pdb=" O ALA C 727 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C1086 " --> pdb=" O PRO C 729 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA C1092 " --> pdb=" O PHE C1109 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE C1109 " --> pdb=" O ALA C1092 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'C' and resid 747 through 750 removed outlier: 4.322A pdb=" N LYS C 747 " --> pdb=" O LEU C 875 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'C' and resid 1134 through 1136 Processing sheet with id=AJ4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AJ5, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.194A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'I' and resid 11 through 12 removed outlier: 7.352A pdb=" N PHE I 101 " --> pdb=" O PHE I 115 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N PHE I 115 " --> pdb=" O PHE I 101 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'I' and resid 135 through 139 removed outlier: 6.214A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'I' and resid 135 through 139 removed outlier: 6.214A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'I' and resid 166 through 169 removed outlier: 4.179A pdb=" N TYR I 209 " --> pdb=" O VAL I 226 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AK2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.747A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'J' and resid 115 through 119 removed outlier: 5.954A pdb=" N TYR J 174 " --> pdb=" O ASN J 139 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'J' and resid 145 through 151 Processing sheet with id=AK5, first strand: chain 'R' and resid 3 through 7 removed outlier: 3.825A pdb=" N GLN R 3 " --> pdb=" O SER R 25 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'R' and resid 10 through 12 removed outlier: 4.388A pdb=" N TYR R 33 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET R 34 " --> pdb=" O VAL R 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL R 50 " --> pdb=" O MET R 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.732A pdb=" N CYS R 95 " --> pdb=" O TRP R 112 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TRP R 112 " --> pdb=" O CYS R 95 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG R 97 " --> pdb=" O ASP R 110 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA R 108 " --> pdb=" O SER R 99 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'R' and resid 129 through 133 removed outlier: 5.953A pdb=" N TYR R 185 " --> pdb=" O ASP R 153 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'R' and resid 129 through 133 removed outlier: 5.953A pdb=" N TYR R 185 " --> pdb=" O ASP R 153 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'R' and resid 160 through 163 removed outlier: 3.585A pdb=" N TYR R 203 " --> pdb=" O VAL R 220 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.630A pdb=" N ASP S 70 " --> pdb=" O SER S 67 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'S' and resid 10 through 13 removed outlier: 3.619A pdb=" N GLU S 107 " --> pdb=" O LEU S 11 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU S 33 " --> pdb=" O SER S 49 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER S 49 " --> pdb=" O LEU S 33 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'S' and resid 116 through 120 removed outlier: 5.744A pdb=" N TYR S 175 " --> pdb=" O ASN S 140 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER S 176 " --> pdb=" O THR S 166 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'S' and resid 155 through 157 removed outlier: 4.155A pdb=" N TRP S 150 " --> pdb=" O GLN S 157 " (cutoff:3.500A) 1994 hydrogen bonds defined for protein. 5259 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: 25.23 Time building geometry restraints manager: 10.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.47: 25894 1.47 - 1.78: 19271 1.78 - 2.08: 224 2.08 - 2.39: 0 2.39 - 2.69: 4 Bond restraints: 45393 Sorted by residual: bond pdb=" C SER A 330 " pdb=" N ASN A 331 " ideal model delta sigma weight residual 1.332 2.694 -1.362 1.40e-02 5.10e+03 9.46e+03 bond pdb=" C SER A 605 " pdb=" N PHE A 606 " ideal model delta sigma weight residual 1.332 2.525 -1.192 1.40e-02 5.10e+03 7.25e+03 bond pdb=" C SER C 605 " pdb=" N PHE C 606 " ideal model delta sigma weight residual 1.332 2.416 -1.083 1.40e-02 5.10e+03 5.99e+03 bond pdb=" C SER B 605 " pdb=" N PHE B 606 " ideal model delta sigma weight residual 1.332 2.400 -1.067 1.40e-02 5.10e+03 5.81e+03 bond pdb=" C PHE B 343 " pdb=" N PRO B 344 " ideal model delta sigma weight residual 1.334 1.874 -0.540 2.34e-02 1.83e+03 5.33e+02 ... (remaining 45388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 17.31: 61745 17.31 - 34.61: 9 34.61 - 51.92: 4 51.92 - 69.22: 0 69.22 - 86.53: 3 Bond angle restraints: 61761 Sorted by residual: angle pdb=" O SER B 605 " pdb=" C SER B 605 " pdb=" N PHE B 606 " ideal model delta sigma weight residual 122.07 35.54 86.53 1.03e+00 9.43e-01 7.06e+03 angle pdb=" O SER C 605 " pdb=" C SER C 605 " pdb=" N PHE C 606 " ideal model delta sigma weight residual 122.07 40.22 81.85 1.03e+00 9.43e-01 6.32e+03 angle pdb=" O SER A 605 " pdb=" C SER A 605 " pdb=" N PHE A 606 " ideal model delta sigma weight residual 122.12 38.47 83.65 1.06e+00 8.90e-01 6.23e+03 angle pdb=" CA SER C 605 " pdb=" C SER C 605 " pdb=" N PHE C 606 " ideal model delta sigma weight residual 117.07 161.42 -44.35 1.14e+00 7.69e-01 1.51e+03 angle pdb=" CA SER A 605 " pdb=" C SER A 605 " pdb=" N PHE A 606 " ideal model delta sigma weight residual 117.30 159.74 -42.44 1.16e+00 7.43e-01 1.34e+03 ... (remaining 61756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 24829 17.80 - 35.61: 1856 35.61 - 53.41: 366 53.41 - 71.21: 97 71.21 - 89.02: 71 Dihedral angle restraints: 27219 sinusoidal: 10566 harmonic: 16653 Sorted by residual: dihedral pdb=" C LYS B 542 " pdb=" N LYS B 542 " pdb=" CA LYS B 542 " pdb=" CB LYS B 542 " ideal model delta harmonic sigma weight residual -122.60 -148.06 25.46 0 2.50e+00 1.60e-01 1.04e+02 dihedral pdb=" CA ASP P 116 " pdb=" C ASP P 116 " pdb=" N PRO P 117 " pdb=" CA PRO P 117 " ideal model delta harmonic sigma weight residual -180.00 -131.40 -48.60 0 5.00e+00 4.00e-02 9.45e+01 dihedral pdb=" CA ASP I 116 " pdb=" C ASP I 116 " pdb=" N PRO I 117 " pdb=" CA PRO I 117 " ideal model delta harmonic sigma weight residual -180.00 -131.43 -48.57 0 5.00e+00 4.00e-02 9.44e+01 ... (remaining 27216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.201: 6970 0.201 - 0.403: 22 0.403 - 0.604: 6 0.604 - 0.806: 0 0.806 - 1.007: 1 Chirality restraints: 6999 Sorted by residual: chirality pdb=" CA LYS B 542 " pdb=" N LYS B 542 " pdb=" C LYS B 542 " pdb=" CB LYS B 542 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.54e+01 chirality pdb=" CA ARG A 333 " pdb=" N ARG A 333 " pdb=" C ARG A 333 " pdb=" CB ARG A 333 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.93e+00 chirality pdb=" CA PHE C 332 " pdb=" N PHE C 332 " pdb=" C PHE C 332 " pdb=" CB PHE C 332 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.54 2.00e-01 2.50e+01 7.42e+00 ... (remaining 6996 not shown) Planarity restraints: 7965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 343 " 0.045 2.00e-02 2.50e+03 8.44e-02 7.13e+01 pdb=" C PHE B 343 " -0.145 2.00e-02 2.50e+03 pdb=" O PHE B 343 " 0.063 2.00e-02 2.50e+03 pdb=" N PRO B 344 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 331 " 0.038 2.00e-02 2.50e+03 7.79e-02 6.07e+01 pdb=" C ASN C 331 " -0.135 2.00e-02 2.50e+03 pdb=" O ASN C 331 " 0.052 2.00e-02 2.50e+03 pdb=" N PHE C 332 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 540 " -0.036 2.00e-02 2.50e+03 6.93e-02 4.81e+01 pdb=" C GLY B 540 " 0.120 2.00e-02 2.50e+03 pdb=" O GLY B 540 " -0.046 2.00e-02 2.50e+03 pdb=" N PRO B 541 " -0.038 2.00e-02 2.50e+03 ... (remaining 7962 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 10 2.11 - 2.81: 12144 2.81 - 3.50: 57570 3.50 - 4.20: 108421 4.20 - 4.90: 186615 Nonbonded interactions: 364760 Sorted by model distance: nonbonded pdb=" CD1 PHE B 59 " pdb=" OE1 GLN C 577 " model vdw 1.412 3.340 nonbonded pdb=" CD1 PHE A 59 " pdb=" OE1 GLN B 577 " model vdw 1.414 3.340 nonbonded pdb=" OE1 GLN A 577 " pdb=" CD1 PHE C 59 " model vdw 1.458 3.340 nonbonded pdb=" CD1 PHE A 59 " pdb=" CD GLN B 577 " model vdw 1.755 3.570 nonbonded pdb=" CD GLN A 577 " pdb=" CD1 PHE C 59 " model vdw 1.773 3.570 ... (remaining 364755 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 388 or resid 390 through 1161 or resid 1201)) selection = (chain 'B' and (resid 33 through 388 or resid 390 through 1161 or resid 1201)) selection = (chain 'C' and (resid 33 through 388 or resid 390 through 1161 or resid 1201)) } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'N' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'Q' } 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=0.50 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: 6.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.030 Extract box with map and model: 1.530 Check model and map are aligned: 0.260 Set scattering table: 0.300 Process input model: 102.060 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.320 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: 0.020 Load rotamer database and sin/cos tables:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3693 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 : 0.013 1.362 45393 Z= 0.761 Angle : 1.120 86.525 61761 Z= 0.814 Chirality : 0.057 1.007 6999 Planarity : 0.007 0.106 7962 Dihedral : 13.793 89.015 16305 Min Nonbonded Distance : 1.412 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.75 % Favored : 96.20 % Rotamer: Outliers : 0.64 % Allowed : 1.80 % Favored : 97.56 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 8.49 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.06 % 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 (0.11), residues: 5656 helix: 0.71 (0.17), residues: 723 sheet: 0.86 (0.12), residues: 1861 loop : -0.81 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 900 HIS 0.030 0.002 HIS C 968 PHE 0.036 0.002 PHE A 332 TYR 0.030 0.002 TYR C1081 ARG 0.014 0.001 ARG B1009 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11312 Ramachandran restraints generated. 5656 Oldfield, 0 Emsley, 5656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11312 Ramachandran restraints generated. 5656 Oldfield, 0 Emsley, 5656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 748 time to evaluate : 3.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7214 (t) cc_final: 0.6967 (m) REVERT: A 69 ASP cc_start: 0.7222 (m-30) cc_final: 0.6935 (t70) REVERT: A 319 SER cc_start: 0.8521 (t) cc_final: 0.8231 (p) REVERT: A 600 ASP cc_start: 0.6998 (t70) cc_final: 0.6712 (t0) REVERT: M 163 TRP cc_start: 0.0210 (m100) cc_final: -0.0072 (t-100) REVERT: N 162 GLN cc_start: 0.0449 (mm-40) cc_final: 0.0088 (tm130) REVERT: N 172 ASP cc_start: 0.3604 (p0) cc_final: 0.3244 (p0) REVERT: B 47 SER cc_start: 0.7263 (t) cc_final: 0.6920 (m) REVERT: B 99 PRO cc_start: 0.6303 (Cg_exo) cc_final: 0.6036 (Cg_endo) REVERT: B 724 ASN cc_start: 0.6988 (p0) cc_final: 0.6768 (p0) REVERT: B 1059 LYS cc_start: 0.7502 (tppt) cc_final: 0.7202 (mmtm) REVERT: P 188 SER cc_start: 0.2618 (p) cc_final: 0.2098 (t) REVERT: C 202 ASN cc_start: 0.6763 (m-40) cc_final: 0.6411 (m110) REVERT: C 283 TYR cc_start: 0.7397 (m-80) cc_final: 0.6482 (m-80) REVERT: C 598 ILE cc_start: 0.7006 (pt) cc_final: 0.6460 (mm) REVERT: C 834 ASP cc_start: 0.7050 (t70) cc_final: 0.6809 (m-30) REVERT: C 964 ASP cc_start: 0.6881 (m-30) cc_final: 0.6630 (m-30) REVERT: C 1134 THR cc_start: 0.5877 (p) cc_final: 0.5472 (t) outliers start: 29 outliers final: 8 residues processed: 772 average time/residue: 1.0470 time to fit residues: 1038.1978 Evaluate side-chains 317 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 309 time to evaluate : 3.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 542 LYS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain C residue 334 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 478 optimal weight: 1.9990 chunk 429 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 289 optimal weight: 0.5980 chunk 229 optimal weight: 20.0000 chunk 444 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 270 optimal weight: 0.5980 chunk 330 optimal weight: 30.0000 chunk 514 optimal weight: 8.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A 348 ASN A 578 GLN A 838 ASN A 927 GLN A 940 GLN L 167 GLN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 ASN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN B 769 GLN B 838 ASN B 886 GLN B 927 GLN B 940 GLN B 968 HIS B1115 HIS Q 167 GLN E 73 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN F 37 GLN F 126 GLN F 149 GLN C 82 HIS C 95 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 838 ASN C 940 GLN C 968 HIS ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 HIS R 73 ASN R 206 ASN ** S 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4108 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 45393 Z= 0.381 Angle : 0.743 16.190 61761 Z= 0.390 Chirality : 0.051 0.373 6999 Planarity : 0.006 0.090 7962 Dihedral : 5.682 55.991 6233 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.90 % Allowed : 9.13 % Favored : 87.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 8.49 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.07 (0.11), residues: 5664 helix: 0.94 (0.19), residues: 701 sheet: 0.79 (0.12), residues: 1881 loop : -0.82 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 900 HIS 0.011 0.002 HIS C 968 PHE 0.066 0.003 PHE B 182 TYR 0.028 0.002 TYR Q 37 ARG 0.015 0.001 ARG S 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 398 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7439 (t) cc_final: 0.7169 (m) REVERT: A 232 GLN cc_start: 0.8455 (tt0) cc_final: 0.7327 (pm20) REVERT: A 319 SER cc_start: 0.8690 (t) cc_final: 0.8299 (p) REVERT: A 660 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7156 (mtp180) REVERT: A 737 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8348 (t) REVERT: A 754 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6530 (ttm) REVERT: A 787 GLU cc_start: 0.7263 (tt0) cc_final: 0.6959 (tt0) REVERT: A 1059 LYS cc_start: 0.8103 (tppt) cc_final: 0.7863 (tmmt) REVERT: A 1085 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8771 (mt0) REVERT: N 100 PHE cc_start: 0.4216 (OUTLIER) cc_final: 0.3428 (t80) REVERT: N 162 GLN cc_start: 0.0803 (mm-40) cc_final: 0.0317 (pt0) REVERT: B 315 CYS cc_start: 0.6073 (t) cc_final: 0.5786 (t) REVERT: B 574 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7224 (mt) REVERT: B 754 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6835 (ttm) REVERT: B 787 GLU cc_start: 0.7387 (tt0) cc_final: 0.7140 (tt0) REVERT: B 828 LYS cc_start: 0.7616 (mmtm) cc_final: 0.6701 (tmmm) REVERT: E 117 MET cc_start: 0.0850 (OUTLIER) cc_final: 0.0081 (pp-130) REVERT: F 151 LYS cc_start: 0.0592 (OUTLIER) cc_final: -0.0442 (mttt) REVERT: C 82 HIS cc_start: 0.5034 (OUTLIER) cc_final: 0.4675 (p-80) REVERT: C 167 MET cc_start: 0.1088 (pp-130) cc_final: 0.0560 (tmm) REVERT: C 202 ASN cc_start: 0.6965 (m-40) cc_final: 0.6557 (m110) REVERT: C 283 TYR cc_start: 0.7654 (m-80) cc_final: 0.7292 (m-80) REVERT: C 574 LEU cc_start: 0.7593 (mt) cc_final: 0.7180 (mp) REVERT: C 598 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7172 (mm) REVERT: C 600 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7369 (m-30) REVERT: C 674 TYR cc_start: 0.8020 (m-80) cc_final: 0.7754 (m-80) REVERT: C 787 GLU cc_start: 0.7474 (tt0) cc_final: 0.7216 (tt0) REVERT: C 1028 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7274 (mtt90) REVERT: J 63 PHE cc_start: 0.1997 (m-80) cc_final: 0.1711 (m-80) outliers start: 143 outliers final: 60 residues processed: 498 average time/residue: 0.9457 time to fit residues: 622.6176 Evaluate side-chains 347 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 275 time to evaluate : 3.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 578 GLN Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 1085 GLN Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 996 SER Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 1132 ASP Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain S residue 34 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 286 optimal weight: 0.5980 chunk 159 optimal weight: 0.5980 chunk 428 optimal weight: 1.9990 chunk 350 optimal weight: 10.0000 chunk 142 optimal weight: 40.0000 chunk 515 optimal weight: 6.9990 chunk 557 optimal weight: 40.0000 chunk 459 optimal weight: 0.7980 chunk 511 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 413 optimal weight: 20.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN A 462 ASN A 776 GLN H 79 GLN ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN B 969 ASN B 971 GLN P 170 ASN E 180 GLN F 149 GLN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1024 GLN I 67 ASN ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 126 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4153 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 45393 Z= 0.334 Angle : 0.673 15.057 61761 Z= 0.352 Chirality : 0.049 0.315 6999 Planarity : 0.005 0.091 7962 Dihedral : 5.175 46.228 6219 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.64 % Allowed : 11.90 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.49 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: 0.04 (0.11), residues: 5664 helix: 1.33 (0.19), residues: 694 sheet: 0.87 (0.12), residues: 1882 loop : -0.83 (0.11), residues: 3088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 450 HIS 0.025 0.001 HIS C 82 PHE 0.031 0.002 PHE P 24 TYR 0.025 0.002 TYR H 160 ARG 0.011 0.001 ARG C 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 311 time to evaluate : 3.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7580 (t) cc_final: 0.7297 (m) REVERT: A 67 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7373 (p) REVERT: A 143 LYS cc_start: 0.7126 (mtmt) cc_final: 0.6696 (tttm) REVERT: A 232 GLN cc_start: 0.8451 (tt0) cc_final: 0.7358 (pm20) REVERT: A 283 TYR cc_start: 0.7450 (m-10) cc_final: 0.7038 (m-80) REVERT: A 319 SER cc_start: 0.8723 (t) cc_final: 0.8367 (p) REVERT: A 583 ILE cc_start: 0.7907 (mm) cc_final: 0.7513 (mm) REVERT: A 585 ASP cc_start: 0.6683 (m-30) cc_final: 0.5885 (t0) REVERT: A 660 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7289 (mtp180) REVERT: A 737 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8355 (t) REVERT: A 768 LEU cc_start: 0.8071 (tt) cc_final: 0.7515 (mp) REVERT: A 787 GLU cc_start: 0.7224 (tt0) cc_final: 0.6818 (tt0) REVERT: A 808 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7816 (tp) REVERT: A 834 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6750 (m-30) REVERT: A 1012 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7634 (t) REVERT: B 68 GLN cc_start: 0.7491 (tm-30) cc_final: 0.7211 (tp-100) REVERT: B 214 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.5061 (t80) REVERT: B 232 GLN cc_start: 0.7943 (tt0) cc_final: 0.7178 (mt0) REVERT: B 583 ILE cc_start: 0.7819 (mm) cc_final: 0.7615 (mm) REVERT: B 711 MET cc_start: 0.8315 (ptm) cc_final: 0.7949 (ptm) REVERT: B 787 GLU cc_start: 0.7236 (tt0) cc_final: 0.7006 (tt0) REVERT: B 794 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7174 (pt0) REVERT: B 808 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7931 (mm) REVERT: B 994 ILE cc_start: 0.6515 (mt) cc_final: 0.6265 (mp) REVERT: B 1100 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7420 (mtmp) REVERT: E 34 MET cc_start: 0.4211 (mmm) cc_final: 0.3320 (mmm) REVERT: E 117 MET cc_start: 0.1278 (tpt) cc_final: 0.0212 (pp-130) REVERT: F 151 LYS cc_start: 0.0410 (OUTLIER) cc_final: -0.0557 (mttt) REVERT: C 202 ASN cc_start: 0.6907 (m-40) cc_final: 0.6418 (m110) REVERT: C 574 LEU cc_start: 0.7901 (mt) cc_final: 0.7654 (mp) REVERT: C 577 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.5739 (mm-40) REVERT: C 674 TYR cc_start: 0.7990 (m-80) cc_final: 0.7725 (m-80) REVERT: C 787 GLU cc_start: 0.7371 (tt0) cc_final: 0.7118 (tt0) REVERT: C 793 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: C 873 THR cc_start: 0.8515 (p) cc_final: 0.8215 (t) REVERT: C 971 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: C 978 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7240 (mptp) REVERT: I 116 ASP cc_start: 0.3585 (OUTLIER) cc_final: 0.3332 (t70) REVERT: I 157 VAL cc_start: -0.1503 (OUTLIER) cc_final: -0.1756 (t) REVERT: J 66 SER cc_start: 0.1137 (OUTLIER) cc_final: 0.0365 (m) outliers start: 130 outliers final: 61 residues processed: 407 average time/residue: 0.9609 time to fit residues: 516.5156 Evaluate side-chains 333 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 254 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1100 LYS Chi-restraints excluded: chain B residue 1106 GLU Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain B residue 1147 VAL Chi-restraints excluded: chain P residue 188 SER Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 793 GLN Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 971 GLN Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 978 LYS Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain S residue 34 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 509 optimal weight: 50.0000 chunk 387 optimal weight: 2.9990 chunk 267 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 346 optimal weight: 5.9990 chunk 517 optimal weight: 30.0000 chunk 548 optimal weight: 20.0000 chunk 270 optimal weight: 1.9990 chunk 490 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN A 793 GLN ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 214 ASN F 37 GLN F 149 GLN C 82 HIS C 129 GLN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4199 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 45393 Z= 0.395 Angle : 0.688 13.369 61761 Z= 0.360 Chirality : 0.050 0.248 6999 Planarity : 0.006 0.089 7962 Dihedral : 5.222 45.597 6219 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.02 % Allowed : 13.46 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.49 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: -0.09 (0.11), residues: 5664 helix: 1.24 (0.19), residues: 671 sheet: 0.83 (0.12), residues: 1835 loop : -0.92 (0.11), residues: 3158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 450 HIS 0.015 0.001 HIS C 82 PHE 0.045 0.002 PHE B 182 TYR 0.026 0.002 TYR C 283 ARG 0.011 0.001 ARG C 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 287 time to evaluate : 3.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7727 (t) cc_final: 0.7370 (m) REVERT: A 67 THR cc_start: 0.7625 (p) cc_final: 0.7402 (p) REVERT: A 232 GLN cc_start: 0.8576 (tt0) cc_final: 0.7696 (pm20) REVERT: A 283 TYR cc_start: 0.7490 (m-10) cc_final: 0.7008 (m-80) REVERT: A 319 SER cc_start: 0.8761 (t) cc_final: 0.8357 (p) REVERT: A 462 ASN cc_start: 0.4083 (t0) cc_final: 0.3846 (t0) REVERT: A 660 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7348 (mtp180) REVERT: A 754 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6645 (ttm) REVERT: A 768 LEU cc_start: 0.8165 (tt) cc_final: 0.7742 (mp) REVERT: A 787 GLU cc_start: 0.7274 (tt0) cc_final: 0.6996 (tt0) REVERT: A 808 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7781 (tp) REVERT: A 834 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7142 (m-30) REVERT: A 1012 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7899 (t) REVERT: A 1085 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8732 (mt0) REVERT: B 68 GLN cc_start: 0.7470 (tm-30) cc_final: 0.7150 (tp-100) REVERT: B 214 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.5445 (t80) REVERT: B 232 GLN cc_start: 0.7979 (tt0) cc_final: 0.7312 (mt0) REVERT: B 558 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7919 (m-40) REVERT: B 660 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7306 (mtm180) REVERT: B 711 MET cc_start: 0.8374 (ptm) cc_final: 0.8053 (ptm) REVERT: B 787 GLU cc_start: 0.7304 (tt0) cc_final: 0.7098 (tt0) REVERT: B 794 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7067 (pt0) REVERT: B 808 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7928 (mm) REVERT: B 834 ASP cc_start: 0.7597 (m-30) cc_final: 0.7340 (m-30) REVERT: B 1100 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7607 (mtmp) REVERT: B 1127 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7943 (mm110) REVERT: Q 188 GLU cc_start: 0.2300 (mp0) cc_final: 0.1605 (pm20) REVERT: F 4 MET cc_start: 0.1778 (mmm) cc_final: 0.1503 (mtp) REVERT: F 149 GLN cc_start: 0.5479 (OUTLIER) cc_final: 0.5262 (pt0) REVERT: F 151 LYS cc_start: 0.0693 (OUTLIER) cc_final: -0.0292 (mttt) REVERT: C 167 MET cc_start: 0.0221 (pp-130) cc_final: -0.0386 (tmm) REVERT: C 202 ASN cc_start: 0.6852 (m-40) cc_final: 0.6202 (m110) REVERT: C 776 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: C 787 GLU cc_start: 0.7510 (tt0) cc_final: 0.7240 (tt0) REVERT: C 793 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: C 873 THR cc_start: 0.8541 (p) cc_final: 0.8240 (t) REVERT: C 971 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: C 978 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7351 (mptp) REVERT: C 998 LEU cc_start: 0.7063 (tp) cc_final: 0.6702 (tp) REVERT: I 116 ASP cc_start: 0.3462 (OUTLIER) cc_final: 0.2915 (t70) REVERT: J 66 SER cc_start: 0.1123 (OUTLIER) cc_final: 0.0243 (m) REVERT: R 13 GLN cc_start: 0.3220 (OUTLIER) cc_final: 0.2901 (pp30) outliers start: 150 outliers final: 68 residues processed: 404 average time/residue: 0.9696 time to fit residues: 517.8091 Evaluate side-chains 335 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 245 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1085 GLN Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 558 ASN Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1100 LYS Chi-restraints excluded: chain B residue 1106 GLU Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1127 GLN Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain B residue 1147 VAL Chi-restraints excluded: chain P residue 188 SER Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 793 GLN Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 971 GLN Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 978 LYS Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain R residue 13 GLN Chi-restraints excluded: chain R residue 74 SER Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 178 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 456 optimal weight: 0.5980 chunk 311 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 408 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 467 optimal weight: 0.8980 chunk 378 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 279 optimal weight: 0.6980 chunk 491 optimal weight: 30.0000 chunk 138 optimal weight: 6.9990 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 HIS H 179 HIS ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN C1024 GLN ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4218 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 45393 Z= 0.422 Angle : 0.684 13.620 61761 Z= 0.356 Chirality : 0.050 0.269 6999 Planarity : 0.006 0.090 7962 Dihedral : 5.198 45.528 6219 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.10 % Favored : 95.88 % Rotamer: Outliers : 2.96 % Allowed : 14.60 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.49 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.11), residues: 5664 helix: 1.20 (0.19), residues: 677 sheet: 0.78 (0.12), residues: 1855 loop : -1.02 (0.11), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 450 HIS 0.009 0.001 HIS B 519 PHE 0.024 0.002 PHE H 27 TYR 0.024 0.002 TYR B 279 ARG 0.011 0.001 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 272 time to evaluate : 3.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7855 (t) cc_final: 0.7465 (m) REVERT: A 232 GLN cc_start: 0.8623 (tt0) cc_final: 0.7793 (pm20) REVERT: A 283 TYR cc_start: 0.7614 (m-10) cc_final: 0.7052 (m-80) REVERT: A 319 SER cc_start: 0.8806 (t) cc_final: 0.8406 (p) REVERT: A 578 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.6835 (mp10) REVERT: A 660 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7367 (mtp180) REVERT: A 754 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6729 (ttm) REVERT: A 768 LEU cc_start: 0.8210 (tt) cc_final: 0.7776 (mp) REVERT: A 787 GLU cc_start: 0.7248 (tt0) cc_final: 0.6970 (tt0) REVERT: A 808 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7793 (tp) REVERT: A 834 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7260 (OUTLIER) REVERT: A 1012 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7972 (t) REVERT: A 1125 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: B 68 GLN cc_start: 0.7403 (tm-30) cc_final: 0.7114 (tp40) REVERT: B 140 VAL cc_start: 0.6247 (t) cc_final: 0.5978 (m) REVERT: B 214 TYR cc_start: 0.6365 (OUTLIER) cc_final: 0.5779 (t80) REVERT: B 232 GLN cc_start: 0.8056 (tt0) cc_final: 0.7536 (mt0) REVERT: B 558 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.7895 (m-40) REVERT: B 574 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7596 (mp) REVERT: B 660 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7312 (mtm180) REVERT: B 711 MET cc_start: 0.8455 (ptm) cc_final: 0.8240 (ptm) REVERT: B 787 GLU cc_start: 0.7312 (tt0) cc_final: 0.7079 (tt0) REVERT: B 808 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7927 (mm) REVERT: B 834 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: B 1100 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7590 (mtmp) REVERT: B 1127 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7925 (mm110) REVERT: P 84 MET cc_start: -0.0040 (ptp) cc_final: -0.0280 (ptp) REVERT: Q 188 GLU cc_start: 0.2301 (mp0) cc_final: 0.1579 (pm20) REVERT: E 117 MET cc_start: 0.0975 (OUTLIER) cc_final: 0.0359 (pp-130) REVERT: F 190 LYS cc_start: 0.3045 (pttp) cc_final: 0.1842 (mmtm) REVERT: C 82 HIS cc_start: 0.5373 (OUTLIER) cc_final: 0.5052 (p90) REVERT: C 167 MET cc_start: -0.0200 (pp-130) cc_final: -0.2299 (tpt) REVERT: C 187 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7586 (mm-40) REVERT: C 202 ASN cc_start: 0.6761 (m-40) cc_final: 0.6066 (m110) REVERT: C 577 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.6015 (mm-40) REVERT: C 672 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8195 (p0) REVERT: C 776 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: C 787 GLU cc_start: 0.7517 (tt0) cc_final: 0.7247 (tt0) REVERT: C 793 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: C 873 THR cc_start: 0.8552 (p) cc_final: 0.8249 (t) REVERT: C 971 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: C 978 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7358 (mptp) REVERT: I 116 ASP cc_start: 0.3379 (OUTLIER) cc_final: 0.2885 (t70) REVERT: J 66 SER cc_start: 0.1233 (OUTLIER) cc_final: 0.0389 (m) REVERT: R 13 GLN cc_start: 0.3176 (OUTLIER) cc_final: 0.2924 (pp30) REVERT: R 109 PHE cc_start: 0.3143 (OUTLIER) cc_final: 0.2778 (m-80) outliers start: 146 outliers final: 81 residues processed: 394 average time/residue: 0.9717 time to fit residues: 505.5653 Evaluate side-chains 357 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 250 time to evaluate : 3.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 578 GLN Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 558 ASN Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 834 ASP Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 886 GLN Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1005 VAL Chi-restraints excluded: chain B residue 1100 LYS Chi-restraints excluded: chain B residue 1106 GLU Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1127 GLN Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain B residue 1147 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 188 SER Chi-restraints excluded: chain P residue 230 SER Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 793 GLN Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 971 GLN Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 978 LYS Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain R residue 13 GLN Chi-restraints excluded: chain R residue 74 SER Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 109 PHE Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 178 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 184 optimal weight: 30.0000 chunk 493 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 321 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 548 optimal weight: 40.0000 chunk 455 optimal weight: 0.5980 chunk 253 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 181 optimal weight: 20.0000 chunk 288 optimal weight: 0.6980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 GLN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN B 971 GLN ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN C 95 ASN ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN C1024 GLN ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4206 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 45393 Z= 0.308 Angle : 0.638 14.424 61761 Z= 0.330 Chirality : 0.047 0.255 6999 Planarity : 0.005 0.090 7962 Dihedral : 4.983 46.224 6218 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.10 % Favored : 95.88 % Rotamer: Outliers : 2.70 % Allowed : 15.42 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.49 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.02 % 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: -0.13 (0.11), residues: 5664 helix: 1.32 (0.19), residues: 696 sheet: 0.76 (0.12), residues: 1908 loop : -1.00 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 450 HIS 0.005 0.001 HIS B 519 PHE 0.056 0.002 PHE B 182 TYR 0.032 0.002 TYR H 111 ARG 0.011 0.001 ARG C 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 266 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7851 (t) cc_final: 0.7459 (m) REVERT: A 232 GLN cc_start: 0.8620 (tt0) cc_final: 0.7775 (pm20) REVERT: A 283 TYR cc_start: 0.7610 (m-10) cc_final: 0.6955 (m-80) REVERT: A 319 SER cc_start: 0.8789 (t) cc_final: 0.8426 (p) REVERT: A 578 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.6905 (mp10) REVERT: A 660 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7438 (mtp180) REVERT: A 716 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7942 (tp30) REVERT: A 737 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8320 (t) REVERT: A 754 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6768 (ttm) REVERT: A 768 LEU cc_start: 0.8185 (tt) cc_final: 0.7787 (mp) REVERT: A 787 GLU cc_start: 0.7207 (tt0) cc_final: 0.6856 (tt0) REVERT: A 808 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7800 (tp) REVERT: A 834 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7019 (m-30) REVERT: A 1019 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7878 (mm-40) REVERT: A 1098 ASP cc_start: 0.8033 (t0) cc_final: 0.7641 (t0) REVERT: A 1125 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: B 68 GLN cc_start: 0.7436 (tm-30) cc_final: 0.7148 (tp40) REVERT: B 140 VAL cc_start: 0.6619 (t) cc_final: 0.6280 (m) REVERT: B 214 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.5820 (t80) REVERT: B 232 GLN cc_start: 0.7983 (tt0) cc_final: 0.7616 (mt0) REVERT: B 660 ARG cc_start: 0.7578 (mmp-170) cc_final: 0.7287 (mtm180) REVERT: B 711 MET cc_start: 0.8453 (ptm) cc_final: 0.8171 (ptm) REVERT: B 776 GLN cc_start: 0.8018 (mt0) cc_final: 0.7730 (mt0) REVERT: B 794 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7106 (pt0) REVERT: B 808 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7934 (mm) REVERT: B 834 ASP cc_start: 0.7718 (m-30) cc_final: 0.7417 (m-30) REVERT: B 1100 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7494 (mtmp) REVERT: Q 188 GLU cc_start: 0.2300 (mp0) cc_final: 0.1578 (pm20) REVERT: E 117 MET cc_start: 0.1051 (tpt) cc_final: 0.0641 (pp-130) REVERT: C 82 HIS cc_start: 0.5619 (OUTLIER) cc_final: 0.5197 (p90) REVERT: C 167 MET cc_start: -0.0190 (pp-130) cc_final: -0.2525 (tpt) REVERT: C 184 TYR cc_start: 0.6477 (t80) cc_final: 0.6263 (t80) REVERT: C 187 GLN cc_start: 0.7962 (tp-100) cc_final: 0.7508 (mm-40) REVERT: C 202 ASN cc_start: 0.6785 (m-40) cc_final: 0.6057 (m110) REVERT: C 585 ASP cc_start: 0.7560 (m-30) cc_final: 0.7226 (t70) REVERT: C 672 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8280 (p0) REVERT: C 674 TYR cc_start: 0.8121 (m-80) cc_final: 0.7906 (m-80) REVERT: C 776 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: C 787 GLU cc_start: 0.7466 (tt0) cc_final: 0.7206 (tt0) REVERT: C 793 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: C 978 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7269 (mptp) REVERT: I 116 ASP cc_start: 0.3169 (OUTLIER) cc_final: 0.2655 (t70) REVERT: J 66 SER cc_start: 0.0914 (OUTLIER) cc_final: 0.0307 (m) REVERT: R 13 GLN cc_start: 0.3102 (OUTLIER) cc_final: 0.2843 (pp30) REVERT: R 109 PHE cc_start: 0.3183 (OUTLIER) cc_final: 0.2831 (m-80) REVERT: S 183 LEU cc_start: 0.0823 (OUTLIER) cc_final: 0.0474 (tp) outliers start: 132 outliers final: 75 residues processed: 373 average time/residue: 0.9770 time to fit residues: 481.3935 Evaluate side-chains 342 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 245 time to evaluate : 3.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 578 GLN Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 886 GLN Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1005 VAL Chi-restraints excluded: chain B residue 1100 LYS Chi-restraints excluded: chain B residue 1106 GLU Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 188 SER Chi-restraints excluded: chain P residue 230 SER Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 793 GLN Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 978 LYS Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain R residue 13 GLN Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 109 PHE Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain S residue 34 HIS Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 528 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 312 optimal weight: 20.0000 chunk 400 optimal weight: 0.9990 chunk 310 optimal weight: 10.0000 chunk 461 optimal weight: 2.9990 chunk 306 optimal weight: 10.0000 chunk 546 optimal weight: 0.5980 chunk 342 optimal weight: 10.0000 chunk 333 optimal weight: 8.9990 chunk 252 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN H 179 HIS ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN B 971 GLN ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN C1024 GLN ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4200 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 45393 Z= 0.268 Angle : 0.619 13.953 61761 Z= 0.319 Chirality : 0.046 0.245 6999 Planarity : 0.005 0.091 7962 Dihedral : 4.868 45.867 6218 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 2.78 % Allowed : 15.75 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.49 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.02 % 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: -0.08 (0.11), residues: 5664 helix: 1.44 (0.20), residues: 706 sheet: 0.82 (0.12), residues: 1904 loop : -1.01 (0.11), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 450 HIS 0.004 0.001 HIS H 103 PHE 0.026 0.002 PHE H 27 TYR 0.023 0.002 TYR B 184 ARG 0.010 0.001 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 270 time to evaluate : 3.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7827 (t) cc_final: 0.7407 (m) REVERT: A 232 GLN cc_start: 0.8640 (tt0) cc_final: 0.7784 (pm20) REVERT: A 283 TYR cc_start: 0.7591 (m-10) cc_final: 0.6964 (m-80) REVERT: A 319 SER cc_start: 0.8788 (t) cc_final: 0.8453 (p) REVERT: A 660 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7385 (mtp180) REVERT: A 716 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7921 (tp30) REVERT: A 737 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8349 (t) REVERT: A 754 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6746 (ttm) REVERT: A 768 LEU cc_start: 0.8207 (tt) cc_final: 0.7804 (mp) REVERT: A 787 GLU cc_start: 0.7220 (tt0) cc_final: 0.6862 (tt0) REVERT: A 808 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7798 (tp) REVERT: A 834 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6999 (m-30) REVERT: A 1019 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7853 (mm-40) REVERT: A 1098 ASP cc_start: 0.8006 (t0) cc_final: 0.7631 (t0) REVERT: A 1125 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: N 100 PHE cc_start: 0.5212 (m-80) cc_final: 0.4133 (t80) REVERT: B 68 GLN cc_start: 0.7443 (tm-30) cc_final: 0.7164 (tp-100) REVERT: B 140 VAL cc_start: 0.6650 (t) cc_final: 0.6421 (m) REVERT: B 214 TYR cc_start: 0.6292 (OUTLIER) cc_final: 0.5784 (t80) REVERT: B 232 GLN cc_start: 0.7922 (tt0) cc_final: 0.7541 (mt0) REVERT: B 660 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7284 (mtm180) REVERT: B 711 MET cc_start: 0.8466 (ptm) cc_final: 0.8244 (ptm) REVERT: B 776 GLN cc_start: 0.8001 (mt0) cc_final: 0.7704 (mt0) REVERT: B 794 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7123 (pt0) REVERT: B 808 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7936 (mm) REVERT: B 834 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: B 997 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6461 (ttp-110) REVERT: B 1100 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7488 (mtmp) REVERT: B 1127 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7854 (mm110) REVERT: Q 188 GLU cc_start: 0.2211 (mp0) cc_final: 0.1523 (pm20) REVERT: E 52 TYR cc_start: 0.2361 (m-10) cc_final: 0.1717 (m-10) REVERT: E 117 MET cc_start: 0.0947 (tpt) cc_final: 0.0571 (pp-130) REVERT: F 4 MET cc_start: 0.1414 (mtm) cc_final: 0.0747 (mmm) REVERT: F 190 LYS cc_start: 0.2958 (pttp) cc_final: 0.1767 (mmtm) REVERT: C 82 HIS cc_start: 0.5543 (OUTLIER) cc_final: 0.5087 (p90) REVERT: C 167 MET cc_start: -0.0171 (pp-130) cc_final: -0.2481 (tpt) REVERT: C 187 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7476 (mm-40) REVERT: C 672 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8281 (p0) REVERT: C 674 TYR cc_start: 0.8097 (m-80) cc_final: 0.7889 (m-80) REVERT: C 776 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: C 787 GLU cc_start: 0.7409 (tt0) cc_final: 0.7160 (tt0) REVERT: C 793 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: C 971 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: C 978 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7306 (mptp) REVERT: C 998 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6775 (tp) REVERT: J 66 SER cc_start: 0.0719 (OUTLIER) cc_final: 0.0363 (m) REVERT: R 13 GLN cc_start: 0.3037 (OUTLIER) cc_final: 0.2824 (pp30) REVERT: R 109 PHE cc_start: 0.3145 (OUTLIER) cc_final: 0.2795 (m-80) REVERT: S 183 LEU cc_start: 0.0977 (OUTLIER) cc_final: 0.0603 (tp) outliers start: 136 outliers final: 78 residues processed: 377 average time/residue: 0.9396 time to fit residues: 470.6534 Evaluate side-chains 356 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 252 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 834 ASP Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 886 GLN Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 997 ARG Chi-restraints excluded: chain B residue 1005 VAL Chi-restraints excluded: chain B residue 1100 LYS Chi-restraints excluded: chain B residue 1106 GLU Chi-restraints excluded: chain B residue 1127 GLN Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain B residue 1147 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 188 SER Chi-restraints excluded: chain P residue 230 SER Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 793 GLN Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 971 GLN Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 978 LYS Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain C residue 1147 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain R residue 13 GLN Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 109 PHE Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain S residue 34 HIS Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 338 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 326 optimal weight: 20.0000 chunk 164 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 347 optimal weight: 5.9990 chunk 372 optimal weight: 30.0000 chunk 270 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 429 optimal weight: 0.6980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN L 125 GLN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS N 191 HIS B 139 ASN B 202 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 ASN P 1 GLN F 149 GLN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN C1024 GLN ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4233 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 45393 Z= 0.403 Angle : 0.682 14.157 61761 Z= 0.352 Chirality : 0.049 0.264 6999 Planarity : 0.005 0.091 7962 Dihedral : 5.114 46.354 6218 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.49 % Favored : 95.50 % Rotamer: Outliers : 2.68 % Allowed : 16.33 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.49 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 5664 helix: 1.15 (0.19), residues: 687 sheet: 0.71 (0.12), residues: 1876 loop : -1.07 (0.11), residues: 3101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 450 HIS 0.013 0.001 HIS B 519 PHE 0.024 0.002 PHE H 27 TYR 0.028 0.002 TYR H 111 ARG 0.008 0.001 ARG C1009 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 266 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7915 (t) cc_final: 0.7421 (m) REVERT: A 232 GLN cc_start: 0.8569 (tt0) cc_final: 0.7729 (pm20) REVERT: A 283 TYR cc_start: 0.7651 (m-10) cc_final: 0.6909 (m-80) REVERT: A 319 SER cc_start: 0.8818 (t) cc_final: 0.8419 (p) REVERT: A 578 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.6898 (mp10) REVERT: A 660 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7377 (mtp180) REVERT: A 716 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7929 (tp30) REVERT: A 754 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6716 (ttm) REVERT: A 768 LEU cc_start: 0.8153 (tt) cc_final: 0.7760 (mp) REVERT: A 787 GLU cc_start: 0.7242 (tt0) cc_final: 0.6939 (tt0) REVERT: A 808 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7791 (tp) REVERT: A 834 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7320 (m-30) REVERT: N 100 PHE cc_start: 0.5196 (m-80) cc_final: 0.4201 (t80) REVERT: B 68 GLN cc_start: 0.7437 (tm-30) cc_final: 0.7122 (tp-100) REVERT: B 140 VAL cc_start: 0.6693 (t) cc_final: 0.6399 (m) REVERT: B 232 GLN cc_start: 0.7871 (tt0) cc_final: 0.7563 (mt0) REVERT: B 378 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6720 (t70) REVERT: B 588 ASP cc_start: 0.7408 (t0) cc_final: 0.7164 (t0) REVERT: B 660 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7315 (mtm180) REVERT: B 794 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7093 (pt0) REVERT: B 808 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7958 (mm) REVERT: B 834 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: B 997 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6499 (ttp-110) REVERT: B 1127 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7877 (mm110) REVERT: Q 188 GLU cc_start: 0.2010 (mp0) cc_final: 0.1362 (pm20) REVERT: F 4 MET cc_start: 0.1570 (mtm) cc_final: 0.0851 (mmm) REVERT: C 82 HIS cc_start: 0.5511 (OUTLIER) cc_final: 0.4993 (p90) REVERT: C 167 MET cc_start: -0.0029 (pp-130) cc_final: -0.2306 (tpt) REVERT: C 187 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7793 (mm-40) REVERT: C 577 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7503 (mt0) REVERT: C 600 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7369 (m-30) REVERT: C 776 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7534 (mm110) REVERT: C 787 GLU cc_start: 0.7544 (tt0) cc_final: 0.7287 (tt0) REVERT: C 793 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: C 927 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8339 (pt0) REVERT: C 971 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: C 978 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7356 (mptp) REVERT: J 66 SER cc_start: 0.0711 (OUTLIER) cc_final: 0.0389 (m) REVERT: R 109 PHE cc_start: 0.3145 (OUTLIER) cc_final: 0.2931 (m-80) REVERT: S 183 LEU cc_start: 0.1255 (OUTLIER) cc_final: 0.0863 (tp) outliers start: 131 outliers final: 79 residues processed: 371 average time/residue: 0.9351 time to fit residues: 461.1181 Evaluate side-chains 345 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 242 time to evaluate : 3.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 578 GLN Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 834 ASP Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 886 GLN Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 997 ARG Chi-restraints excluded: chain B residue 1005 VAL Chi-restraints excluded: chain B residue 1106 GLU Chi-restraints excluded: chain B residue 1127 GLN Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain B residue 1147 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 188 SER Chi-restraints excluded: chain P residue 230 SER Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 793 GLN Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 927 GLN Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 971 GLN Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 978 LYS Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain C residue 1147 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 109 PHE Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain S residue 34 HIS Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 497 optimal weight: 50.0000 chunk 523 optimal weight: 0.9990 chunk 477 optimal weight: 0.9990 chunk 509 optimal weight: 10.0000 chunk 306 optimal weight: 30.0000 chunk 221 optimal weight: 4.9990 chunk 399 optimal weight: 0.8980 chunk 156 optimal weight: 30.0000 chunk 460 optimal weight: 3.9990 chunk 481 optimal weight: 0.2980 chunk 507 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS H 214 ASN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 GLN F 149 GLN C 95 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4203 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 45393 Z= 0.240 Angle : 0.615 13.697 61761 Z= 0.315 Chirality : 0.046 0.254 6999 Planarity : 0.005 0.093 7962 Dihedral : 4.820 45.964 6217 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 2.18 % Allowed : 17.01 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.49 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.02 % 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: -0.09 (0.11), residues: 5664 helix: 1.40 (0.20), residues: 712 sheet: 0.81 (0.12), residues: 1877 loop : -1.00 (0.11), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 36 HIS 0.013 0.001 HIS B 519 PHE 0.027 0.002 PHE H 27 TYR 0.024 0.001 TYR N 142 ARG 0.011 0.001 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 262 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7881 (t) cc_final: 0.7419 (m) REVERT: A 232 GLN cc_start: 0.8567 (tt0) cc_final: 0.7752 (pm20) REVERT: A 283 TYR cc_start: 0.7643 (m-10) cc_final: 0.6930 (m-80) REVERT: A 298 THR cc_start: 0.7371 (OUTLIER) cc_final: 0.7018 (t) REVERT: A 319 SER cc_start: 0.8794 (t) cc_final: 0.8464 (p) REVERT: A 578 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7036 (mp10) REVERT: A 660 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7440 (mtp180) REVERT: A 754 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6797 (ttm) REVERT: A 768 LEU cc_start: 0.8157 (tt) cc_final: 0.7802 (mp) REVERT: A 787 GLU cc_start: 0.7203 (tt0) cc_final: 0.6852 (tt0) REVERT: A 800 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7588 (pmtt) REVERT: A 808 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7876 (tp) REVERT: A 834 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6875 (m-30) REVERT: A 1019 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7773 (mm-40) REVERT: A 1098 ASP cc_start: 0.7948 (t0) cc_final: 0.7571 (OUTLIER) REVERT: N 100 PHE cc_start: 0.5225 (m-80) cc_final: 0.4233 (t80) REVERT: B 68 GLN cc_start: 0.7430 (tm-30) cc_final: 0.7144 (tp-100) REVERT: B 167 MET cc_start: 0.1511 (pmm) cc_final: 0.1141 (pmm) REVERT: B 184 TYR cc_start: 0.6616 (t80) cc_final: 0.6390 (t80) REVERT: B 232 GLN cc_start: 0.7872 (tt0) cc_final: 0.7627 (mt0) REVERT: B 378 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6711 (t70) REVERT: B 588 ASP cc_start: 0.7441 (t0) cc_final: 0.7125 (t0) REVERT: B 660 ARG cc_start: 0.7577 (mmp-170) cc_final: 0.7281 (mtm180) REVERT: B 794 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7159 (pt0) REVERT: B 808 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7917 (mm) REVERT: B 834 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: B 997 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6506 (ttp-110) REVERT: B 1127 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7854 (mm110) REVERT: P 84 MET cc_start: 0.0124 (ptp) cc_final: -0.0147 (ptp) REVERT: Q 188 GLU cc_start: 0.2085 (mp0) cc_final: 0.1364 (pm20) REVERT: F 4 MET cc_start: 0.1319 (mtm) cc_final: 0.0680 (mmm) REVERT: C 140 VAL cc_start: 0.6427 (t) cc_final: 0.6164 (t) REVERT: C 187 GLN cc_start: 0.8089 (tp-100) cc_final: 0.7816 (mm-40) REVERT: C 674 TYR cc_start: 0.8140 (m-80) cc_final: 0.7829 (m-80) REVERT: C 776 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7536 (mm110) REVERT: C 787 GLU cc_start: 0.7402 (tt0) cc_final: 0.7147 (tt0) REVERT: C 808 ILE cc_start: 0.8624 (mm) cc_final: 0.8320 (tp) REVERT: J 66 SER cc_start: 0.0796 (OUTLIER) cc_final: 0.0514 (m) REVERT: R 109 PHE cc_start: 0.3016 (OUTLIER) cc_final: 0.2728 (m-80) outliers start: 106 outliers final: 69 residues processed: 341 average time/residue: 0.9666 time to fit residues: 436.3205 Evaluate side-chains 335 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 251 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 578 GLN Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 800 LYS Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 834 ASP Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 886 GLN Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 997 ARG Chi-restraints excluded: chain B residue 1106 GLU Chi-restraints excluded: chain B residue 1127 GLN Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 188 SER Chi-restraints excluded: chain P residue 230 SER Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1147 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 109 PHE Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain S residue 34 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 334 optimal weight: 30.0000 chunk 538 optimal weight: 50.0000 chunk 328 optimal weight: 9.9990 chunk 255 optimal weight: 5.9990 chunk 374 optimal weight: 5.9990 chunk 564 optimal weight: 9.9990 chunk 519 optimal weight: 3.9990 chunk 449 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 275 optimal weight: 0.4980 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS F 149 GLN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1024 GLN ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4251 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 45393 Z= 0.482 Angle : 0.716 13.949 61761 Z= 0.374 Chirality : 0.052 0.462 6999 Planarity : 0.006 0.094 7962 Dihedral : 5.189 46.821 6217 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 95.00 % Rotamer: Outliers : 2.26 % Allowed : 17.25 % Favored : 80.49 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 8.49 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.04 % 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: -0.36 (0.11), residues: 5664 helix: 0.92 (0.19), residues: 690 sheet: 0.66 (0.12), residues: 1844 loop : -1.09 (0.11), residues: 3130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP L 36 HIS 0.010 0.001 HIS B 519 PHE 0.122 0.003 PHE C 182 TYR 0.041 0.002 TYR C 184 ARG 0.010 0.001 ARG A 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 254 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLN cc_start: 0.8539 (tt0) cc_final: 0.7770 (pm20) REVERT: A 283 TYR cc_start: 0.7663 (m-10) cc_final: 0.6913 (m-80) REVERT: A 319 SER cc_start: 0.8825 (t) cc_final: 0.8390 (p) REVERT: A 578 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.6979 (mp10) REVERT: A 660 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7392 (mtp180) REVERT: A 754 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6707 (ttm) REVERT: A 787 GLU cc_start: 0.7260 (tt0) cc_final: 0.6953 (tt0) REVERT: A 800 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7706 (pmtt) REVERT: A 808 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7789 (tp) REVERT: A 834 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7385 (m-30) REVERT: A 1125 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: B 68 GLN cc_start: 0.7405 (tm-30) cc_final: 0.7081 (tp-100) REVERT: B 167 MET cc_start: 0.1515 (pmm) cc_final: 0.1215 (pmm) REVERT: B 378 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.6800 (t70) REVERT: B 588 ASP cc_start: 0.7395 (t0) cc_final: 0.7189 (t0) REVERT: B 660 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7324 (mtm180) REVERT: B 776 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: B 794 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7095 (pt0) REVERT: B 834 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: B 997 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6528 (ttp-110) REVERT: B 1127 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7928 (mm110) REVERT: Q 188 GLU cc_start: 0.2241 (mp0) cc_final: 0.1508 (pm20) REVERT: F 4 MET cc_start: 0.1434 (mtm) cc_final: 0.0656 (mmm) REVERT: C 187 GLN cc_start: 0.7929 (tp-100) cc_final: 0.7632 (mm-40) REVERT: C 519 HIS cc_start: 0.3053 (OUTLIER) cc_final: 0.2764 (m170) REVERT: C 560 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7060 (pt) REVERT: C 600 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7386 (m-30) REVERT: C 776 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7538 (mm110) REVERT: C 787 GLU cc_start: 0.7539 (tt0) cc_final: 0.7277 (tt0) REVERT: J 66 SER cc_start: 0.0631 (OUTLIER) cc_final: 0.0383 (m) REVERT: S 149 GLN cc_start: 0.3148 (tp-100) cc_final: 0.2944 (pt0) REVERT: S 183 LEU cc_start: 0.1532 (OUTLIER) cc_final: 0.1127 (tp) outliers start: 110 outliers final: 71 residues processed: 339 average time/residue: 0.9219 time to fit residues: 418.1587 Evaluate side-chains 335 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 244 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 578 GLN Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 800 LYS Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 776 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 834 ASP Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 886 GLN Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 997 ARG Chi-restraints excluded: chain B residue 1106 GLU Chi-restraints excluded: chain B residue 1127 GLN Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain B residue 1147 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 188 SER Chi-restraints excluded: chain P residue 230 SER Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1147 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain S residue 34 HIS Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 357 optimal weight: 4.9990 chunk 479 optimal weight: 0.7980 chunk 137 optimal weight: 40.0000 chunk 414 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 125 optimal weight: 40.0000 chunk 450 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 462 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.220566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.205896 restraints weight = 107027.610| |-----------------------------------------------------------------------------| r_work (start): 0.4616 rms_B_bonded: 1.13 r_work: 0.4160 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3915 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work: 0.3825 rms_B_bonded: 4.37 restraints_weight: 0.1250 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 45393 Z= 0.250 Angle : 0.639 14.823 61761 Z= 0.331 Chirality : 0.047 0.413 6999 Planarity : 0.005 0.091 7962 Dihedral : 4.909 46.773 6217 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.67 % Favored : 96.31 % Rotamer: Outliers : 1.90 % Allowed : 17.75 % Favored : 80.35 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 8.49 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.04 % 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: -0.17 (0.11), residues: 5664 helix: 1.29 (0.20), residues: 707 sheet: 0.73 (0.12), residues: 1876 loop : -1.03 (0.11), residues: 3081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP L 36 HIS 0.011 0.001 HIS B 519 PHE 0.127 0.002 PHE A 182 TYR 0.027 0.001 TYR H 111 ARG 0.010 0.001 ARG A 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11660.90 seconds wall clock time: 204 minutes 24.55 seconds (12264.55 seconds total)