Starting phenix.real_space_refine on Sun Mar 10 21:18:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpq_34940/03_2024/8hpq_34940.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpq_34940/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpq_34940/03_2024/8hpq_34940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpq_34940/03_2024/8hpq_34940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpq_34940/03_2024/8hpq_34940.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpq_34940/03_2024/8hpq_34940.pdb" } 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 Residue "A GLU 485": "OE1" <-> "OE2" Residue "A TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 25.75, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1201 " - " ASN A 357 " " NAG B1201 " - " ASN B 357 " " NAG C1201 " - " ASN C 357 " Time building additional restraints: 13.19 Conformation dependent library (CDL) restraints added in 9.4 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: 4.34 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: 20.88 Time building geometry restraints manager: 14.61 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: 35.54 - 60.72: 3 60.72 - 85.90: 1 85.90 - 111.07: 17699 111.07 - 136.25: 44044 136.25 - 161.42: 14 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: 1.40 - 2.10: 14 2.10 - 2.80: 11642 2.80 - 3.50: 57650 3.50 - 4.20: 108519 4.20 - 4.90: 186952 Nonbonded interactions: 364777 Sorted by model distance: nonbonded pdb=" ND2 ASN A 374 " pdb=" CE1 PHE C 182 " model vdw 1.403 3.420 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=" CE1 PHE A 182 " pdb=" ND2 ASN B 374 " model vdw 1.662 3.420 ... (remaining 364772 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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: 5.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.030 Extract box with map and model: 27.430 Check model and map are aligned: 0.500 Set scattering table: 0.340 Process input model: 110.070 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.890 ------------------------------------------------------------------------------- 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= 0.740 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 : 1.403 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 fitting. rotamer outliers: 29 poor density : 748 time to evaluate : 3.714 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: 1.0548 time to fit residues: 1040.6615 Evaluate side-chains 317 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 309 time to evaluate : 3.741 ------------------------------------------------------------------------------- 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: 0.6980 chunk 429 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 289 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 444 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 270 optimal weight: 0.8980 chunk 330 optimal weight: 30.0000 chunk 514 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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** ** 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 E 73 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN F 126 GLN F 149 GLN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN C 507 GLN ** 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** R 73 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4129 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 45393 Z= 0.412 Angle : 0.743 16.062 61761 Z= 0.390 Chirality : 0.051 0.315 6999 Planarity : 0.006 0.089 7962 Dihedral : 5.669 52.925 6233 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.00 % Allowed : 9.48 % Favored : 87.52 % Cbeta Deviations : 0.00 % 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: -0.15 (0.11), residues: 5664 helix: 0.91 (0.19), residues: 703 sheet: 0.77 (0.12), residues: 1904 loop : -0.92 (0.11), residues: 3057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 900 HIS 0.012 0.002 HIS C 968 PHE 0.029 0.003 PHE S 71 TYR 0.027 0.002 TYR B 279 ARG 0.009 0.001 ARG C 371 *********************** 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 548 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 400 time to evaluate : 3.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7564 (t) cc_final: 0.7303 (m) REVERT: A 67 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7310 (p) REVERT: A 70 LEU cc_start: 0.7698 (mm) cc_final: 0.7357 (mm) REVERT: A 232 GLN cc_start: 0.8435 (tt0) cc_final: 0.7317 (pm20) REVERT: A 283 TYR cc_start: 0.7495 (m-10) cc_final: 0.6956 (m-80) REVERT: A 295 GLU cc_start: 0.6360 (pp20) cc_final: 0.6153 (pp20) REVERT: A 319 SER cc_start: 0.8761 (t) cc_final: 0.8384 (p) REVERT: A 660 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7213 (mtp180) REVERT: A 754 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6601 (ttm) REVERT: A 768 LEU cc_start: 0.7964 (tt) cc_final: 0.7284 (mp) REVERT: A 787 GLU cc_start: 0.7348 (tt0) cc_final: 0.6940 (tt0) REVERT: A 1085 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8626 (mt0) REVERT: N 39 LYS cc_start: 0.2444 (OUTLIER) cc_final: 0.2066 (mmmt) REVERT: N 162 GLN cc_start: 0.0713 (mm-40) cc_final: -0.0006 (tm130) REVERT: B 68 GLN cc_start: 0.7380 (tm-30) cc_final: 0.7128 (tp40) REVERT: B 232 GLN cc_start: 0.7951 (tt0) cc_final: 0.7106 (mt0) REVERT: B 754 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7110 (ttm) REVERT: B 787 GLU cc_start: 0.7330 (tt0) cc_final: 0.7107 (tt0) REVERT: B 794 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: B 808 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7893 (mm) REVERT: B 828 LYS cc_start: 0.7745 (mmtm) cc_final: 0.7480 (ttmt) REVERT: P 188 SER cc_start: 0.3027 (p) cc_final: 0.2419 (t) REVERT: E 117 MET cc_start: 0.0942 (OUTLIER) cc_final: 0.0173 (pp-130) REVERT: F 151 LYS cc_start: 0.0610 (OUTLIER) cc_final: -0.0420 (mttt) REVERT: C 82 HIS cc_start: 0.4778 (OUTLIER) cc_final: 0.4493 (p90) REVERT: C 202 ASN cc_start: 0.6974 (m-40) cc_final: 0.6560 (m-40) REVERT: C 574 LEU cc_start: 0.7683 (mt) cc_final: 0.7294 (mp) REVERT: C 579 PHE cc_start: 0.7612 (p90) cc_final: 0.7379 (p90) REVERT: C 598 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7204 (mm) REVERT: C 600 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: C 787 GLU cc_start: 0.7434 (tt0) cc_final: 0.7195 (tt0) REVERT: C 873 THR cc_start: 0.8573 (p) cc_final: 0.8230 (t) REVERT: C 964 ASP cc_start: 0.7284 (m-30) cc_final: 0.6966 (m-30) REVERT: J 63 PHE cc_start: 0.2004 (m-80) cc_final: 0.1746 (m-80) outliers start: 148 outliers final: 60 residues processed: 507 average time/residue: 0.9620 time to fit residues: 641.7958 Evaluate side-chains 354 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 281 time to evaluate : 3.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 202 ASN 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 464 ASN 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 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 953 SER 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 22 CYS Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 75 ILE 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 587 THR Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 759 ASP 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 948 ILE Chi-restraints excluded: chain B residue 975 THR 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 Q residue 5 THR 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 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: 1.9990 chunk 159 optimal weight: 0.1980 chunk 428 optimal weight: 0.0470 chunk 350 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 515 optimal weight: 20.0000 chunk 557 optimal weight: 6.9990 chunk 459 optimal weight: 1.9990 chunk 511 optimal weight: 0.9980 chunk 175 optimal weight: 20.0000 chunk 413 optimal weight: 4.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 73 ASN ** M 81 GLN ** 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 818 GLN B 949 GLN B 969 ASN B 971 GLN B1016 GLN E 180 GLN F 34 HIS F 149 GLN C 82 HIS ** 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** ** R 180 GLN ** 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: 0.4112 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 45393 Z= 0.208 Angle : 0.606 14.732 61761 Z= 0.312 Chirality : 0.045 0.225 6999 Planarity : 0.005 0.087 7962 Dihedral : 4.945 44.191 6219 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.96 % Allowed : 12.74 % Favored : 85.30 % Cbeta Deviations : 0.00 % 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: 0.14 (0.11), residues: 5664 helix: 1.64 (0.19), residues: 689 sheet: 0.86 (0.12), residues: 1891 loop : -0.79 (0.11), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 450 HIS 0.011 0.001 HIS B 221 PHE 0.026 0.002 PHE H 27 TYR 0.033 0.001 TYR H 96 ARG 0.011 0.000 ARG B 204 *********************** 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 402 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 306 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7464 (t) cc_final: 0.7223 (m) REVERT: A 67 THR cc_start: 0.7586 (OUTLIER) cc_final: 0.7316 (p) REVERT: A 143 LYS cc_start: 0.7005 (mtmt) cc_final: 0.6627 (tttm) REVERT: A 203 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6192 (tt) REVERT: A 232 GLN cc_start: 0.8410 (tt0) cc_final: 0.7319 (pm20) REVERT: A 283 TYR cc_start: 0.7529 (m-10) cc_final: 0.6934 (m-80) REVERT: A 319 SER cc_start: 0.8730 (t) cc_final: 0.8402 (p) REVERT: A 600 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: A 768 LEU cc_start: 0.8049 (tt) cc_final: 0.7444 (mp) REVERT: A 787 GLU cc_start: 0.7214 (tt0) cc_final: 0.6939 (tt0) REVERT: A 808 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7841 (tp) REVERT: A 834 ASP cc_start: 0.6905 (t0) cc_final: 0.6468 (m-30) REVERT: A 1098 ASP cc_start: 0.7878 (t0) cc_final: 0.7555 (t0) REVERT: N 100 PHE cc_start: 0.4780 (OUTLIER) cc_final: 0.3917 (t80) REVERT: B 68 GLN cc_start: 0.7401 (tm-30) cc_final: 0.7186 (tp40) REVERT: B 214 TYR cc_start: 0.6258 (OUTLIER) cc_final: 0.5147 (t80) REVERT: B 232 GLN cc_start: 0.7920 (tt0) cc_final: 0.7131 (mt0) REVERT: B 597 GLU cc_start: 0.7439 (tp30) cc_final: 0.7221 (tt0) REVERT: B 794 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7124 (pt0) REVERT: B 808 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7919 (mm) REVERT: B 828 LYS cc_start: 0.7796 (mmtm) cc_final: 0.7563 (ttmt) REVERT: B 994 ILE cc_start: 0.6303 (mt) cc_final: 0.6022 (mp) REVERT: B 1052 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8262 (mmtm) REVERT: E 34 MET cc_start: 0.4031 (mmm) cc_final: 0.3035 (mmm) REVERT: E 117 MET cc_start: 0.1049 (tpt) cc_final: 0.0180 (pp-130) REVERT: F 149 GLN cc_start: 0.5515 (OUTLIER) cc_final: 0.5257 (pt0) REVERT: F 151 LYS cc_start: 0.0555 (OUTLIER) cc_final: -0.0355 (mttt) REVERT: C 82 HIS cc_start: 0.5114 (OUTLIER) cc_final: 0.4681 (p-80) REVERT: C 167 MET cc_start: 0.0991 (pp-130) cc_final: 0.0473 (tmm) REVERT: C 202 ASN cc_start: 0.6879 (m-40) cc_final: 0.6404 (m110) REVERT: C 574 LEU cc_start: 0.7772 (mt) cc_final: 0.7547 (mp) REVERT: C 579 PHE cc_start: 0.7524 (p90) cc_final: 0.7305 (p90) REVERT: C 674 TYR cc_start: 0.7814 (m-80) cc_final: 0.7326 (m-10) REVERT: C 787 GLU cc_start: 0.7303 (tt0) cc_final: 0.7032 (tt0) REVERT: C 873 THR cc_start: 0.8589 (p) cc_final: 0.8371 (t) REVERT: C 971 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: C 978 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7065 (mptp) REVERT: I 157 VAL cc_start: -0.1538 (OUTLIER) cc_final: -0.1784 (t) REVERT: J 66 SER cc_start: 0.1211 (OUTLIER) cc_final: 0.0335 (m) outliers start: 96 outliers final: 44 residues processed: 375 average time/residue: 0.8987 time to fit residues: 452.0745 Evaluate side-chains 321 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 262 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 203 LEU 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 600 ASP Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 192 THR 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 214 TYR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 545 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 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 975 THR Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1106 GLU Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain E residue 207 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 C residue 67 THR Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 186 SER 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 567 THR Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 971 GLN Chi-restraints excluded: chain C residue 978 LYS Chi-restraints excluded: chain C residue 1132 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 82 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 509 optimal weight: 9.9990 chunk 387 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 246 optimal weight: 5.9990 chunk 346 optimal weight: 3.9990 chunk 517 optimal weight: 6.9990 chunk 548 optimal weight: 9.9990 chunk 270 optimal weight: 0.9990 chunk 490 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 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** N 191 HIS B 210 ASN B 776 GLN ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN Q 167 GLN F 149 GLN 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 38 GLN J 39 GLN ** R 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4181 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 45393 Z= 0.375 Angle : 0.659 13.757 61761 Z= 0.342 Chirality : 0.048 0.207 6999 Planarity : 0.005 0.088 7962 Dihedral : 5.067 43.316 6219 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.70 % Allowed : 13.52 % Favored : 83.77 % 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: 0.03 (0.11), residues: 5664 helix: 1.48 (0.19), residues: 669 sheet: 0.86 (0.12), residues: 1882 loop : -0.87 (0.11), residues: 3113 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 0.024 0.002 PHE H 27 TYR 0.026 0.002 TYR B 279 ARG 0.011 0.001 ARG A 997 *********************** 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 422 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 289 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7643 (t) cc_final: 0.7358 (m) REVERT: A 67 THR cc_start: 0.7658 (p) cc_final: 0.7424 (p) REVERT: A 143 LYS cc_start: 0.7111 (mtmt) cc_final: 0.6580 (tttm) REVERT: A 232 GLN cc_start: 0.8542 (tt0) cc_final: 0.7630 (pm20) REVERT: A 283 TYR cc_start: 0.7558 (m-10) cc_final: 0.6926 (m-80) REVERT: A 319 SER cc_start: 0.8752 (t) cc_final: 0.8384 (p) REVERT: A 583 ILE cc_start: 0.8360 (mm) cc_final: 0.7985 (mm) REVERT: A 585 ASP cc_start: 0.6907 (m-30) cc_final: 0.6542 (t0) REVERT: A 600 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: A 660 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7351 (mtp180) REVERT: A 716 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7859 (tp30) REVERT: A 754 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6759 (ttm) REVERT: A 768 LEU cc_start: 0.8174 (tt) cc_final: 0.7656 (mp) REVERT: A 787 GLU cc_start: 0.7278 (tt0) cc_final: 0.7033 (tt0) REVERT: A 808 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7830 (tp) REVERT: A 834 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7066 (m-30) REVERT: A 1012 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7733 (t) REVERT: A 1125 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: N 100 PHE cc_start: 0.5033 (OUTLIER) cc_final: 0.4077 (t80) REVERT: B 68 GLN cc_start: 0.7427 (tm-30) cc_final: 0.7145 (tp40) REVERT: B 214 TYR cc_start: 0.6479 (OUTLIER) cc_final: 0.5376 (t80) REVERT: B 232 GLN cc_start: 0.7916 (tt0) cc_final: 0.7280 (mt0) REVERT: B 660 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7271 (mtm180) REVERT: B 711 MET cc_start: 0.8367 (ptm) cc_final: 0.8055 (ptm) REVERT: B 766 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6875 (tt) REVERT: B 808 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7990 (mm) REVERT: B 828 LYS cc_start: 0.7738 (mmtm) cc_final: 0.7488 (ttpm) REVERT: B 834 ASP cc_start: 0.7309 (m-30) cc_final: 0.7006 (m-30) REVERT: B 994 ILE cc_start: 0.6425 (mt) cc_final: 0.6126 (mp) REVERT: Q 188 GLU cc_start: 0.2448 (mp0) cc_final: 0.1743 (pm20) REVERT: E 34 MET cc_start: 0.4180 (mmm) cc_final: 0.3221 (mmm) REVERT: F 151 LYS cc_start: 0.0686 (OUTLIER) cc_final: -0.0266 (mttt) REVERT: C 167 MET cc_start: 0.0588 (pp-130) cc_final: 0.0123 (tmm) REVERT: C 202 ASN cc_start: 0.6809 (m-40) cc_final: 0.6161 (m110) REVERT: C 579 PHE cc_start: 0.7726 (p90) cc_final: 0.7525 (p90) REVERT: C 787 GLU cc_start: 0.7445 (tt0) cc_final: 0.7189 (tt0) REVERT: C 873 THR cc_start: 0.8602 (p) cc_final: 0.8350 (t) REVERT: C 971 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: C 978 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7393 (mptp) REVERT: I 116 ASP cc_start: 0.3519 (OUTLIER) cc_final: 0.3003 (t70) REVERT: I 157 VAL cc_start: -0.1401 (OUTLIER) cc_final: -0.1679 (t) REVERT: S 39 LYS cc_start: 0.1479 (mmmt) cc_final: 0.1226 (pttt) outliers start: 133 outliers final: 68 residues processed: 389 average time/residue: 0.9695 time to fit residues: 494.6843 Evaluate side-chains 328 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 242 time to evaluate : 3.728 ------------------------------------------------------------------------------- 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 464 ASN 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 600 ASP 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 973 LEU 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 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 M residue 192 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain N residue 187 ASP 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 393 CYS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 553 VAL 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 759 ASP Chi-restraints excluded: chain B residue 766 LEU 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 953 SER 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 24 PHE Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain E residue 82 MET 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 C residue 82 HIS Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 186 SER 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 737 THR Chi-restraints excluded: chain C residue 748 THR 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 1132 ASP 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 77 THR Chi-restraints excluded: chain R residue 82 MET 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: 0.8980 chunk 7 optimal weight: 9.9990 chunk 408 optimal weight: 5.9990 chunk 226 optimal weight: 0.5980 chunk 467 optimal weight: 0.9980 chunk 378 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 279 optimal weight: 0.7980 chunk 491 optimal weight: 2.9990 chunk 138 optimal weight: 40.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 GLN ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN M 81 GLN M 83 ASN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1024 GLN I 99 HIS J 38 GLN ** R 180 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: 0.4140 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 45393 Z= 0.179 Angle : 0.569 13.073 61761 Z= 0.293 Chirality : 0.044 0.192 6999 Planarity : 0.005 0.086 7962 Dihedral : 4.693 39.561 6219 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.25 % Favored : 96.73 % Rotamer: Outliers : 2.10 % Allowed : 14.82 % Favored : 83.07 % Cbeta Deviations : 0.00 % 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: 0.21 (0.11), residues: 5664 helix: 1.85 (0.20), residues: 686 sheet: 0.93 (0.12), residues: 1891 loop : -0.78 (0.11), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 450 HIS 0.007 0.001 HIS C 82 PHE 0.028 0.001 PHE H 27 TYR 0.026 0.001 TYR H 111 ARG 0.008 0.000 ARG B1009 *********************** 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 371 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 268 time to evaluate : 3.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7553 (t) cc_final: 0.7284 (m) REVERT: A 232 GLN cc_start: 0.8572 (tt0) cc_final: 0.7652 (pm20) REVERT: A 283 TYR cc_start: 0.7508 (m-10) cc_final: 0.6956 (m-80) REVERT: A 319 SER cc_start: 0.8778 (t) cc_final: 0.8473 (p) REVERT: A 583 ILE cc_start: 0.8346 (mm) cc_final: 0.8009 (mm) REVERT: A 585 ASP cc_start: 0.6906 (m-30) cc_final: 0.6662 (t0) REVERT: A 600 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: A 660 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7388 (mtp180) REVERT: A 716 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: A 768 LEU cc_start: 0.8177 (tt) cc_final: 0.7718 (mp) REVERT: A 787 GLU cc_start: 0.7195 (tt0) cc_final: 0.6944 (tt0) REVERT: A 808 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7835 (tp) REVERT: A 834 ASP cc_start: 0.7002 (t0) cc_final: 0.6654 (m-30) REVERT: A 1098 ASP cc_start: 0.7884 (t0) cc_final: 0.7581 (t0) REVERT: B 68 GLN cc_start: 0.7422 (tm-30) cc_final: 0.7184 (tp40) REVERT: B 140 VAL cc_start: 0.5886 (t) cc_final: 0.5389 (m) REVERT: B 184 TYR cc_start: 0.6772 (t80) cc_final: 0.6571 (t80) REVERT: B 214 TYR cc_start: 0.6276 (OUTLIER) cc_final: 0.5233 (t80) REVERT: B 232 GLN cc_start: 0.7965 (tt0) cc_final: 0.7332 (mt0) REVERT: B 558 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.7886 (m-40) REVERT: B 588 ASP cc_start: 0.7601 (t0) cc_final: 0.7269 (t0) REVERT: B 660 ARG cc_start: 0.7545 (mmp-170) cc_final: 0.7331 (mtm180) REVERT: B 711 MET cc_start: 0.8304 (ptm) cc_final: 0.7945 (ptm) REVERT: B 794 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7126 (pt0) REVERT: B 808 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7915 (mm) REVERT: B 828 LYS cc_start: 0.7754 (mmtm) cc_final: 0.7521 (ttpm) REVERT: B 834 ASP cc_start: 0.7066 (m-30) cc_final: 0.6854 (m-30) REVERT: B 1052 LYS cc_start: 0.8649 (mmtm) cc_final: 0.8271 (mmtm) REVERT: B 1127 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: Q 33 TYR cc_start: 0.2324 (OUTLIER) cc_final: 0.1245 (m-10) REVERT: Q 188 GLU cc_start: 0.2382 (mp0) cc_final: 0.1708 (pm20) REVERT: E 34 MET cc_start: 0.4255 (mmm) cc_final: 0.3307 (mmm) REVERT: F 151 LYS cc_start: 0.0416 (OUTLIER) cc_final: -0.0296 (mttt) REVERT: C 167 MET cc_start: 0.0385 (pp-130) cc_final: -0.0061 (tmm) REVERT: C 202 ASN cc_start: 0.6785 (m-40) cc_final: 0.6121 (m110) REVERT: C 579 PHE cc_start: 0.7707 (p90) cc_final: 0.7488 (p90) REVERT: C 600 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7687 (t70) REVERT: C 674 TYR cc_start: 0.7754 (m-80) cc_final: 0.7543 (m-80) REVERT: C 787 GLU cc_start: 0.7312 (tt0) cc_final: 0.7053 (tt0) REVERT: C 971 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: C 978 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7211 (mptp) REVERT: I 116 ASP cc_start: 0.2928 (OUTLIER) cc_final: 0.2433 (t70) REVERT: J 66 SER cc_start: 0.1135 (OUTLIER) cc_final: 0.0264 (m) REVERT: R 109 PHE cc_start: 0.3167 (OUTLIER) cc_final: 0.2817 (m-80) outliers start: 103 outliers final: 42 residues processed: 347 average time/residue: 0.9785 time to fit residues: 446.6580 Evaluate side-chains 299 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 240 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 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 600 ASP 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 808 ILE Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 120 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 214 TYR 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 554 ASN Chi-restraints excluded: chain B residue 558 ASN Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 712 SER 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 990 VAL Chi-restraints excluded: chain B residue 1106 GLU Chi-restraints excluded: chain B residue 1127 GLN Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain Q residue 33 TYR 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 151 LYS Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain C residue 186 SER 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 567 THR Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 971 GLN Chi-restraints excluded: chain C residue 978 LYS 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 29 VAL Chi-restraints excluded: chain R residue 109 PHE Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain S residue 34 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 184 optimal weight: 0.6980 chunk 493 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 321 optimal weight: 30.0000 chunk 135 optimal weight: 6.9990 chunk 548 optimal weight: 10.0000 chunk 455 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 288 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 793 GLN ** H 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN M 83 ASN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN F 37 GLN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1024 GLN I 99 HIS J 38 GLN ** R 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4176 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 45393 Z= 0.273 Angle : 0.601 12.867 61761 Z= 0.310 Chirality : 0.046 0.195 6999 Planarity : 0.005 0.087 7962 Dihedral : 4.736 39.306 6219 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.99 % Favored : 95.99 % Rotamer: Outliers : 2.76 % Allowed : 14.78 % Favored : 82.45 % 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: 0.17 (0.11), residues: 5664 helix: 1.72 (0.20), residues: 694 sheet: 0.93 (0.12), residues: 1891 loop : -0.81 (0.11), residues: 3079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 450 HIS 0.008 0.001 HIS H 103 PHE 0.031 0.002 PHE I 100 TYR 0.021 0.001 TYR B 279 ARG 0.007 0.001 ARG H 68 *********************** 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 402 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 267 time to evaluate : 3.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7687 (t) cc_final: 0.7364 (m) REVERT: A 232 GLN cc_start: 0.8625 (tt0) cc_final: 0.7758 (pm20) REVERT: A 283 TYR cc_start: 0.7562 (m-10) cc_final: 0.6926 (m-80) REVERT: A 319 SER cc_start: 0.8755 (t) cc_final: 0.8436 (p) REVERT: A 600 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: A 660 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7409 (mtp180) REVERT: A 716 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7920 (tp30) REVERT: A 737 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8353 (t) REVERT: A 754 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6775 (ttm) REVERT: A 768 LEU cc_start: 0.8198 (tt) cc_final: 0.7755 (mp) REVERT: A 787 GLU cc_start: 0.7246 (tt0) cc_final: 0.6911 (tt0) REVERT: A 808 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7877 (tp) REVERT: A 834 ASP cc_start: 0.7324 (t0) cc_final: 0.6927 (m-30) REVERT: A 1098 ASP cc_start: 0.7981 (t0) cc_final: 0.7632 (OUTLIER) REVERT: B 68 GLN cc_start: 0.7356 (tm-30) cc_final: 0.7042 (tp40) REVERT: B 140 VAL cc_start: 0.6041 (t) cc_final: 0.5513 (m) REVERT: B 214 TYR cc_start: 0.6313 (OUTLIER) cc_final: 0.5406 (t80) REVERT: B 232 GLN cc_start: 0.8009 (tt0) cc_final: 0.7376 (mt0) REVERT: B 558 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.7969 (m-40) REVERT: B 588 ASP cc_start: 0.7597 (t0) cc_final: 0.7159 (t0) REVERT: B 660 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7376 (mtm180) REVERT: B 711 MET cc_start: 0.8358 (ptm) cc_final: 0.8065 (ptm) REVERT: B 794 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: B 808 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7931 (mm) REVERT: B 828 LYS cc_start: 0.7894 (mmtm) cc_final: 0.7606 (ttpm) REVERT: B 834 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7068 (m-30) REVERT: B 1127 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: Q 188 GLU cc_start: 0.2352 (mp0) cc_final: 0.1697 (pm20) REVERT: E 34 MET cc_start: 0.4262 (mmm) cc_final: 0.3368 (mmm) REVERT: E 117 MET cc_start: 0.0780 (OUTLIER) cc_final: 0.0385 (pp-130) REVERT: F 4 MET cc_start: 0.1193 (mtp) cc_final: 0.0976 (mtp) REVERT: F 151 LYS cc_start: 0.0662 (OUTLIER) cc_final: -0.0039 (mttt) REVERT: C 82 HIS cc_start: 0.5288 (OUTLIER) cc_final: 0.5009 (p90) REVERT: C 167 MET cc_start: -0.0232 (pp-130) cc_final: -0.1225 (tmt) REVERT: C 202 ASN cc_start: 0.6812 (m-40) cc_final: 0.6114 (m110) REVERT: C 583 ILE cc_start: 0.8293 (mm) cc_final: 0.8077 (mm) REVERT: C 776 GLN cc_start: 0.7870 (tt0) cc_final: 0.7488 (pt0) REVERT: C 787 GLU cc_start: 0.7388 (tt0) cc_final: 0.7132 (tt0) REVERT: C 971 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: C 978 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7274 (mptp) REVERT: J 66 SER cc_start: 0.1215 (OUTLIER) cc_final: 0.0451 (m) outliers start: 135 outliers final: 70 residues processed: 372 average time/residue: 0.9252 time to fit residues: 457.4066 Evaluate side-chains 333 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 245 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 346 ILE 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 600 ASP 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 973 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 192 THR 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 315 CYS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 558 ASN 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 759 ASP 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 834 ASP Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 990 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 Q residue 33 TYR Chi-restraints excluded: chain E residue 117 MET 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 151 LYS Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 186 SER 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 737 THR Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 827 SER 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 1132 ASP Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 99 HIS 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 29 VAL Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain S residue 34 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 528 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 312 optimal weight: 30.0000 chunk 400 optimal weight: 1.9990 chunk 310 optimal weight: 30.0000 chunk 461 optimal weight: 2.9990 chunk 306 optimal weight: 6.9990 chunk 546 optimal weight: 10.0000 chunk 342 optimal weight: 20.0000 chunk 333 optimal weight: 8.9990 chunk 252 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 HIS ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN L 90 GLN M 81 GLN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 GLN B 971 GLN P 1 GLN ** 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 ** R 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 191 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4221 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 45393 Z= 0.442 Angle : 0.679 13.053 61761 Z= 0.352 Chirality : 0.050 0.204 6999 Planarity : 0.005 0.087 7962 Dihedral : 5.025 41.558 6218 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.38 % Favored : 95.60 % Rotamer: Outliers : 2.76 % Allowed : 15.40 % Favored : 81.83 % 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: 1.31 (0.19), residues: 691 sheet: 0.79 (0.12), residues: 1875 loop : -0.94 (0.11), residues: 3098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 118 HIS 0.041 0.002 HIS I 99 PHE 0.044 0.002 PHE I 101 TYR 0.024 0.002 TYR B 279 ARG 0.011 0.001 ARG C1009 *********************** 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 407 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 272 time to evaluate : 3.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7858 (t) cc_final: 0.7442 (m) REVERT: A 232 GLN cc_start: 0.8614 (tt0) cc_final: 0.7788 (pm20) REVERT: A 283 TYR cc_start: 0.7643 (m-10) cc_final: 0.6902 (m-80) REVERT: A 319 SER cc_start: 0.8818 (t) cc_final: 0.8414 (p) REVERT: A 600 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: A 660 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7435 (mtp180) REVERT: A 716 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7883 (tp30) REVERT: A 754 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6775 (ttm) REVERT: A 787 GLU cc_start: 0.7297 (tt0) cc_final: 0.7049 (tt0) REVERT: A 808 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7804 (tp) REVERT: B 68 GLN cc_start: 0.7320 (tm-30) cc_final: 0.6957 (tp-100) REVERT: B 140 VAL cc_start: 0.6238 (t) cc_final: 0.5942 (m) REVERT: B 214 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.5724 (t80) REVERT: B 232 GLN cc_start: 0.8009 (tt0) cc_final: 0.7555 (mt0) REVERT: B 558 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7983 (m-40) REVERT: B 588 ASP cc_start: 0.7603 (t0) cc_final: 0.7132 (t0) REVERT: B 660 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7316 (mtm180) REVERT: B 711 MET cc_start: 0.8424 (ptm) cc_final: 0.8201 (ptm) REVERT: B 776 GLN cc_start: 0.8041 (mt0) cc_final: 0.7744 (tt0) REVERT: B 808 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7961 (mm) REVERT: B 828 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7674 (ttpm) REVERT: B 834 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: B 1127 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7841 (mt0) REVERT: Q 188 GLU cc_start: 0.2316 (mp0) cc_final: 0.1676 (pm20) REVERT: E 117 MET cc_start: 0.1035 (tpt) cc_final: 0.0466 (pp-130) REVERT: F 4 MET cc_start: 0.1474 (mtp) cc_final: 0.1253 (mtp) REVERT: F 151 LYS cc_start: 0.0700 (OUTLIER) cc_final: 0.0003 (mttt) REVERT: C 82 HIS cc_start: 0.5346 (OUTLIER) cc_final: 0.5006 (p90) REVERT: C 167 MET cc_start: -0.0457 (pp-130) cc_final: -0.2731 (tpt) REVERT: C 172 ARG cc_start: 0.4670 (mtt90) cc_final: 0.4446 (mtp-110) REVERT: C 187 GLN cc_start: 0.7835 (tp40) cc_final: 0.7592 (tp-100) REVERT: C 202 ASN cc_start: 0.6659 (m-40) cc_final: 0.5945 (m110) REVERT: C 577 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6024 (mm-40) REVERT: C 585 ASP cc_start: 0.7869 (m-30) cc_final: 0.7368 (t0) REVERT: C 600 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: C 672 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8099 (p0) REVERT: C 776 GLN cc_start: 0.7903 (tt0) cc_final: 0.7528 (pt0) REVERT: C 787 GLU cc_start: 0.7459 (tt0) cc_final: 0.7198 (tt0) REVERT: C 793 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: C 971 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: C 978 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7411 (mptp) REVERT: C 998 LEU cc_start: 0.7416 (mm) cc_final: 0.7103 (tp) REVERT: C 1009 ARG cc_start: 0.7220 (mtm110) cc_final: 0.6867 (mtp-110) REVERT: J 66 SER cc_start: 0.1030 (OUTLIER) cc_final: 0.0244 (m) outliers start: 135 outliers final: 76 residues processed: 382 average time/residue: 0.9176 time to fit residues: 466.1212 Evaluate side-chains 353 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 257 time to evaluate : 4.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 464 ASN 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 600 ASP 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 973 LEU Chi-restraints excluded: chain A residue 1016 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 116 ASP Chi-restraints excluded: chain H residue 157 VAL 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 192 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 315 CYS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 558 ASN 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 759 ASP 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 953 SER Chi-restraints excluded: chain B residue 990 VAL 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 230 SER Chi-restraints excluded: chain Q residue 33 TYR 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 151 LYS Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 186 SER 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 554 ASN 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 737 THR Chi-restraints excluded: chain C residue 745 MET 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 982 SER Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 100 PHE 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 12 VAL Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain S residue 34 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 338 optimal weight: 40.0000 chunk 218 optimal weight: 20.0000 chunk 326 optimal weight: 30.0000 chunk 164 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 347 optimal weight: 7.9990 chunk 372 optimal weight: 9.9990 chunk 270 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 429 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN M 81 GLN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS N 79 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN B 462 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN ** C 135 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** ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 HIS J 39 GLN R 13 GLN ** S 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4247 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 45393 Z= 0.520 Angle : 0.716 15.241 61761 Z= 0.372 Chirality : 0.052 0.269 6999 Planarity : 0.006 0.088 7962 Dihedral : 5.261 42.648 6218 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.96 % Favored : 95.02 % Rotamer: Outliers : 2.82 % Allowed : 15.91 % Favored : 81.27 % 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: -0.34 (0.11), residues: 5664 helix: 0.96 (0.19), residues: 684 sheet: 0.67 (0.12), residues: 1869 loop : -1.10 (0.11), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 36 HIS 0.018 0.002 HIS B 519 PHE 0.047 0.003 PHE I 100 TYR 0.027 0.002 TYR B 279 ARG 0.006 0.001 ARG C 997 *********************** 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 415 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 277 time to evaluate : 4.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 TYR cc_start: 0.7506 (m-80) cc_final: 0.6958 (m-80) REVERT: A 232 GLN cc_start: 0.8568 (tt0) cc_final: 0.7742 (pm20) REVERT: A 283 TYR cc_start: 0.7704 (m-10) cc_final: 0.6740 (m-80) REVERT: A 600 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7418 (m-30) REVERT: A 660 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7432 (mtp180) REVERT: A 716 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: A 754 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6722 (ttm) REVERT: A 787 GLU cc_start: 0.7313 (tt0) cc_final: 0.7061 (tt0) REVERT: A 808 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7818 (tp) REVERT: A 834 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: N 100 PHE cc_start: 0.5122 (OUTLIER) cc_final: 0.4521 (t80) REVERT: B 68 GLN cc_start: 0.7276 (tm-30) cc_final: 0.6926 (tp-100) REVERT: B 116 ARG cc_start: 0.5498 (OUTLIER) cc_final: 0.4858 (mpt90) REVERT: B 140 VAL cc_start: 0.6574 (t) cc_final: 0.6316 (m) REVERT: B 232 GLN cc_start: 0.7896 (tt0) cc_final: 0.7590 (mt0) REVERT: B 558 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7883 (m-40) REVERT: B 588 ASP cc_start: 0.7595 (t0) cc_final: 0.7136 (t0) REVERT: B 660 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7331 (mtm180) REVERT: B 711 MET cc_start: 0.8429 (ptm) cc_final: 0.8209 (ptm) REVERT: B 794 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7099 (pt0) REVERT: B 828 LYS cc_start: 0.8013 (mmtm) cc_final: 0.7656 (ttpm) REVERT: B 834 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: B 1127 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7906 (mm110) REVERT: Q 188 GLU cc_start: 0.2270 (mp0) cc_final: 0.1633 (pm20) REVERT: E 52 TYR cc_start: 0.2602 (m-10) cc_final: 0.2210 (m-10) REVERT: E 117 MET cc_start: 0.1092 (tpt) cc_final: 0.0551 (pp-130) REVERT: F 151 LYS cc_start: 0.0803 (OUTLIER) cc_final: 0.0098 (mttt) REVERT: C 82 HIS cc_start: 0.5433 (OUTLIER) cc_final: 0.4965 (p90) REVERT: C 167 MET cc_start: -0.0376 (pp-130) cc_final: -0.2655 (tpt) REVERT: C 187 GLN cc_start: 0.7906 (tp40) cc_final: 0.7300 (mm-40) REVERT: C 202 ASN cc_start: 0.6729 (m-40) cc_final: 0.5985 (m110) REVERT: C 560 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7095 (pt) REVERT: C 577 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: C 776 GLN cc_start: 0.7876 (tt0) cc_final: 0.7528 (pt0) REVERT: C 787 GLU cc_start: 0.7524 (tt0) cc_final: 0.7266 (tt0) REVERT: C 793 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: C 971 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: C 978 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7347 (mptp) REVERT: C 1009 ARG cc_start: 0.7294 (mtm110) cc_final: 0.6892 (mtp-110) REVERT: J 66 SER cc_start: 0.0901 (OUTLIER) cc_final: 0.0221 (m) outliers start: 138 outliers final: 87 residues processed: 390 average time/residue: 0.9954 time to fit residues: 516.4606 Evaluate side-chains 361 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 253 time to evaluate : 3.811 ------------------------------------------------------------------------------- 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 380 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 432 ILE 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 600 ASP 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 973 LEU Chi-restraints excluded: chain A residue 1016 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 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 88 GLU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 100 PHE 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 116 ARG Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 558 ASN 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 759 ASP Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 GLU 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 953 SER Chi-restraints excluded: chain B residue 990 VAL 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 230 SER Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 33 TYR 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 151 LYS 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 186 SER 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 554 ASN Chi-restraints excluded: chain C residue 560 LEU 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 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 1012 THR Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 100 PHE 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 12 VAL 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 S residue 34 HIS Chi-restraints excluded: chain S residue 75 ILE 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: 5.9990 chunk 477 optimal weight: 0.9980 chunk 509 optimal weight: 8.9990 chunk 306 optimal weight: 50.0000 chunk 221 optimal weight: 0.0770 chunk 399 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 460 optimal weight: 0.5980 chunk 481 optimal weight: 0.3980 chunk 507 optimal weight: 7.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 179 HIS H 214 ASN M 81 GLN M 83 ASN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN ** C 135 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** C 672 ASN C1024 GLN I 99 HIS R 13 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4176 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 45393 Z= 0.173 Angle : 0.586 14.001 61761 Z= 0.301 Chirality : 0.045 0.294 6999 Planarity : 0.005 0.089 7962 Dihedral : 4.697 41.975 6217 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.39 % Favored : 96.59 % Rotamer: Outliers : 1.66 % Allowed : 17.53 % 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: 0.06 (0.11), residues: 5664 helix: 1.78 (0.20), residues: 693 sheet: 0.86 (0.12), residues: 1887 loop : -0.93 (0.11), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L 36 HIS 0.015 0.001 HIS B 519 PHE 0.031 0.001 PHE I 100 TYR 0.017 0.001 TYR B1081 ARG 0.011 0.000 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 350 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 270 time to evaluate : 3.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASN cc_start: 0.6572 (OUTLIER) cc_final: 0.6061 (t0) REVERT: A 232 GLN cc_start: 0.8584 (tt0) cc_final: 0.7777 (pm20) REVERT: A 241 VAL cc_start: 0.7575 (t) cc_final: 0.7294 (m) REVERT: A 243 LEU cc_start: 0.7149 (mp) cc_final: 0.6910 (mp) REVERT: A 283 TYR cc_start: 0.7664 (m-10) cc_final: 0.6918 (m-80) REVERT: A 319 SER cc_start: 0.8814 (t) cc_final: 0.8507 (p) REVERT: A 660 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7417 (mtp180) REVERT: A 754 MET cc_start: 0.7067 (mtp) cc_final: 0.6825 (ttm) REVERT: A 768 LEU cc_start: 0.8168 (tt) cc_final: 0.7822 (mp) REVERT: A 787 GLU cc_start: 0.7183 (tt0) cc_final: 0.6940 (tt0) REVERT: A 834 ASP cc_start: 0.7090 (t0) cc_final: 0.6737 (m-30) REVERT: A 1098 ASP cc_start: 0.7904 (t0) cc_final: 0.7531 (OUTLIER) REVERT: N 100 PHE cc_start: 0.5084 (m-80) cc_final: 0.4467 (t80) REVERT: B 68 GLN cc_start: 0.7282 (tm-30) cc_final: 0.6960 (tp40) REVERT: B 140 VAL cc_start: 0.6656 (t) cc_final: 0.6415 (m) REVERT: B 232 GLN cc_start: 0.7856 (tt0) cc_final: 0.7627 (mm-40) REVERT: B 558 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7798 (m-40) REVERT: B 588 ASP cc_start: 0.7544 (t0) cc_final: 0.7190 (t0) REVERT: B 660 ARG cc_start: 0.7572 (mmp-170) cc_final: 0.7349 (mtm180) REVERT: B 794 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7137 (pt0) REVERT: B 828 LYS cc_start: 0.7967 (mmtm) cc_final: 0.7655 (ttpm) REVERT: B 834 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7273 (m-30) REVERT: B 984 PHE cc_start: 0.6538 (m-80) cc_final: 0.6302 (m-80) REVERT: Q 188 GLU cc_start: 0.2323 (mp0) cc_final: 0.1642 (pm20) REVERT: E 117 MET cc_start: 0.1141 (tpt) cc_final: 0.0698 (pp-130) REVERT: F 151 LYS cc_start: 0.0714 (OUTLIER) cc_final: 0.0136 (mttt) REVERT: C 167 MET cc_start: -0.0486 (pp-130) cc_final: -0.2860 (tpt) REVERT: C 184 TYR cc_start: 0.6669 (t80) cc_final: 0.6440 (t80) REVERT: C 187 GLN cc_start: 0.7766 (tp40) cc_final: 0.7264 (mm-40) REVERT: C 672 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8141 (p0) REVERT: C 776 GLN cc_start: 0.7840 (tt0) cc_final: 0.7547 (pt0) REVERT: C 787 GLU cc_start: 0.7357 (tt0) cc_final: 0.7093 (tt0) REVERT: C 808 ILE cc_start: 0.8619 (mm) cc_final: 0.8296 (tp) REVERT: C 997 ARG cc_start: 0.7281 (mmt-90) cc_final: 0.7046 (mmt-90) REVERT: C 1009 ARG cc_start: 0.7172 (mtm110) cc_final: 0.6889 (mtp-110) REVERT: I 116 ASP cc_start: 0.3458 (OUTLIER) cc_final: 0.3033 (t70) REVERT: I 165 VAL cc_start: -0.0163 (OUTLIER) cc_final: -0.0403 (p) REVERT: J 66 SER cc_start: 0.0539 (OUTLIER) cc_final: 0.0193 (m) REVERT: S 34 HIS cc_start: 0.3482 (OUTLIER) cc_final: 0.3233 (m90) REVERT: S 183 LEU cc_start: 0.1072 (OUTLIER) cc_final: 0.0823 (tt) outliers start: 80 outliers final: 48 residues processed: 333 average time/residue: 0.9524 time to fit residues: 422.8190 Evaluate side-chains 317 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 258 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASN 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 563 THR Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 157 VAL 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 192 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 558 ASN 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 759 ASP Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 834 ASP Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain Q residue 33 TYR 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 151 LYS Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 554 ASN Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 165 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 12 VAL Chi-restraints excluded: chain R residue 116 THR 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 334 optimal weight: 0.5980 chunk 538 optimal weight: 0.9990 chunk 328 optimal weight: 20.0000 chunk 255 optimal weight: 0.8980 chunk 374 optimal weight: 20.0000 chunk 564 optimal weight: 2.9990 chunk 519 optimal weight: 0.6980 chunk 449 optimal weight: 0.0170 chunk 46 optimal weight: 8.9990 chunk 347 optimal weight: 10.0000 chunk 275 optimal weight: 5.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 179 HIS M 81 GLN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN F 149 GLN ** C 135 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** C 672 ASN I 99 HIS ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4177 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.165 45393 Z= 0.214 Angle : 0.676 59.186 61761 Z= 0.369 Chirality : 0.046 0.869 6999 Planarity : 0.005 0.158 7962 Dihedral : 4.686 41.961 6216 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.37 % Favored : 96.61 % Rotamer: Outliers : 1.56 % Allowed : 17.67 % Favored : 80.77 % Cbeta Deviations : 0.04 % 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: 0.07 (0.11), residues: 5664 helix: 1.82 (0.20), residues: 693 sheet: 0.87 (0.12), residues: 1858 loop : -0.92 (0.11), residues: 3113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP R 36 HIS 0.013 0.001 HIS B 519 PHE 0.342 0.002 PHE I 100 TYR 0.045 0.001 TYR R 93 ARG 0.017 0.000 ARG R 97 ********************** 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 333 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 258 time to evaluate : 3.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASN cc_start: 0.6573 (OUTLIER) cc_final: 0.6065 (t0) REVERT: A 232 GLN cc_start: 0.8584 (tt0) cc_final: 0.7776 (pm20) REVERT: A 241 VAL cc_start: 0.7576 (t) cc_final: 0.7294 (m) REVERT: A 243 LEU cc_start: 0.7148 (mp) cc_final: 0.6911 (mp) REVERT: A 283 TYR cc_start: 0.7664 (m-10) cc_final: 0.6920 (m-80) REVERT: A 319 SER cc_start: 0.8812 (t) cc_final: 0.8505 (p) REVERT: A 660 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7416 (mtp180) REVERT: A 754 MET cc_start: 0.7070 (mtp) cc_final: 0.6824 (ttm) REVERT: A 768 LEU cc_start: 0.8170 (tt) cc_final: 0.7821 (mp) REVERT: A 787 GLU cc_start: 0.7184 (tt0) cc_final: 0.6943 (tt0) REVERT: A 834 ASP cc_start: 0.7088 (t0) cc_final: 0.6736 (m-30) REVERT: A 1098 ASP cc_start: 0.7902 (t0) cc_final: 0.7530 (OUTLIER) REVERT: B 68 GLN cc_start: 0.7281 (tm-30) cc_final: 0.6961 (tp40) REVERT: B 140 VAL cc_start: 0.6645 (t) cc_final: 0.6413 (m) REVERT: B 232 GLN cc_start: 0.7856 (tt0) cc_final: 0.7628 (mm-40) REVERT: B 558 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7798 (m-40) REVERT: B 660 ARG cc_start: 0.7572 (mmp-170) cc_final: 0.7350 (mtm180) REVERT: B 794 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7137 (pt0) REVERT: B 828 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7655 (ttpm) REVERT: B 834 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: B 984 PHE cc_start: 0.6542 (m-80) cc_final: 0.6296 (m-80) REVERT: Q 188 GLU cc_start: 0.2323 (mp0) cc_final: 0.1643 (pm20) REVERT: E 117 MET cc_start: 0.1142 (tpt) cc_final: 0.0696 (pp-130) REVERT: F 151 LYS cc_start: 0.0708 (OUTLIER) cc_final: 0.0133 (mttt) REVERT: C 167 MET cc_start: -0.0487 (pp-130) cc_final: -0.2859 (tpt) REVERT: C 187 GLN cc_start: 0.7764 (tp40) cc_final: 0.7256 (mm-40) REVERT: C 776 GLN cc_start: 0.7843 (tt0) cc_final: 0.7549 (pt0) REVERT: C 787 GLU cc_start: 0.7356 (tt0) cc_final: 0.7093 (tt0) REVERT: C 808 ILE cc_start: 0.8618 (mm) cc_final: 0.8295 (tp) REVERT: C 1009 ARG cc_start: 0.7173 (mtm110) cc_final: 0.6889 (mtp-110) REVERT: I 116 ASP cc_start: 0.3434 (OUTLIER) cc_final: 0.3031 (t70) REVERT: I 165 VAL cc_start: -0.0161 (OUTLIER) cc_final: -0.0402 (p) REVERT: J 66 SER cc_start: 0.0540 (OUTLIER) cc_final: 0.0194 (m) REVERT: R 93 TYR cc_start: 0.2685 (OUTLIER) cc_final: 0.2145 (m-10) REVERT: S 34 HIS cc_start: 0.3487 (OUTLIER) cc_final: 0.3231 (m90) REVERT: S 183 LEU cc_start: 0.1076 (OUTLIER) cc_final: 0.0823 (tt) outliers start: 75 outliers final: 58 residues processed: 319 average time/residue: 0.9526 time to fit residues: 403.0664 Evaluate side-chains 326 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 257 time to evaluate : 3.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 545 THR 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 873 THR Chi-restraints excluded: chain A residue 1142 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 192 THR Chi-restraints excluded: chain N residue 142 TYR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 558 ASN 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 759 ASP Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 834 ASP Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain Q residue 33 TYR 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 F residue 111 THR Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 554 ASN Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 1142 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 165 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 12 VAL Chi-restraints excluded: chain R residue 13 GLN Chi-restraints excluded: chain R residue 93 TYR Chi-restraints excluded: chain R residue 116 THR 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: 8.9990 chunk 479 optimal weight: 0.0980 chunk 137 optimal weight: 50.0000 chunk 414 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 125 optimal weight: 40.0000 chunk 450 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 462 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 82 optimal weight: 0.0870 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 179 HIS M 81 GLN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN F 149 GLN ** C 135 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** C 672 ASN I 99 HIS ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.221226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.206685 restraints weight = 107638.959| |-----------------------------------------------------------------------------| r_work (start): 0.4625 rms_B_bonded: 1.13 r_work: 0.4177 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.4059 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work: 0.3958 rms_B_bonded: 4.08 restraints_weight: 0.1250 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.232 45393 Z= 0.252 Angle : 0.739 59.152 61761 Z= 0.412 Chirality : 0.045 0.487 6999 Planarity : 0.005 0.159 7962 Dihedral : 4.694 41.953 6216 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.39 % Favored : 96.59 % Rotamer: Outliers : 1.66 % Allowed : 17.61 % Favored : 80.73 % Cbeta Deviations : 0.06 % 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: 1.83 (0.20), residues: 693 sheet: 0.88 (0.12), residues: 1887 loop : -0.92 (0.11), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP R 36 HIS 0.012 0.001 HIS B 519 PHE 0.333 0.002 PHE I 100 TYR 0.042 0.001 TYR R 93 ARG 0.020 0.000 ARG R 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12565.57 seconds wall clock time: 220 minutes 52.18 seconds (13252.18 seconds total)