Starting phenix.real_space_refine on Sat Oct 31 14:17:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sh2_54887/10_2026/9sh2_54887.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sh2_54887/10_2026/9sh2_54887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sh2_54887/10_2026/9sh2_54887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sh2_54887/10_2026/9sh2_54887.map" model { file = "/net/cci-nas-00/data/ceres_data/9sh2_54887/10_2026/9sh2_54887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sh2_54887/10_2026/9sh2_54887.cif" } resolution = 2.14 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 27020 2.51 5 N 7518 2.21 5 O 8456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43120 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Chain: "B" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Chain: "C" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Chain: "D" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Chain: "E" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Chain: "F" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Chain: "G" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Chain: "H" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Chain: "I" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Chain: "J" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Chain: "K" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Chain: "L" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Chain: "M" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Chain: "N" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3080 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Time building chain proxies: 9.30, per 1000 atoms: 0.22 Number of scatterers: 43120 At special positions: 0 Unit cell: (153.45, 156.24, 171.12, 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 126 16.00 O 8456 8.00 N 7518 7.00 C 27020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 345 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 345 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 345 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 345 " distance=2.03 Simple disulfide: pdb=" SG CYS H 336 " - pdb=" SG CYS H 345 " distance=2.03 Simple disulfide: pdb=" SG CYS I 336 " - pdb=" SG CYS I 345 " distance=2.03 Simple disulfide: pdb=" SG CYS J 336 " - pdb=" SG CYS J 345 " distance=2.03 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 345 " distance=2.03 Simple disulfide: pdb=" SG CYS L 336 " - pdb=" SG CYS L 345 " distance=2.03 Simple disulfide: pdb=" SG CYS M 336 " - pdb=" SG CYS M 345 " distance=2.03 Simple disulfide: pdb=" SG CYS N 336 " - pdb=" SG CYS N 345 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 2.0 seconds 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10444 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 44 sheets defined 19.6% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.962A pdb=" N LEU A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 removed outlier: 4.495A pdb=" N ARG A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 93 removed outlier: 3.608A pdb=" N ALA A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 removed outlier: 4.347A pdb=" N SER A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 200 through 203 removed outlier: 3.927A pdb=" N THR A 203 " --> pdb=" O LYS A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 203' Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.949A pdb=" N LEU B 15 " --> pdb=" O ILE B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 55 Processing helix chain 'B' and resid 72 through 93 removed outlier: 3.525A pdb=" N ALA B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 removed outlier: 4.402A pdb=" N SER B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 200 through 203 removed outlier: 3.914A pdb=" N THR B 203 " --> pdb=" O LYS B 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.921A pdb=" N LEU C 15 " --> pdb=" O ILE C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 55 Processing helix chain 'C' and resid 72 through 93 removed outlier: 3.663A pdb=" N ALA C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 149 through 164 Processing helix chain 'C' and resid 200 through 203 removed outlier: 3.915A pdb=" N THR C 203 " --> pdb=" O LYS C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 200 through 203' Processing helix chain 'C' and resid 388 through 392 removed outlier: 4.124A pdb=" N LEU C 392 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.920A pdb=" N LEU D 15 " --> pdb=" O ILE D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 55 Processing helix chain 'D' and resid 72 through 93 removed outlier: 4.145A pdb=" N ALA D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 109 through 114 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 200 through 203 removed outlier: 3.916A pdb=" N THR D 203 " --> pdb=" O LYS D 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 200 through 203' Processing helix chain 'D' and resid 388 through 392 removed outlier: 4.113A pdb=" N LEU D 392 " --> pdb=" O ILE D 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 22 removed outlier: 3.897A pdb=" N LEU E 15 " --> pdb=" O ILE E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 4.463A pdb=" N ARG E 56 " --> pdb=" O VAL E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 93 removed outlier: 3.940A pdb=" N ALA E 90 " --> pdb=" O GLU E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'E' and resid 149 through 164 Processing helix chain 'E' and resid 200 through 203 removed outlier: 3.927A pdb=" N THR E 203 " --> pdb=" O LYS E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 200 through 203' Processing helix chain 'E' and resid 388 through 392 removed outlier: 4.087A pdb=" N LEU E 392 " --> pdb=" O ILE E 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 22 removed outlier: 3.894A pdb=" N LEU F 15 " --> pdb=" O ILE F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 55 Processing helix chain 'F' and resid 72 through 93 removed outlier: 3.989A pdb=" N ALA F 90 " --> pdb=" O GLU F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 109 through 114 Processing helix chain 'F' and resid 149 through 164 Processing helix chain 'F' and resid 200 through 203 removed outlier: 3.912A pdb=" N THR F 203 " --> pdb=" O LYS F 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 200 through 203' Processing helix chain 'F' and resid 388 through 392 removed outlier: 4.122A pdb=" N LEU F 392 " --> pdb=" O ILE F 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 22 removed outlier: 3.909A pdb=" N LEU G 15 " --> pdb=" O ILE G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 55 Processing helix chain 'G' and resid 72 through 93 removed outlier: 4.020A pdb=" N ALA G 90 " --> pdb=" O GLU G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 108 No H-bonds generated for 'chain 'G' and resid 106 through 108' Processing helix chain 'G' and resid 109 through 114 Processing helix chain 'G' and resid 149 through 164 Processing helix chain 'G' and resid 200 through 203 removed outlier: 3.883A pdb=" N THR G 203 " --> pdb=" O LYS G 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 203' Processing helix chain 'G' and resid 390 through 392 No H-bonds generated for 'chain 'G' and resid 390 through 392' Processing helix chain 'H' and resid 10 through 22 removed outlier: 3.946A pdb=" N LEU H 15 " --> pdb=" O ILE H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 55 Processing helix chain 'H' and resid 72 through 93 Processing helix chain 'H' and resid 108 through 114 removed outlier: 4.400A pdb=" N SER H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 164 Processing helix chain 'H' and resid 200 through 203 removed outlier: 3.908A pdb=" N THR H 203 " --> pdb=" O LYS H 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 200 through 203' Processing helix chain 'H' and resid 390 through 392 No H-bonds generated for 'chain 'H' and resid 390 through 392' Processing helix chain 'I' and resid 10 through 22 removed outlier: 3.951A pdb=" N LEU I 15 " --> pdb=" O ILE I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 56 removed outlier: 4.468A pdb=" N ARG I 56 " --> pdb=" O VAL I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 93 Processing helix chain 'I' and resid 108 through 114 removed outlier: 4.375A pdb=" N SER I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 164 Processing helix chain 'I' and resid 200 through 203 removed outlier: 3.911A pdb=" N THR I 203 " --> pdb=" O LYS I 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 200 through 203' Processing helix chain 'I' and resid 390 through 392 No H-bonds generated for 'chain 'I' and resid 390 through 392' Processing helix chain 'J' and resid 10 through 22 removed outlier: 3.942A pdb=" N LEU J 15 " --> pdb=" O ILE J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 56 removed outlier: 4.460A pdb=" N ARG J 56 " --> pdb=" O VAL J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 93 removed outlier: 3.560A pdb=" N GLY J 93 " --> pdb=" O ILE J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 108 No H-bonds generated for 'chain 'J' and resid 106 through 108' Processing helix chain 'J' and resid 109 through 114 Processing helix chain 'J' and resid 149 through 164 Processing helix chain 'J' and resid 200 through 203 removed outlier: 3.907A pdb=" N THR J 203 " --> pdb=" O LYS J 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 200 through 203' Processing helix chain 'J' and resid 390 through 392 No H-bonds generated for 'chain 'J' and resid 390 through 392' Processing helix chain 'K' and resid 10 through 22 removed outlier: 3.901A pdb=" N LEU K 15 " --> pdb=" O ILE K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 55 Processing helix chain 'K' and resid 72 through 93 removed outlier: 3.993A pdb=" N ALA K 90 " --> pdb=" O GLU K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 108 No H-bonds generated for 'chain 'K' and resid 106 through 108' Processing helix chain 'K' and resid 109 through 114 Processing helix chain 'K' and resid 149 through 164 Processing helix chain 'K' and resid 200 through 203 removed outlier: 3.924A pdb=" N THR K 203 " --> pdb=" O LYS K 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 200 through 203' Processing helix chain 'K' and resid 390 through 392 No H-bonds generated for 'chain 'K' and resid 390 through 392' Processing helix chain 'L' and resid 10 through 22 removed outlier: 3.939A pdb=" N LEU L 15 " --> pdb=" O ILE L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 56 removed outlier: 4.420A pdb=" N ARG L 56 " --> pdb=" O VAL L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 93 removed outlier: 3.991A pdb=" N ALA L 90 " --> pdb=" O GLU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 108 No H-bonds generated for 'chain 'L' and resid 106 through 108' Processing helix chain 'L' and resid 109 through 114 Processing helix chain 'L' and resid 149 through 164 Processing helix chain 'L' and resid 200 through 203 removed outlier: 3.921A pdb=" N THR L 203 " --> pdb=" O LYS L 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 200 through 203' Processing helix chain 'L' and resid 390 through 392 No H-bonds generated for 'chain 'L' and resid 390 through 392' Processing helix chain 'M' and resid 10 through 22 removed outlier: 3.941A pdb=" N LEU M 15 " --> pdb=" O ILE M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 56 removed outlier: 4.502A pdb=" N ARG M 56 " --> pdb=" O VAL M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 92 Processing helix chain 'M' and resid 106 through 108 No H-bonds generated for 'chain 'M' and resid 106 through 108' Processing helix chain 'M' and resid 109 through 114 Processing helix chain 'M' and resid 149 through 164 Processing helix chain 'M' and resid 200 through 203 removed outlier: 3.846A pdb=" N THR M 203 " --> pdb=" O LYS M 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 200 through 203' Processing helix chain 'M' and resid 390 through 392 No H-bonds generated for 'chain 'M' and resid 390 through 392' Processing helix chain 'N' and resid 10 through 22 removed outlier: 3.942A pdb=" N LEU N 15 " --> pdb=" O ILE N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 55 Processing helix chain 'N' and resid 72 through 93 Processing helix chain 'N' and resid 108 through 114 removed outlier: 4.382A pdb=" N SER N 112 " --> pdb=" O GLU N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 164 Processing helix chain 'N' and resid 200 through 203 removed outlier: 3.927A pdb=" N THR N 203 " --> pdb=" O LYS N 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 200 through 203' Processing helix chain 'N' and resid 390 through 392 No H-bonds generated for 'chain 'N' and resid 390 through 392' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 7.715A pdb=" N SER A 3 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.947A pdb=" N ASN A 25 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ILE A 69 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL A 27 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 61 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 70 " --> pdb=" O ASP A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 101 removed outlier: 3.562A pdb=" N SER A 134 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 198 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 205 through 212 current: chain 'A' and resid 246 through 272 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 246 through 272 current: chain 'A' and resid 394 through 413 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 394 through 413 current: chain 'B' and resid 205 through 212 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 205 through 212 current: chain 'B' and resid 246 through 272 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 246 through 272 current: chain 'B' and resid 394 through 413 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 394 through 413 current: chain 'C' and resid 205 through 212 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 205 through 212 current: chain 'C' and resid 246 through 272 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 246 through 272 current: chain 'C' and resid 394 through 413 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 394 through 413 current: chain 'D' and resid 205 through 212 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 205 through 212 current: chain 'D' and resid 246 through 272 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 246 through 272 current: chain 'D' and resid 394 through 413 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 394 through 413 current: chain 'E' and resid 205 through 212 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 205 through 212 current: chain 'E' and resid 246 through 272 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 246 through 272 current: chain 'E' and resid 394 through 413 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 394 through 413 current: chain 'F' and resid 205 through 212 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 205 through 212 current: chain 'F' and resid 246 through 272 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 246 through 272 current: chain 'F' and resid 394 through 413 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 394 through 413 current: chain 'G' and resid 205 through 212 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 205 through 212 current: chain 'G' and resid 246 through 272 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 246 through 272 current: chain 'G' and resid 394 through 413 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 394 through 413 current: chain 'H' and resid 205 through 212 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 205 through 212 current: chain 'H' and resid 246 through 272 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 246 through 272 current: chain 'H' and resid 394 through 413 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 394 through 413 current: chain 'I' and resid 205 through 212 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 205 through 212 current: chain 'I' and resid 246 through 272 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 246 through 272 current: chain 'I' and resid 394 through 413 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 394 through 413 current: chain 'J' and resid 205 through 212 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 205 through 212 current: chain 'J' and resid 246 through 272 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 246 through 272 current: chain 'J' and resid 394 through 413 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 394 through 413 current: chain 'K' and resid 205 through 212 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 205 through 212 current: chain 'K' and resid 246 through 272 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 246 through 272 current: chain 'K' and resid 394 through 413 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 394 through 413 current: chain 'L' and resid 205 through 212 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 205 through 212 current: chain 'L' and resid 246 through 272 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 246 through 272 current: chain 'L' and resid 394 through 413 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 394 through 413 current: chain 'M' and resid 205 through 212 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 205 through 212 current: chain 'M' and resid 246 through 272 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 246 through 272 current: chain 'M' and resid 394 through 413 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 394 through 413 current: chain 'N' and resid 205 through 212 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 205 through 212 current: chain 'N' and resid 246 through 272 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 246 through 272 current: chain 'N' and resid 394 through 413 Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 286 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 321 through 330 current: chain 'A' and resid 342 through 348 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 342 through 348 current: chain 'B' and resid 277 through 286 removed outlier: 3.509A pdb=" N THR B 325 " --> pdb=" O THR B 313 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 321 through 330 current: chain 'B' and resid 342 through 348 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 342 through 348 current: chain 'C' and resid 277 through 286 removed outlier: 3.522A pdb=" N THR C 325 " --> pdb=" O THR C 313 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 321 through 330 current: chain 'C' and resid 342 through 358 removed outlier: 7.555A pdb=" N LEU C 344 " --> pdb=" O PRO D 286 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 321 through 330 current: chain 'D' and resid 342 through 348 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 342 through 348 current: chain 'E' and resid 277 through 286 removed outlier: 19.851A pdb=" N LEU E 303 " --> pdb=" O GLN E 335 " (cutoff:3.500A) removed outlier: 17.378A pdb=" N GLN E 335 " --> pdb=" O LEU E 303 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N LYS E 305 " --> pdb=" O PRO E 333 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR E 325 " --> pdb=" O THR E 313 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS E 345 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU E 344 " --> pdb=" O PRO F 286 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 321 through 330 current: chain 'F' and resid 342 through 348 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 342 through 348 current: chain 'G' and resid 277 through 286 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 321 through 330 current: chain 'G' and resid 342 through 358 removed outlier: 7.605A pdb=" N LEU G 344 " --> pdb=" O PRO H 286 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE G 346 " --> pdb=" O GLU H 284 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 321 through 330 current: chain 'H' and resid 342 through 358 removed outlier: 7.588A pdb=" N LEU H 344 " --> pdb=" O PRO I 286 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 321 through 330 current: chain 'I' and resid 342 through 348 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 342 through 348 current: chain 'J' and resid 277 through 279 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 277 through 279 current: chain 'J' and resid 303 through 316 removed outlier: 20.100A pdb=" N LEU J 303 " --> pdb=" O GLN J 335 " (cutoff:3.500A) removed outlier: 16.942A pdb=" N GLN J 335 " --> pdb=" O LEU J 303 " (cutoff:3.500A) removed outlier: 12.087A pdb=" N LYS J 305 " --> pdb=" O PRO J 333 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU J 344 " --> pdb=" O PRO K 286 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE J 346 " --> pdb=" O GLU K 284 " (cutoff:3.500A) removed outlier: 19.901A pdb=" N LEU K 303 " --> pdb=" O GLN K 335 " (cutoff:3.500A) removed outlier: 17.216A pdb=" N GLN K 335 " --> pdb=" O LEU K 303 " (cutoff:3.500A) removed outlier: 12.146A pdb=" N LYS K 305 " --> pdb=" O PRO K 333 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR K 325 " --> pdb=" O THR K 313 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS K 345 " --> pdb=" O ALA K 334 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU K 344 " --> pdb=" O PRO L 286 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 321 through 330 current: chain 'L' and resid 342 through 358 removed outlier: 7.679A pdb=" N LEU L 344 " --> pdb=" O PRO M 286 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE L 346 " --> pdb=" O GLU M 284 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR M 325 " --> pdb=" O THR M 313 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 321 through 330 current: chain 'M' and resid 342 through 348 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 342 through 348 current: chain 'N' and resid 277 through 286 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 321 through 330 current: chain 'N' and resid 342 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 7 removed outlier: 7.776A pdb=" N SER B 3 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 28 removed outlier: 7.864A pdb=" N VAL B 27 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 68 " --> pdb=" O ARG B 61 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG B 61 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 70 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 101 removed outlier: 3.593A pdb=" N SER B 134 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 7 removed outlier: 7.780A pdb=" N SER C 3 " --> pdb=" O ASP C 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 27 through 28 removed outlier: 7.877A pdb=" N VAL C 27 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN C 68 " --> pdb=" O ARG C 61 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG C 61 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 70 " --> pdb=" O ASP C 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 101 removed outlier: 3.635A pdb=" N SER C 134 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 7 removed outlier: 7.782A pdb=" N SER D 3 " --> pdb=" O ASP D 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 27 through 28 removed outlier: 7.924A pdb=" N VAL D 27 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN D 68 " --> pdb=" O ARG D 61 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG D 61 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA D 70 " --> pdb=" O ASP D 59 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 96 through 101 removed outlier: 3.664A pdb=" N SER D 134 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 2 through 7 removed outlier: 7.799A pdb=" N SER E 3 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 25 through 28 removed outlier: 3.734A pdb=" N ASN E 68 " --> pdb=" O ARG E 61 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG E 61 " --> pdb=" O ASN E 68 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA E 70 " --> pdb=" O ASP E 59 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 96 through 101 removed outlier: 3.682A pdb=" N SER E 134 " --> pdb=" O THR E 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 2 through 7 removed outlier: 7.807A pdb=" N SER F 3 " --> pdb=" O ASP F 42 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 25 through 28 removed outlier: 3.894A pdb=" N ASN F 68 " --> pdb=" O ARG F 61 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG F 61 " --> pdb=" O ASN F 68 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA F 70 " --> pdb=" O ASP F 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 96 through 101 removed outlier: 3.663A pdb=" N SER F 134 " --> pdb=" O THR F 147 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 2 through 7 removed outlier: 7.801A pdb=" N SER G 3 " --> pdb=" O ASP G 42 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 27 through 28 removed outlier: 7.878A pdb=" N VAL G 27 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN G 68 " --> pdb=" O ARG G 61 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG G 61 " --> pdb=" O ASN G 68 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA G 70 " --> pdb=" O ASP G 59 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 96 through 101 removed outlier: 3.673A pdb=" N SER G 134 " --> pdb=" O THR G 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 2 through 7 removed outlier: 7.799A pdb=" N SER H 3 " --> pdb=" O ASP H 42 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 27 through 28 removed outlier: 7.905A pdb=" N VAL H 27 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN H 68 " --> pdb=" O ARG H 61 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG H 61 " --> pdb=" O ASN H 68 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA H 70 " --> pdb=" O ASP H 59 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 96 through 101 removed outlier: 3.681A pdb=" N SER H 134 " --> pdb=" O THR H 147 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 2 through 7 removed outlier: 7.775A pdb=" N SER I 3 " --> pdb=" O ASP I 42 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 27 through 28 removed outlier: 7.916A pdb=" N VAL I 27 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN I 68 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG I 61 " --> pdb=" O ASN I 68 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA I 70 " --> pdb=" O ASP I 59 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 96 through 101 removed outlier: 3.651A pdb=" N SER I 134 " --> pdb=" O THR I 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 2 through 7 removed outlier: 7.774A pdb=" N SER J 3 " --> pdb=" O ASP J 42 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 27 through 28 removed outlier: 7.918A pdb=" N VAL J 27 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN J 68 " --> pdb=" O ARG J 61 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG J 61 " --> pdb=" O ASN J 68 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA J 70 " --> pdb=" O ASP J 59 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 96 through 101 removed outlier: 3.631A pdb=" N SER J 134 " --> pdb=" O THR J 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 2 through 7 removed outlier: 7.793A pdb=" N SER K 3 " --> pdb=" O ASP K 42 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 25 through 28 removed outlier: 3.810A pdb=" N ASN K 68 " --> pdb=" O ARG K 61 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG K 61 " --> pdb=" O ASN K 68 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA K 70 " --> pdb=" O ASP K 59 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 96 through 101 removed outlier: 3.601A pdb=" N SER K 134 " --> pdb=" O THR K 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 2 through 7 removed outlier: 7.798A pdb=" N SER L 3 " --> pdb=" O ASP L 42 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 27 through 28 removed outlier: 7.987A pdb=" N VAL L 27 " --> pdb=" O ILE L 69 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN L 68 " --> pdb=" O ARG L 61 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG L 61 " --> pdb=" O ASN L 68 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA L 70 " --> pdb=" O ASP L 59 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 96 through 101 removed outlier: 3.547A pdb=" N SER L 134 " --> pdb=" O THR L 147 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 2 through 7 removed outlier: 7.804A pdb=" N SER M 3 " --> pdb=" O ASP M 42 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 27 through 28 removed outlier: 8.047A pdb=" N VAL M 27 " --> pdb=" O ILE M 69 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN M 68 " --> pdb=" O ARG M 61 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG M 61 " --> pdb=" O ASN M 68 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA M 70 " --> pdb=" O ASP M 59 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 96 through 101 removed outlier: 3.667A pdb=" N SER M 134 " --> pdb=" O THR M 147 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 2 through 7 removed outlier: 7.810A pdb=" N SER N 3 " --> pdb=" O ASP N 42 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 27 through 28 removed outlier: 7.983A pdb=" N VAL N 27 " --> pdb=" O ILE N 69 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN N 68 " --> pdb=" O ARG N 61 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG N 61 " --> pdb=" O ASN N 68 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA N 70 " --> pdb=" O ASP N 59 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 96 through 101 removed outlier: 3.725A pdb=" N SER N 134 " --> pdb=" O THR N 147 " (cutoff:3.500A) 1290 hydrogen bonds defined for protein. 3651 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: 9.29 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14572 1.34 - 1.46: 7735 1.46 - 1.58: 21036 1.58 - 1.70: 1 1.70 - 1.82: 224 Bond restraints: 43568 Sorted by residual: bond pdb=" CB ASP L 91 " pdb=" CG ASP L 91 " ideal model delta sigma weight residual 1.516 1.581 -0.065 2.50e-02 1.60e+03 6.85e+00 bond pdb=" CB ASP K 91 " pdb=" CG ASP K 91 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.86e+00 bond pdb=" CB GLN A 84 " pdb=" CG GLN A 84 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.28e+00 bond pdb=" CA ASP K 91 " pdb=" CB ASP K 91 " ideal model delta sigma weight residual 1.528 1.550 -0.022 1.59e-02 3.96e+03 1.84e+00 bond pdb=" CB GLN A 16 " pdb=" CG GLN A 16 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 ... (remaining 43563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 58193 2.36 - 4.73: 527 4.73 - 7.09: 86 7.09 - 9.46: 24 9.46 - 11.82: 12 Bond angle restraints: 58842 Sorted by residual: angle pdb=" CA GLN A 16 " pdb=" CB GLN A 16 " pdb=" CG GLN A 16 " ideal model delta sigma weight residual 114.10 122.98 -8.88 2.00e+00 2.50e-01 1.97e+01 angle pdb=" C ASN D 294 " pdb=" N GLY D 295 " pdb=" CA GLY D 295 " ideal model delta sigma weight residual 121.41 113.71 7.70 1.96e+00 2.60e-01 1.54e+01 angle pdb=" CA GLN A 84 " pdb=" CB GLN A 84 " pdb=" CG GLN A 84 " ideal model delta sigma weight residual 114.10 121.75 -7.65 2.00e+00 2.50e-01 1.46e+01 angle pdb=" CA MET C 24 " pdb=" CB MET C 24 " pdb=" CG MET C 24 " ideal model delta sigma weight residual 114.10 121.65 -7.55 2.00e+00 2.50e-01 1.42e+01 angle pdb=" C ILE J 292 " pdb=" N ALA J 293 " pdb=" CA ALA J 293 " ideal model delta sigma weight residual 122.16 127.01 -4.85 1.32e+00 5.74e-01 1.35e+01 ... (remaining 58837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 24343 18.00 - 35.99: 1902 35.99 - 53.99: 559 53.99 - 71.98: 118 71.98 - 89.98: 42 Dihedral angle restraints: 26964 sinusoidal: 10850 harmonic: 16114 Sorted by residual: dihedral pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 345 " pdb=" CB CYS G 345 " ideal model delta sinusoidal sigma weight residual -86.00 -164.14 78.14 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CA GLN K 335 " pdb=" C GLN K 335 " pdb=" N CYS K 336 " pdb=" CA CYS K 336 " ideal model delta harmonic sigma weight residual -180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA MET L 24 " pdb=" C MET L 24 " pdb=" N ASN L 25 " pdb=" CA ASN L 25 " ideal model delta harmonic sigma weight residual -180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 26961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 6004 0.057 - 0.115: 998 0.115 - 0.172: 83 0.172 - 0.229: 8 0.229 - 0.286: 5 Chirality restraints: 7098 Sorted by residual: chirality pdb=" CB THR J 290 " pdb=" CA THR J 290 " pdb=" OG1 THR J 290 " pdb=" CG2 THR J 290 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB THR C 290 " pdb=" CA THR C 290 " pdb=" OG1 THR C 290 " pdb=" CG2 THR C 290 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB THR D 290 " pdb=" CA THR D 290 " pdb=" OG1 THR D 290 " pdb=" CG2 THR D 290 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 7095 not shown) Planarity restraints: 7588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 208 " 0.015 2.00e-02 2.50e+03 1.64e-02 6.72e+00 pdb=" CG TRP G 208 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP G 208 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP G 208 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 208 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 208 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 208 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 208 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 208 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP G 208 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 208 " -0.015 2.00e-02 2.50e+03 1.64e-02 6.69e+00 pdb=" CG TRP H 208 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP H 208 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP H 208 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 208 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 208 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 208 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 208 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 208 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 208 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 208 " 0.015 2.00e-02 2.50e+03 1.58e-02 6.26e+00 pdb=" CG TRP F 208 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP F 208 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP F 208 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 208 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 208 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 208 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 208 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 208 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 208 " 0.000 2.00e-02 2.50e+03 ... (remaining 7585 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 1126 2.67 - 3.23: 40163 3.23 - 3.79: 66730 3.79 - 4.34: 91358 4.34 - 4.90: 152236 Nonbonded interactions: 351613 Sorted by model distance: nonbonded pdb=" O SER I 291 " pdb=" OG SER I 298 " model vdw 2.118 3.040 nonbonded pdb=" O SER L 291 " pdb=" OG SER L 298 " model vdw 2.130 3.040 nonbonded pdb=" O SER B 291 " pdb=" OG SER B 298 " model vdw 2.162 3.040 nonbonded pdb=" O SER E 291 " pdb=" OG SER E 298 " model vdw 2.164 3.040 nonbonded pdb=" O SER F 291 " pdb=" OG SER F 298 " model vdw 2.164 3.040 ... (remaining 351608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.160 Process input model: 40.020 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.190 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:9.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 43582 Z= 0.118 Angle : 0.609 11.824 58870 Z= 0.317 Chirality : 0.044 0.286 7098 Planarity : 0.003 0.043 7588 Dihedral : 14.850 89.978 16478 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.93 % Favored : 95.82 % Rotamer: Outliers : 0.69 % Allowed : 15.85 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.12), residues: 5572 helix: 1.34 (0.18), residues: 924 sheet: 1.09 (0.10), residues: 2604 loop : -1.24 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 150 TYR 0.015 0.001 TYR H 96 PHE 0.027 0.001 PHE L 82 TRP 0.044 0.002 TRP G 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (43568) covalent geometry : angle 0.60742 / 0.32 (58842) SS BOND : bond 0.00112 / 0.07 ( 14) SS BOND : angle 2.27091 / 1.43 ( 28) hydrogen bonds : bond 0.19807 / 13.01 ( 1290) hydrogen bonds : angle 8.98582 / 6.21 ( 3651) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 1427 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8099 (mm110) REVERT: A 350 ASN cc_start: 0.8186 (p0) cc_final: 0.7946 (p0) REVERT: A 371 GLU cc_start: 0.8443 (tt0) cc_final: 0.8212 (tt0) REVERT: B 10 GLU cc_start: 0.5357 (mt-10) cc_final: 0.5127 (pt0) REVERT: B 99 ASN cc_start: 0.8188 (m-40) cc_final: 0.7916 (m110) REVERT: B 115 ARG cc_start: 0.7729 (mtp85) cc_final: 0.7461 (mtt90) REVERT: B 138 ASP cc_start: 0.8007 (t0) cc_final: 0.7754 (t0) REVERT: B 154 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6162 (mm-30) REVERT: B 157 ARG cc_start: 0.7082 (ttp80) cc_final: 0.6698 (ttp80) REVERT: B 197 LYS cc_start: 0.6846 (ttmm) cc_final: 0.6552 (ttmm) REVERT: B 241 ARG cc_start: 0.7596 (ttt90) cc_final: 0.7254 (ttt90) REVERT: B 350 ASN cc_start: 0.8358 (p0) cc_final: 0.8154 (p0) REVERT: B 399 LYS cc_start: 0.7893 (mttm) cc_final: 0.7688 (ttmm) REVERT: B 412 ARG cc_start: 0.7492 (mtm-85) cc_final: 0.7132 (ttm-80) REVERT: C 82 PHE cc_start: 0.6338 (t80) cc_final: 0.5890 (t80) REVERT: C 112 SER cc_start: 0.8336 (m) cc_final: 0.8124 (p) REVERT: C 198 LYS cc_start: 0.7296 (tptm) cc_final: 0.7054 (tppp) REVERT: C 220 TRP cc_start: 0.7167 (t60) cc_final: 0.6421 (t60) REVERT: C 239 LEU cc_start: 0.7548 (mt) cc_final: 0.7315 (mp) REVERT: C 256 GLU cc_start: 0.8061 (tt0) cc_final: 0.7858 (tt0) REVERT: C 264 LEU cc_start: 0.8367 (tp) cc_final: 0.8144 (tt) REVERT: C 404 GLU cc_start: 0.8056 (tt0) cc_final: 0.7822 (tp30) REVERT: D 86 GLU cc_start: 0.7791 (pt0) cc_final: 0.7516 (pt0) REVERT: D 101 GLN cc_start: 0.8501 (tt0) cc_final: 0.8263 (tt0) REVERT: D 103 LYS cc_start: 0.8301 (mtmm) cc_final: 0.8068 (mtmm) REVERT: D 115 ARG cc_start: 0.7687 (mmm-85) cc_final: 0.7397 (mtm-85) REVERT: D 128 LEU cc_start: 0.7535 (mm) cc_final: 0.7260 (mt) REVERT: D 132 ARG cc_start: 0.7252 (ptm-80) cc_final: 0.7000 (ptm-80) REVERT: D 154 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6189 (mm-30) REVERT: D 158 LYS cc_start: 0.7508 (mttp) cc_final: 0.7277 (mtpt) REVERT: D 161 ASP cc_start: 0.7923 (t70) cc_final: 0.7622 (t0) REVERT: D 168 GLN cc_start: 0.8326 (mt0) cc_final: 0.8118 (mt0) REVERT: D 198 LYS cc_start: 0.7241 (tptm) cc_final: 0.7041 (tppp) REVERT: D 220 TRP cc_start: 0.7244 (t60) cc_final: 0.6681 (t60) REVERT: D 262 LYS cc_start: 0.7807 (tptm) cc_final: 0.7447 (tptm) REVERT: D 264 LEU cc_start: 0.8366 (tp) cc_final: 0.8096 (tp) REVERT: D 266 ASN cc_start: 0.8383 (m-40) cc_final: 0.8164 (m110) REVERT: D 268 ARG cc_start: 0.8514 (ptt-90) cc_final: 0.8305 (ptt-90) REVERT: D 350 ASN cc_start: 0.8604 (p0) cc_final: 0.8289 (p0) REVERT: D 398 LYS cc_start: 0.8261 (tttt) cc_final: 0.7995 (tttp) REVERT: E 10 GLU cc_start: 0.5823 (mt-10) cc_final: 0.5599 (mt-10) REVERT: E 53 MET cc_start: 0.3816 (mmt) cc_final: 0.3300 (tpt) REVERT: E 154 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6394 (mm-30) REVERT: E 157 ARG cc_start: 0.7385 (ttp80) cc_final: 0.7087 (ttp80) REVERT: E 162 GLU cc_start: 0.7927 (tt0) cc_final: 0.7710 (tt0) REVERT: E 181 ASP cc_start: 0.7866 (m-30) cc_final: 0.7631 (m-30) REVERT: E 198 LYS cc_start: 0.7409 (tptm) cc_final: 0.7069 (tmtt) REVERT: E 225 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7440 (mmtt) REVERT: E 241 ARG cc_start: 0.6954 (ttt90) cc_final: 0.6723 (ttt90) REVERT: E 266 ASN cc_start: 0.8262 (m-40) cc_final: 0.8024 (m-40) REVERT: E 280 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7722 (mt-10) REVERT: E 404 GLU cc_start: 0.7833 (tt0) cc_final: 0.7560 (tt0) REVERT: F 10 GLU cc_start: 0.5566 (mt-10) cc_final: 0.5364 (mt-10) REVERT: F 53 MET cc_start: 0.4293 (mmt) cc_final: 0.3658 (tpt) REVERT: F 60 MET cc_start: 0.3940 (mmm) cc_final: 0.3325 (tpp) REVERT: F 67 VAL cc_start: 0.6096 (m) cc_final: 0.5631 (m) REVERT: F 69 ILE cc_start: 0.5320 (mp) cc_final: 0.5029 (pt) REVERT: F 115 ARG cc_start: 0.7502 (mmm-85) cc_final: 0.7261 (mtm-85) REVERT: F 132 ARG cc_start: 0.7112 (ptm160) cc_final: 0.6867 (ptm-80) REVERT: F 138 ASP cc_start: 0.7559 (t0) cc_final: 0.7295 (t0) REVERT: F 178 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7624 (mt-10) REVERT: F 185 ARG cc_start: 0.7782 (ttp80) cc_final: 0.7362 (ttp80) REVERT: F 198 LYS cc_start: 0.7387 (tptm) cc_final: 0.7131 (mmmt) REVERT: F 220 TRP cc_start: 0.7077 (t60) cc_final: 0.6501 (t60) REVERT: F 225 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7434 (mmpt) REVERT: F 235 ASN cc_start: 0.7783 (m-40) cc_final: 0.7548 (m-40) REVERT: F 305 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8154 (mtpp) REVERT: F 358 GLU cc_start: 0.8234 (pt0) cc_final: 0.8023 (pt0) REVERT: F 404 GLU cc_start: 0.8138 (tt0) cc_final: 0.7869 (tt0) REVERT: G 10 GLU cc_start: 0.5786 (mt-10) cc_final: 0.5531 (mt-10) REVERT: G 24 MET cc_start: 0.4209 (tmt) cc_final: 0.3194 (tmt) REVERT: G 60 MET cc_start: 0.3561 (mmm) cc_final: 0.3233 (tpp) REVERT: G 115 ARG cc_start: 0.7747 (mtp85) cc_final: 0.7433 (mtt90) REVERT: G 178 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7707 (mt-10) REVERT: G 191 PHE cc_start: 0.7811 (t80) cc_final: 0.7589 (t80) REVERT: G 235 ASN cc_start: 0.7923 (m-40) cc_final: 0.7695 (m-40) REVERT: G 239 LEU cc_start: 0.7430 (mt) cc_final: 0.7208 (mp) REVERT: G 241 ARG cc_start: 0.7070 (ttt90) cc_final: 0.6769 (ttt90) REVERT: G 256 GLU cc_start: 0.8008 (tt0) cc_final: 0.7802 (tt0) REVERT: G 280 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8094 (mt-10) REVERT: G 321 GLN cc_start: 0.8000 (mt0) cc_final: 0.7781 (mt0) REVERT: G 342 THR cc_start: 0.7742 (m) cc_final: 0.7336 (t) REVERT: G 398 LYS cc_start: 0.8319 (tttt) cc_final: 0.8050 (tttm) REVERT: H 16 GLN cc_start: 0.9025 (tp40) cc_final: 0.8810 (pt0) REVERT: H 82 PHE cc_start: 0.6113 (t80) cc_final: 0.5828 (t80) REVERT: H 115 ARG cc_start: 0.7782 (mmm-85) cc_final: 0.7495 (mtm-85) REVERT: H 173 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7432 (tm-30) REVERT: H 191 PHE cc_start: 0.7674 (t80) cc_final: 0.7428 (t80) REVERT: H 225 LYS cc_start: 0.7827 (mmtt) cc_final: 0.7615 (mmmt) REVERT: H 256 GLU cc_start: 0.8105 (tt0) cc_final: 0.7773 (tt0) REVERT: H 260 LYS cc_start: 0.8073 (mtpp) cc_final: 0.7862 (mtpp) REVERT: H 321 GLN cc_start: 0.7749 (mt0) cc_final: 0.7535 (mt0) REVERT: H 404 GLU cc_start: 0.8093 (tt0) cc_final: 0.7845 (tp30) REVERT: I 108 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7695 (mm-30) REVERT: I 132 ARG cc_start: 0.7748 (ttp-110) cc_final: 0.7468 (ttp-110) REVERT: I 138 ASP cc_start: 0.8058 (t0) cc_final: 0.7403 (t0) REVERT: I 185 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7561 (ttp80) REVERT: I 197 LYS cc_start: 0.6741 (ttmm) cc_final: 0.6473 (ttmm) REVERT: I 241 ARG cc_start: 0.6938 (ttt90) cc_final: 0.6432 (ttt90) REVERT: I 256 GLU cc_start: 0.8140 (tt0) cc_final: 0.7882 (tt0) REVERT: I 262 LYS cc_start: 0.7633 (tptm) cc_final: 0.7423 (tmtm) REVERT: I 280 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8127 (mt-10) REVERT: I 305 LYS cc_start: 0.7770 (mttm) cc_final: 0.7518 (mttm) REVERT: I 356 MET cc_start: 0.8747 (ttp) cc_final: 0.8521 (ttm) REVERT: I 394 LYS cc_start: 0.7440 (mtmt) cc_final: 0.7178 (mtpt) REVERT: J 132 ARG cc_start: 0.7935 (ptm160) cc_final: 0.7380 (ptm-80) REVERT: J 147 THR cc_start: 0.7982 (m) cc_final: 0.7681 (p) REVERT: J 154 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6510 (mm-30) REVERT: J 164 ASP cc_start: 0.8056 (t0) cc_final: 0.7522 (t0) REVERT: J 198 LYS cc_start: 0.7263 (tptm) cc_final: 0.7006 (tmtt) REVERT: J 231 THR cc_start: 0.7111 (p) cc_final: 0.6881 (p) REVERT: J 251 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6952 (mt-10) REVERT: J 394 LYS cc_start: 0.7335 (mtmt) cc_final: 0.7025 (mtmt) REVERT: J 396 ARG cc_start: 0.7679 (mtp85) cc_final: 0.7401 (mtp180) REVERT: K 86 GLU cc_start: 0.7865 (pt0) cc_final: 0.7636 (pt0) REVERT: K 103 LYS cc_start: 0.8241 (mtmm) cc_final: 0.8015 (mtmm) REVERT: K 132 ARG cc_start: 0.7333 (ttp-170) cc_final: 0.7076 (ttp-170) REVERT: K 154 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6537 (mm-30) REVERT: K 164 ASP cc_start: 0.7415 (t0) cc_final: 0.7182 (t0) REVERT: K 181 ASP cc_start: 0.8025 (m-30) cc_final: 0.7556 (m-30) REVERT: K 185 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7494 (ttp80) REVERT: K 198 LYS cc_start: 0.7345 (tptm) cc_final: 0.6976 (tmtt) REVERT: K 252 LEU cc_start: 0.7774 (mp) cc_final: 0.7550 (mm) REVERT: K 260 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7835 (ttmm) REVERT: K 262 LYS cc_start: 0.7934 (tptm) cc_final: 0.7620 (tmtt) REVERT: K 268 ARG cc_start: 0.8526 (ptt180) cc_final: 0.8276 (ptt-90) REVERT: K 358 GLU cc_start: 0.8220 (pt0) cc_final: 0.8001 (pt0) REVERT: K 401 ASP cc_start: 0.7478 (m-30) cc_final: 0.7273 (m-30) REVERT: L 115 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7436 (mtt90) REVERT: L 198 LYS cc_start: 0.7158 (tptm) cc_final: 0.6774 (tmtt) REVERT: L 260 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7596 (ttpp) REVERT: L 266 ASN cc_start: 0.8112 (m-40) cc_final: 0.7847 (m110) REVERT: L 335 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7977 (mm110) REVERT: M 112 SER cc_start: 0.8208 (m) cc_final: 0.7883 (p) REVERT: M 138 ASP cc_start: 0.7767 (t0) cc_final: 0.7507 (t0) REVERT: M 220 TRP cc_start: 0.6838 (t60) cc_final: 0.6414 (t60) REVERT: M 315 ASN cc_start: 0.7944 (m-40) cc_final: 0.7704 (m110) REVERT: M 399 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7779 (mtmm) REVERT: N 16 GLN cc_start: 0.8905 (tp40) cc_final: 0.8679 (pt0) REVERT: N 47 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8242 (mp-120) REVERT: N 60 MET cc_start: 0.3410 (mmm) cc_final: 0.2652 (mmp) REVERT: N 108 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7459 (mm-30) REVERT: N 138 ASP cc_start: 0.7872 (t0) cc_final: 0.7321 (t0) REVERT: N 161 ASP cc_start: 0.7643 (t70) cc_final: 0.7391 (t70) REVERT: N 256 GLU cc_start: 0.7976 (tt0) cc_final: 0.7710 (tt0) outliers start: 33 outliers final: 15 residues processed: 1452 average time/residue: 0.8737 time to fit residues: 1504.8623 Evaluate side-chains 1275 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 1260 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 340 ASN Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain I residue 340 ASN Chi-restraints excluded: chain I residue 382 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain N residue 340 ASN Chi-restraints excluded: chain N residue 382 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: [394, 430, 41, 265, 523, 497, 414, 310, 488, 366, 223] chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 0.9990 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 0.8980 chunk 310 optimal weight: 0.1980 chunk 488 optimal weight: 2.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN B 101 GLN B 169 GLN B 329 ASN B 373 ASN C 101 GLN C 169 GLN C 329 ASN C 354 GLN C 375 ASN D 99 ASN D 169 GLN ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN D 350 ASN D 373 ASN E 84 GLN E 98 GLN E 169 GLN E 315 ASN E 354 GLN F 84 GLN F 169 GLN F 329 ASN F 352 ASN F 354 GLN G 169 GLN G 329 ASN G 354 GLN H 169 GLN H 340 ASN I 16 GLN I 169 GLN I 272 GLN I 321 GLN I 375 ASN J 16 GLN J 99 ASN ** J 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 GLN K 329 ASN K 352 ASN K 373 ASN L 329 ASN L 354 GLN M 16 GLN M 169 GLN M 321 GLN M 329 ASN M 354 GLN M 375 ASN N 98 GLN N 315 ASN N 329 ASN N 340 ASN N 350 ASN N 354 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.200283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.171408 restraints weight = 56404.654| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 1.88 r_work: 0.4163 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4041 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 43582 Z= 0.217 Angle : 0.681 11.296 58870 Z= 0.344 Chirality : 0.047 0.232 7098 Planarity : 0.004 0.051 7588 Dihedral : 4.900 53.725 5963 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.34 % Favored : 95.41 % Rotamer: Outliers : 4.89 % Allowed : 18.76 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.11), residues: 5572 helix: 0.87 (0.17), residues: 924 sheet: 0.71 (0.10), residues: 2716 loop : -1.17 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 72 TYR 0.008 0.001 TYR N 283 PHE 0.018 0.002 PHE M 408 TRP 0.029 0.002 TRP E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (43568) covalent geometry : angle 0.68021 / 0.34 (58842) SS BOND : bond 0.00486 / 0.32 ( 14) SS BOND : angle 1.76269 / 1.14 ( 28) hydrogen bonds : bond 0.04143 / 2.71 ( 1290) hydrogen bonds : angle 6.08985 / 4.21 ( 3651) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1675 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 1441 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7787 (ptm160) REVERT: A 335 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8187 (mm110) REVERT: B 24 MET cc_start: 0.1615 (tmt) cc_final: 0.0655 (tmt) REVERT: B 132 ARG cc_start: 0.8204 (ptm-80) cc_final: 0.7899 (ttp-110) REVERT: B 241 ARG cc_start: 0.8068 (ttt90) cc_final: 0.7842 (ttt90) REVERT: C 10 GLU cc_start: 0.5479 (OUTLIER) cc_final: 0.5279 (pm20) REVERT: C 24 MET cc_start: 0.2595 (tmt) cc_final: 0.1556 (tmt) REVERT: C 53 MET cc_start: 0.4393 (OUTLIER) cc_final: 0.3866 (tmm) REVERT: C 164 ASP cc_start: 0.8059 (t0) cc_final: 0.7849 (t0) REVERT: D 24 MET cc_start: 0.2353 (tmt) cc_final: 0.1706 (tmt) REVERT: D 25 ASN cc_start: 0.5384 (p0) cc_final: 0.5081 (p0) REVERT: D 115 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7661 (mtm-85) REVERT: D 154 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7199 (mm-30) REVERT: E 17 ILE cc_start: 0.8858 (mm) cc_final: 0.8555 (pp) REVERT: E 53 MET cc_start: 0.4406 (OUTLIER) cc_final: 0.4087 (tpp) REVERT: E 67 VAL cc_start: 0.7027 (OUTLIER) cc_final: 0.6803 (p) REVERT: E 173 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: E 194 THR cc_start: 0.8486 (p) cc_final: 0.7987 (t) REVERT: F 302 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6586 (tm-30) REVERT: G 115 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7874 (mtt90) REVERT: G 262 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8024 (tmtm) REVERT: G 343 ILE cc_start: 0.8745 (pt) cc_final: 0.8437 (pt) REVERT: H 24 MET cc_start: 0.2248 (tmt) cc_final: 0.1636 (tmt) REVERT: H 284 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7855 (mt-10) REVERT: I 24 MET cc_start: 0.1489 (tmt) cc_final: 0.1140 (tmt) REVERT: I 101 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8173 (tp-100) REVERT: I 141 THR cc_start: 0.8454 (p) cc_final: 0.8210 (p) REVERT: I 154 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7063 (mm-30) REVERT: J 24 MET cc_start: 0.0254 (tmt) cc_final: -0.0574 (tmt) REVERT: J 138 ASP cc_start: 0.7877 (t0) cc_final: 0.7613 (t0) REVERT: J 141 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8327 (p) REVERT: J 154 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7216 (mm-30) REVERT: J 164 ASP cc_start: 0.8067 (t0) cc_final: 0.7817 (t0) REVERT: J 396 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7902 (mtp85) REVERT: K 154 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6988 (mm-30) REVERT: K 181 ASP cc_start: 0.7967 (m-30) cc_final: 0.7704 (m-30) REVERT: L 24 MET cc_start: 0.1049 (tmt) cc_final: 0.0047 (tmt) REVERT: L 132 ARG cc_start: 0.8232 (ttp80) cc_final: 0.8027 (ptm-80) REVERT: L 154 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7217 (mm-30) REVERT: L 185 ARG cc_start: 0.8358 (ttp80) cc_final: 0.7934 (ttp80) REVERT: L 274 ARG cc_start: 0.8668 (mtt180) cc_final: 0.8358 (mtt180) REVERT: L 350 ASN cc_start: 0.8104 (p0) cc_final: 0.7888 (p0) REVERT: M 24 MET cc_start: 0.1207 (tmt) cc_final: -0.0101 (tmt) REVERT: M 53 MET cc_start: 0.4281 (OUTLIER) cc_final: 0.2621 (tmm) REVERT: M 154 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7114 (mm-30) REVERT: M 173 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: M 185 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7865 (ttp80) REVERT: M 404 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: N 24 MET cc_start: 0.1911 (tmt) cc_final: 0.0934 (tmt) REVERT: N 154 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7116 (mm-30) outliers start: 234 outliers final: 93 residues processed: 1562 average time/residue: 0.8606 time to fit residues: 1597.0517 Evaluate side-chains 1452 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 1346 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 ASN Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain G residue 262 LYS Chi-restraints excluded: chain G residue 278 LYS Chi-restraints excluded: chain G residue 324 MET Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 363 LEU Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 382 LEU Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 340 ASN Chi-restraints excluded: chain H residue 344 LEU Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain I residue 128 LEU Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 340 ASN Chi-restraints excluded: chain I residue 382 LEU Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 352 ASN Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 53 MET Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 244 SER Chi-restraints excluded: chain K residue 382 LEU Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain L residue 161 ASP Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 118 ASN Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 164 ASP Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 404 GLU Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 340 ASN Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 410 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: [59, 193, 440, 46, 408, 524, 99, 501, 293, 305, 219] chunk 59 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 440 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 408 optimal weight: 4.9990 chunk 524 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 501 optimal weight: 0.9990 chunk 293 optimal weight: 2.9990 chunk 305 optimal weight: 0.6980 chunk 219 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN A 169 GLN B 101 GLN B 169 GLN B 315 ASN C 16 GLN C 84 GLN C 169 GLN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN C 354 GLN D 101 GLN D 169 GLN ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN D 329 ASN D 352 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN E 169 GLN E 315 ASN E 321 GLN E 329 ASN E 352 ASN E 354 GLN F 16 GLN F 84 GLN F 329 ASN F 352 ASN F 354 GLN G 84 GLN G 169 GLN G 335 GLN G 354 GLN H 101 GLN H 169 GLN H 329 ASN H 352 ASN I 169 GLN I 272 GLN I 329 ASN J 99 ASN J 169 GLN J 350 ASN K 169 GLN K 329 ASN K 340 ASN L 169 GLN L 329 ASN L 341 GLN M 329 ASN M 354 GLN N 169 GLN N 315 ASN N 354 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.195967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.167752 restraints weight = 55774.888| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 1.85 r_work: 0.4126 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 43582 Z= 0.227 Angle : 0.684 12.130 58870 Z= 0.345 Chirality : 0.047 0.223 7098 Planarity : 0.004 0.044 7588 Dihedral : 5.075 55.858 5955 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.61 % Favored : 95.14 % Rotamer: Outliers : 5.12 % Allowed : 20.93 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.11), residues: 5572 helix: 0.04 (0.15), residues: 966 sheet: 0.47 (0.10), residues: 2716 loop : -1.42 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 150 TYR 0.009 0.001 TYR I 283 PHE 0.026 0.002 PHE N 82 TRP 0.021 0.002 TRP E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 (43568) covalent geometry : angle 0.68120 / 0.34 (58842) SS BOND : bond 0.00359 / 0.23 ( 14) SS BOND : angle 2.87422 / 1.91 ( 28) hydrogen bonds : bond 0.03677 / 2.40 ( 1290) hydrogen bonds : angle 5.69053 / 3.93 ( 3651) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1649 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 1404 time to evaluate : 1.543 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 10 GLU cc_start: 0.5669 (OUTLIER) cc_final: 0.5446 (pm20) REVERT: A 132 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7543 (ptm160) REVERT: A 335 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8166 (mm110) REVERT: B 24 MET cc_start: 0.1562 (tmt) cc_final: 0.0397 (tmt) REVERT: B 53 MET cc_start: 0.4533 (OUTLIER) cc_final: 0.4143 (tpt) REVERT: B 132 ARG cc_start: 0.8405 (ptm-80) cc_final: 0.8089 (ttp-110) REVERT: B 241 ARG cc_start: 0.8107 (ttt90) cc_final: 0.7877 (ttt90) REVERT: B 280 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7182 (mt-10) REVERT: C 10 GLU cc_start: 0.5542 (OUTLIER) cc_final: 0.5325 (pm20) REVERT: C 24 MET cc_start: 0.2927 (tmt) cc_final: 0.0894 (tmt) REVERT: C 220 TRP cc_start: 0.8545 (t60) cc_final: 0.8214 (t60) REVERT: C 304 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8344 (mmtm) REVERT: D 115 ARG cc_start: 0.8052 (mmm-85) cc_final: 0.7717 (mtm-85) REVERT: D 154 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7156 (mm-30) REVERT: D 223 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7192 (mm-30) REVERT: E 86 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6085 (mp0) REVERT: E 154 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7205 (mm-30) REVERT: E 173 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7198 (tt0) REVERT: E 278 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8252 (ttpp) REVERT: F 26 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7884 (mp) REVERT: F 185 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7720 (ttp80) REVERT: F 302 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6562 (tm-30) REVERT: F 304 LYS cc_start: 0.8756 (mmtm) cc_final: 0.8555 (mmtt) REVERT: G 115 ARG cc_start: 0.8103 (mtp85) cc_final: 0.7889 (mtt90) REVERT: H 10 GLU cc_start: 0.5986 (mp0) cc_final: 0.5677 (mp0) REVERT: H 24 MET cc_start: 0.1885 (tmt) cc_final: 0.0631 (tmt) REVERT: I 24 MET cc_start: 0.1835 (tmt) cc_final: 0.0858 (tmt) REVERT: I 154 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7098 (mm-30) REVERT: I 302 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5888 (tm-30) REVERT: J 24 MET cc_start: 0.0475 (tmt) cc_final: -0.0184 (tmt) REVERT: J 138 ASP cc_start: 0.7857 (t0) cc_final: 0.7569 (t0) REVERT: J 141 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8287 (p) REVERT: J 164 ASP cc_start: 0.8081 (t0) cc_final: 0.7837 (t0) REVERT: K 115 ARG cc_start: 0.7884 (mmm-85) cc_final: 0.7627 (mtm-85) REVERT: K 132 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8088 (ttp-110) REVERT: K 154 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6967 (mm-30) REVERT: K 304 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8444 (mmtt) REVERT: L 24 MET cc_start: 0.1156 (tmt) cc_final: 0.0004 (tmt) REVERT: L 132 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7751 (ttp-110) REVERT: L 154 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7189 (mm-30) REVERT: L 185 ARG cc_start: 0.8337 (ttp80) cc_final: 0.7946 (ttp80) REVERT: L 268 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8100 (ptt180) REVERT: L 402 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7545 (ttp80) REVERT: M 24 MET cc_start: 0.1499 (tmt) cc_final: 0.0703 (tmt) REVERT: M 154 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7154 (mm-30) REVERT: M 175 ARG cc_start: 0.7683 (ttp-110) cc_final: 0.7445 (ttp-110) REVERT: M 185 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7894 (ttp80) REVERT: M 404 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7325 (tp30) REVERT: N 24 MET cc_start: 0.1933 (tmt) cc_final: 0.0642 (tmt) REVERT: N 185 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7482 (ttp80) outliers start: 245 outliers final: 119 residues processed: 1549 average time/residue: 0.8567 time to fit residues: 1574.8736 Evaluate side-chains 1499 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1367 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 352 ASN Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain G residue 278 LYS Chi-restraints excluded: chain G residue 324 MET Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 382 LEU Chi-restraints excluded: chain G residue 399 LYS Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 352 ASN Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain I residue 5 ASP Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain I residue 153 ILE Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 382 LEU Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain J residue 5 ASP Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 196 LYS Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain K residue 53 MET Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 132 ARG Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 244 SER Chi-restraints excluded: chain K residue 262 LYS Chi-restraints excluded: chain K residue 340 ASN Chi-restraints excluded: chain K residue 372 ASP Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 161 ASP Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 268 ARG Chi-restraints excluded: chain L residue 402 ARG Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 402 ARG Chi-restraints excluded: chain M residue 404 GLU Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 410 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: [6, 409, 490, 156, 179, 261, 481, 380, 229, 456, 103] chunk 6 optimal weight: 0.7980 chunk 409 optimal weight: 1.9990 chunk 490 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 481 optimal weight: 0.7980 chunk 380 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 456 optimal weight: 4.9990 chunk 103 optimal weight: 0.0570 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 GLN A 101 GLN A 169 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN B 16 GLN B 101 GLN B 169 GLN B 315 ASN B 329 ASN C 169 GLN C 272 GLN C 321 GLN C 354 GLN C 391 ASN D 16 GLN D 169 GLN ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D 329 ASN E 84 GLN E 272 GLN E 315 ASN E 321 GLN E 354 GLN F 169 GLN F 329 ASN F 352 ASN F 354 GLN G 16 GLN G 84 GLN G 354 GLN H 47 GLN H 84 GLN H 101 GLN H 272 GLN H 329 ASN H 354 GLN I 169 GLN I 272 GLN I 354 GLN J 84 GLN J 99 ASN J 169 GLN J 329 ASN J 341 GLN J 352 ASN J 354 GLN K 16 GLN K 101 GLN K 169 GLN K 340 ASN K 352 ASN L 169 GLN L 329 ASN ** L 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 GLN M 329 ASN M 352 ASN M 354 GLN N 169 GLN N 354 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.195990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.168117 restraints weight = 55459.737| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 1.84 r_work: 0.4133 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.4008 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 43582 Z= 0.173 Angle : 0.653 12.149 58870 Z= 0.327 Chirality : 0.046 0.200 7098 Planarity : 0.004 0.054 7588 Dihedral : 4.784 40.339 5949 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.45 % Favored : 95.30 % Rotamer: Outliers : 5.08 % Allowed : 22.28 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.11), residues: 5572 helix: 0.07 (0.16), residues: 966 sheet: 0.40 (0.10), residues: 2562 loop : -1.44 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 396 TYR 0.010 0.001 TYR J 96 PHE 0.031 0.001 PHE F 82 TRP 0.014 0.001 TRP C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (43568) covalent geometry : angle 0.65152 / 0.33 (58842) SS BOND : bond 0.00543 / 0.32 ( 14) SS BOND : angle 2.05284 / 1.26 ( 28) hydrogen bonds : bond 0.03405 / 2.23 ( 1290) hydrogen bonds : angle 5.46256 / 3.77 ( 3651) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1644 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 1401 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.5655 (OUTLIER) cc_final: 0.5356 (pm20) REVERT: A 335 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8211 (mm110) REVERT: B 24 MET cc_start: 0.1525 (tmt) cc_final: 0.1016 (tmt) REVERT: B 53 MET cc_start: 0.5091 (OUTLIER) cc_final: 0.4519 (tpt) REVERT: B 241 ARG cc_start: 0.8112 (ttt90) cc_final: 0.7876 (ttt90) REVERT: B 402 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7520 (ttp80) REVERT: C 10 GLU cc_start: 0.5773 (OUTLIER) cc_final: 0.5561 (pm20) REVERT: C 24 MET cc_start: 0.3105 (tmt) cc_final: 0.1440 (tmt) REVERT: C 25 ASN cc_start: 0.5978 (p0) cc_final: 0.5313 (p0) REVERT: C 220 TRP cc_start: 0.8579 (t60) cc_final: 0.8193 (t60) REVERT: C 304 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8412 (mmtm) REVERT: C 349 LYS cc_start: 0.8270 (mtmm) cc_final: 0.8067 (mttp) REVERT: D 24 MET cc_start: 0.1925 (tmt) cc_final: 0.0008 (tmt) REVERT: D 53 MET cc_start: 0.4879 (OUTLIER) cc_final: 0.3735 (tmm) REVERT: D 115 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7706 (mtm-85) REVERT: D 154 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7171 (mm-30) REVERT: D 223 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7117 (mm-30) REVERT: D 225 LYS cc_start: 0.8373 (mmtt) cc_final: 0.8091 (mmtt) REVERT: E 154 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7167 (mm-30) REVERT: E 173 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7166 (tt0) REVERT: E 241 ARG cc_start: 0.7625 (ttt90) cc_final: 0.7220 (mtp-110) REVERT: F 302 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6594 (tm-30) REVERT: G 10 GLU cc_start: 0.5553 (mp0) cc_final: 0.5262 (mp0) REVERT: G 115 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7883 (mtt90) REVERT: G 185 ARG cc_start: 0.7635 (ttp80) cc_final: 0.6809 (ttp80) REVERT: H 10 GLU cc_start: 0.5456 (mp0) cc_final: 0.5160 (mp0) REVERT: H 82 PHE cc_start: 0.5790 (t80) cc_final: 0.5400 (t80) REVERT: I 24 MET cc_start: 0.1792 (tmt) cc_final: 0.1108 (tmt) REVERT: I 154 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7061 (mm-30) REVERT: I 302 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5927 (tm-30) REVERT: J 10 GLU cc_start: 0.5750 (mp0) cc_final: 0.5148 (mp0) REVERT: J 24 MET cc_start: 0.0372 (tmt) cc_final: -0.0019 (tmt) REVERT: J 138 ASP cc_start: 0.7793 (t0) cc_final: 0.7507 (t0) REVERT: J 141 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8317 (p) REVERT: J 164 ASP cc_start: 0.8075 (t0) cc_final: 0.7819 (t0) REVERT: J 302 GLU cc_start: 0.4934 (OUTLIER) cc_final: 0.4655 (pm20) REVERT: J 396 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7820 (mtp180) REVERT: K 10 GLU cc_start: 0.5346 (mp0) cc_final: 0.5111 (mp0) REVERT: K 101 GLN cc_start: 0.8596 (tt0) cc_final: 0.8332 (tt0) REVERT: K 115 ARG cc_start: 0.7866 (mmm-85) cc_final: 0.7605 (mtm-85) REVERT: K 154 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6988 (mm-30) REVERT: L 24 MET cc_start: 0.0972 (tmt) cc_final: 0.0003 (tmt) REVERT: L 154 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7226 (mm-30) REVERT: L 185 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7908 (ttp80) REVERT: M 10 GLU cc_start: 0.5354 (OUTLIER) cc_final: 0.5093 (pm20) REVERT: M 24 MET cc_start: 0.1621 (tmt) cc_final: 0.1265 (tmt) REVERT: M 154 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7207 (mm-30) REVERT: M 185 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7829 (ttp80) REVERT: N 24 MET cc_start: 0.2318 (tmt) cc_final: 0.1399 (tmt) REVERT: N 185 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7368 (ttp80) outliers start: 243 outliers final: 127 residues processed: 1542 average time/residue: 0.8663 time to fit residues: 1585.4052 Evaluate side-chains 1499 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 1361 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 262 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain G residue 278 LYS Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 399 LYS Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 340 ASN Chi-restraints excluded: chain H residue 358 GLU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain I residue 153 ILE Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 382 LEU Chi-restraints excluded: chain I residue 409 ILE Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain J residue 302 GLU Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain K residue 53 MET Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 244 SER Chi-restraints excluded: chain K residue 262 LYS Chi-restraints excluded: chain K residue 340 ASN Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 392 LEU Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 340 ASN Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 399 LYS Chi-restraints excluded: chain N residue 410 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: [200, 180, 265, 396, 18, 60, 84, 288, 520, 240, 442] chunk 200 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 265 optimal weight: 0.7980 chunk 396 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 288 optimal weight: 3.9990 chunk 520 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 442 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN A 169 GLN A 329 ASN B 16 GLN B 101 GLN B 169 GLN C 101 GLN C 169 GLN C 329 ASN C 350 ASN C 354 GLN D 84 GLN D 169 GLN D 211 ASN D 321 GLN D 329 ASN D 352 ASN E 84 GLN E 315 ASN E 321 GLN E 352 ASN E 354 GLN F 25 ASN F 84 GLN F 101 GLN F 329 ASN F 352 ASN F 354 GLN G 169 GLN G 354 GLN H 84 GLN H 101 GLN H 329 ASN H 354 GLN I 169 GLN I 272 GLN I 352 ASN J 84 GLN J 169 GLN ** J 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 352 ASN K 169 GLN L 169 GLN L 329 ASN L 350 ASN L 352 ASN M 101 GLN M 169 GLN M 329 ASN M 352 ASN N 16 GLN N 169 GLN N 249 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.189288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.162306 restraints weight = 55521.794| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 1.84 r_work: 0.4074 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 43582 Z= 0.383 Angle : 0.801 10.552 58870 Z= 0.403 Chirality : 0.050 0.244 7098 Planarity : 0.005 0.060 7588 Dihedral : 5.516 42.515 5949 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.28 % Favored : 94.47 % Rotamer: Outliers : 5.70 % Allowed : 23.10 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.11), residues: 5572 helix: -1.08 (0.15), residues: 1036 sheet: 0.37 (0.10), residues: 2450 loop : -1.90 (0.12), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 150 TYR 0.015 0.002 TYR J 96 PHE 0.040 0.003 PHE F 82 TRP 0.028 0.003 TRP J 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00902 / 0.38 (43568) covalent geometry : angle 0.79662 / 0.40 (58842) SS BOND : bond 0.00550 / 0.28 ( 14) SS BOND : angle 3.89797 / 2.64 ( 28) hydrogen bonds : bond 0.04158 / 2.74 ( 1290) hydrogen bonds : angle 5.89664 / 4.09 ( 3651) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1729 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 273 poor density : 1456 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ILE cc_start: 0.6516 (mm) cc_final: 0.6207 (mm) REVERT: A 82 PHE cc_start: 0.6455 (t80) cc_final: 0.5864 (t80) REVERT: A 335 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8267 (mm110) REVERT: B 53 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4907 (tpp) REVERT: B 241 ARG cc_start: 0.8144 (ttt90) cc_final: 0.7920 (ttt90) REVERT: B 303 LEU cc_start: 0.8635 (mp) cc_final: 0.8388 (mm) REVERT: B 402 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7634 (ttp80) REVERT: C 10 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.6023 (pm20) REVERT: C 24 MET cc_start: 0.3527 (tmt) cc_final: 0.2246 (tmt) REVERT: C 115 ARG cc_start: 0.7968 (mmm-85) cc_final: 0.7652 (mtm-85) REVERT: C 132 ARG cc_start: 0.8664 (ptm-80) cc_final: 0.8437 (ptm160) REVERT: D 10 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6099 (pm20) REVERT: D 24 MET cc_start: 0.2382 (tmt) cc_final: 0.0589 (tmt) REVERT: D 53 MET cc_start: 0.5305 (OUTLIER) cc_final: 0.4624 (tpt) REVERT: D 115 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.7718 (mtm-85) REVERT: D 132 ARG cc_start: 0.8462 (ptm-80) cc_final: 0.8255 (ttp-110) REVERT: D 154 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7288 (mm-30) REVERT: D 393 PHE cc_start: 0.8515 (m-80) cc_final: 0.8315 (m-80) REVERT: E 10 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.6097 (pm20) REVERT: E 69 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7536 (mm) REVERT: E 173 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7197 (tt0) REVERT: F 98 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: F 302 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: F 304 LYS cc_start: 0.8815 (mmtm) cc_final: 0.8576 (mmtt) REVERT: G 10 GLU cc_start: 0.5444 (mp0) cc_final: 0.5208 (mp0) REVERT: H 82 PHE cc_start: 0.6479 (t80) cc_final: 0.6137 (t80) REVERT: H 198 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7843 (tmtt) REVERT: I 10 GLU cc_start: 0.5990 (mp0) cc_final: 0.5685 (mp0) REVERT: I 24 MET cc_start: 0.2363 (OUTLIER) cc_final: 0.1883 (tmt) REVERT: I 154 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7155 (mm-30) REVERT: I 304 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8403 (mmtp) REVERT: J 138 ASP cc_start: 0.7870 (t0) cc_final: 0.7616 (t0) REVERT: J 164 ASP cc_start: 0.8217 (t0) cc_final: 0.7991 (t0) REVERT: J 302 GLU cc_start: 0.5721 (OUTLIER) cc_final: 0.5404 (pm20) REVERT: K 10 GLU cc_start: 0.5566 (mp0) cc_final: 0.5213 (mp0) REVERT: K 60 MET cc_start: 0.6075 (tmm) cc_final: 0.5265 (tmm) REVERT: K 69 ILE cc_start: 0.7519 (mp) cc_final: 0.7293 (mm) REVERT: K 154 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7106 (tm-30) REVERT: K 191 PHE cc_start: 0.8054 (t80) cc_final: 0.7791 (t80) REVERT: L 24 MET cc_start: 0.1600 (tmt) cc_final: 0.0762 (tmt) REVERT: L 154 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7272 (tm-30) REVERT: L 268 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8010 (ptt180) REVERT: L 347 SER cc_start: 0.8283 (t) cc_final: 0.8031 (p) REVERT: M 10 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5875 (pm20) REVERT: M 404 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: N 24 MET cc_start: 0.2932 (tmt) cc_final: 0.2372 (tmt) REVERT: N 154 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7200 (mm-30) REVERT: N 185 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7783 (ttp80) outliers start: 273 outliers final: 142 residues processed: 1593 average time/residue: 0.8447 time to fit residues: 1599.8778 Evaluate side-chains 1562 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1404 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 98 GLN Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 399 LYS Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain G residue 278 LYS Chi-restraints excluded: chain G residue 324 MET Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 382 LEU Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 358 GLU Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain I residue 153 ILE Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 352 ASN Chi-restraints excluded: chain I residue 399 LYS Chi-restraints excluded: chain I residue 409 ILE Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain J residue 302 GLU Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 53 MET Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 260 LYS Chi-restraints excluded: chain K residue 262 LYS Chi-restraints excluded: chain K residue 349 LYS Chi-restraints excluded: chain K residue 372 ASP Chi-restraints excluded: chain K residue 382 LEU Chi-restraints excluded: chain K residue 392 LEU Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 268 ARG Chi-restraints excluded: chain L residue 352 ASN Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 292 ILE Chi-restraints excluded: chain M residue 324 MET Chi-restraints excluded: chain M residue 352 ASN Chi-restraints excluded: chain M residue 358 GLU Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 392 LEU Chi-restraints excluded: chain M residue 404 GLU Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 399 LYS Chi-restraints excluded: chain N residue 409 ILE Chi-restraints excluded: chain N residue 410 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: [31, 79, 449, 113, 268, 513, 438, 7, 186, 264, 97] chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 449 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 268 optimal weight: 30.0000 chunk 513 optimal weight: 0.9990 chunk 438 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN B 16 GLN B 101 GLN B 169 GLN B 272 GLN C 169 GLN C 321 GLN C 341 GLN C 350 ASN C 354 GLN D 169 GLN D 272 GLN E 84 GLN E 315 ASN E 321 GLN F 84 GLN F 329 ASN F 352 ASN F 354 GLN G 169 GLN G 354 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 GLN I 169 GLN I 272 GLN I 352 ASN J 16 GLN J 352 ASN J 354 GLN K 101 GLN K 169 GLN K 272 GLN L 16 GLN L 169 GLN L 329 ASN M 169 GLN M 329 ASN M 354 GLN N 169 GLN N 329 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.190567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.163636 restraints weight = 55519.491| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 1.84 r_work: 0.4092 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 43582 Z= 0.232 Angle : 0.705 10.625 58870 Z= 0.355 Chirality : 0.047 0.197 7098 Planarity : 0.004 0.045 7588 Dihedral : 5.058 39.996 5943 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.63 % Favored : 95.12 % Rotamer: Outliers : 4.85 % Allowed : 25.58 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.11), residues: 5572 helix: -0.94 (0.15), residues: 1036 sheet: 0.28 (0.10), residues: 2436 loop : -1.88 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 241 TYR 0.010 0.001 TYR C 96 PHE 0.045 0.002 PHE F 82 TRP 0.013 0.002 TRP E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (43568) covalent geometry : angle 0.70273 / 0.35 (58842) SS BOND : bond 0.00485 / 0.35 ( 14) SS BOND : angle 2.86561 / 1.80 ( 28) hydrogen bonds : bond 0.03641 / 2.41 ( 1290) hydrogen bonds : angle 5.64191 / 3.90 ( 3651) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1663 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 1431 time to evaluate : 1.171 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 24 MET cc_start: 0.5141 (tmm) cc_final: 0.4268 (tmm) REVERT: A 132 ARG cc_start: 0.8336 (ptm-80) cc_final: 0.8075 (ptm-80) REVERT: A 335 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8232 (mm110) REVERT: A 402 ARG cc_start: 0.8157 (mtm-85) cc_final: 0.7878 (ttp80) REVERT: B 241 ARG cc_start: 0.8105 (ttt90) cc_final: 0.7886 (ttt90) REVERT: B 402 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7600 (ttp80) REVERT: C 10 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.6090 (pm20) REVERT: C 115 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.7657 (mtm-85) REVERT: C 132 ARG cc_start: 0.8570 (ptm-80) cc_final: 0.8363 (ptm160) REVERT: D 16 GLN cc_start: 0.8386 (tp40) cc_final: 0.8143 (tp40) REVERT: D 24 MET cc_start: 0.2417 (tmt) cc_final: 0.0684 (tmt) REVERT: D 53 MET cc_start: 0.4806 (OUTLIER) cc_final: 0.4503 (tpt) REVERT: D 115 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7697 (mtm-85) REVERT: D 132 ARG cc_start: 0.8380 (ptm-80) cc_final: 0.8130 (ttp-110) REVERT: D 154 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7224 (mm-30) REVERT: E 82 PHE cc_start: 0.6297 (t80) cc_final: 0.5993 (t80) REVERT: E 154 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7236 (tm-30) REVERT: F 302 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6565 (tm-30) REVERT: G 69 ILE cc_start: 0.7807 (mm) cc_final: 0.7558 (mp) REVERT: H 198 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7856 (tmtt) REVERT: I 24 MET cc_start: 0.2146 (OUTLIER) cc_final: 0.1686 (tmt) REVERT: I 30 ASP cc_start: 0.5856 (t0) cc_final: 0.5625 (t70) REVERT: I 154 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7105 (mm-30) REVERT: I 304 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8321 (mmtp) REVERT: J 10 GLU cc_start: 0.6114 (mp0) cc_final: 0.5388 (mp0) REVERT: J 164 ASP cc_start: 0.8166 (t0) cc_final: 0.7940 (t0) REVERT: J 302 GLU cc_start: 0.5795 (OUTLIER) cc_final: 0.5465 (pm20) REVERT: J 396 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7877 (mtp180) REVERT: K 10 GLU cc_start: 0.5462 (mp0) cc_final: 0.5234 (mp0) REVERT: K 69 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7445 (mm) REVERT: K 154 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7034 (tm-30) REVERT: K 191 PHE cc_start: 0.8028 (t80) cc_final: 0.7768 (t80) REVERT: L 24 MET cc_start: 0.1595 (tmt) cc_final: 0.0895 (tmt) REVERT: L 154 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7256 (tm-30) REVERT: M 10 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5742 (pm20) REVERT: M 67 VAL cc_start: 0.6532 (m) cc_final: 0.6321 (m) REVERT: N 24 MET cc_start: 0.2569 (tmt) cc_final: 0.2269 (tmt) REVERT: N 26 ILE cc_start: 0.8360 (tp) cc_final: 0.8037 (mp) REVERT: N 154 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7110 (mm-30) outliers start: 232 outliers final: 133 residues processed: 1565 average time/residue: 0.8757 time to fit residues: 1629.8781 Evaluate side-chains 1527 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1385 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 262 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 ASN Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 278 LYS Chi-restraints excluded: chain G residue 324 MET Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 382 LEU Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 352 ASN Chi-restraints excluded: chain H residue 358 GLU Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain I residue 153 ILE Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 352 ASN Chi-restraints excluded: chain I residue 382 LEU Chi-restraints excluded: chain I residue 409 ILE Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain J residue 302 GLU Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 53 MET Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 262 LYS Chi-restraints excluded: chain K residue 372 ASP Chi-restraints excluded: chain K residue 382 LEU Chi-restraints excluded: chain K residue 392 LEU Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 260 LYS Chi-restraints excluded: chain L residue 262 LYS Chi-restraints excluded: chain L residue 372 ASP Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 292 ILE Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 392 LEU Chi-restraints excluded: chain M residue 402 ARG Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 382 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: [338, 28, 359, 523, 184, 525, 264, 18, 432, 496, 188] chunk 338 optimal weight: 5.9990 chunk 28 optimal weight: 50.0000 chunk 359 optimal weight: 2.9990 chunk 523 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 525 optimal weight: 5.9990 chunk 264 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 432 optimal weight: 0.0040 chunk 496 optimal weight: 5.9990 chunk 188 optimal weight: 30.0000 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN B 169 GLN C 101 GLN C 169 GLN C 350 ASN C 354 GLN D 16 GLN D 169 GLN D 321 GLN D 352 ASN E 84 GLN E 315 ASN E 321 GLN F 169 GLN F 329 ASN F 354 GLN G 169 GLN G 354 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 GLN H 329 ASN I 169 GLN I 272 GLN J 169 GLN J 352 ASN J 354 GLN K 101 GLN K 169 GLN L 169 GLN L 329 ASN M 84 GLN M 101 GLN M 169 GLN M 329 ASN N 169 GLN N 340 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.186845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.160439 restraints weight = 55213.121| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 1.83 r_work: 0.4067 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 43582 Z= 0.367 Angle : 0.792 12.205 58870 Z= 0.399 Chirality : 0.050 0.218 7098 Planarity : 0.005 0.062 7588 Dihedral : 5.446 44.310 5943 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.17 % Favored : 93.58 % Rotamer: Outliers : 5.16 % Allowed : 25.77 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.11), residues: 5572 helix: -1.19 (0.15), residues: 1036 sheet: 0.10 (0.10), residues: 2436 loop : -2.08 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 150 TYR 0.018 0.002 TYR E 96 PHE 0.040 0.002 PHE F 82 TRP 0.021 0.002 TRP J 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00865 / 0.37 (43568) covalent geometry : angle 0.78877 / 0.40 (58842) SS BOND : bond 0.00689 / 0.43 ( 14) SS BOND : angle 3.43482 / 2.28 ( 28) hydrogen bonds : bond 0.04081 / 2.73 ( 1290) hydrogen bonds : angle 5.92036 / 4.11 ( 3651) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1661 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 1414 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8217 (mp10) cc_final: 0.7917 (mp-120) REVERT: A 335 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8312 (mm110) REVERT: A 402 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7881 (ttp80) REVERT: A 403 ARG cc_start: 0.7998 (ttp-110) cc_final: 0.7731 (ttp-110) REVERT: B 10 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.5620 (mp0) REVERT: B 241 ARG cc_start: 0.8114 (ttt90) cc_final: 0.7889 (ttt90) REVERT: B 303 LEU cc_start: 0.8740 (mp) cc_final: 0.8472 (mm) REVERT: B 402 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7554 (ttp80) REVERT: C 24 MET cc_start: 0.3679 (tmt) cc_final: 0.2728 (tmt) REVERT: C 115 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7680 (mtm-85) REVERT: C 349 LYS cc_start: 0.8331 (mtmm) cc_final: 0.8096 (mttp) REVERT: D 24 MET cc_start: 0.2736 (tmt) cc_final: 0.1113 (tmt) REVERT: D 115 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7720 (mtm-85) REVERT: D 154 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7318 (mm-30) REVERT: E 53 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.5492 (ttt) REVERT: E 280 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7358 (mt-10) REVERT: E 335 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8175 (mm-40) REVERT: I 24 MET cc_start: 0.2668 (OUTLIER) cc_final: 0.2152 (tmt) REVERT: I 154 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7085 (mm-30) REVERT: I 302 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6205 (tm-30) REVERT: I 304 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8284 (mmtp) REVERT: J 10 GLU cc_start: 0.6439 (mp0) cc_final: 0.5728 (mp0) REVERT: J 53 MET cc_start: 0.4456 (OUTLIER) cc_final: 0.4057 (tpt) REVERT: J 164 ASP cc_start: 0.8124 (t0) cc_final: 0.7923 (t0) REVERT: J 302 GLU cc_start: 0.6025 (OUTLIER) cc_final: 0.5673 (pm20) REVERT: J 396 ARG cc_start: 0.8338 (mtp85) cc_final: 0.7931 (mtp180) REVERT: K 10 GLU cc_start: 0.5788 (mp0) cc_final: 0.5474 (mp0) REVERT: K 60 MET cc_start: 0.6043 (tmm) cc_final: 0.5105 (tmm) REVERT: K 154 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7127 (tm-30) REVERT: L 24 MET cc_start: 0.2319 (tmt) cc_final: 0.1793 (tmt) REVERT: L 60 MET cc_start: 0.4450 (tmm) cc_final: 0.3886 (tmm) REVERT: L 154 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7276 (mm-30) REVERT: L 185 ARG cc_start: 0.8298 (ttp80) cc_final: 0.7824 (ttp80) REVERT: L 402 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7694 (ttp80) REVERT: M 10 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.5630 (pm20) REVERT: M 24 MET cc_start: 0.1268 (OUTLIER) cc_final: 0.0925 (tmt) REVERT: M 53 MET cc_start: 0.5333 (OUTLIER) cc_final: 0.5039 (tpp) REVERT: M 67 VAL cc_start: 0.6557 (m) cc_final: 0.6323 (m) REVERT: M 69 ILE cc_start: 0.7403 (mp) cc_final: 0.7134 (mm) REVERT: M 412 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7402 (mtm-85) REVERT: N 26 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8163 (mp) REVERT: N 154 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7126 (mm-30) REVERT: N 185 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7760 (ttp80) outliers start: 247 outliers final: 154 residues processed: 1551 average time/residue: 0.8324 time to fit residues: 1533.1512 Evaluate side-chains 1562 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1396 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 60 MET Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 262 LYS Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 278 LYS Chi-restraints excluded: chain G residue 324 MET Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 382 LEU Chi-restraints excluded: chain G residue 392 LEU Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 352 ASN Chi-restraints excluded: chain H residue 358 GLU Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain I residue 153 ILE Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 382 LEU Chi-restraints excluded: chain I residue 409 ILE Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 302 GLU Chi-restraints excluded: chain J residue 354 GLN Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 53 MET Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 262 LYS Chi-restraints excluded: chain K residue 372 ASP Chi-restraints excluded: chain K residue 382 LEU Chi-restraints excluded: chain K residue 392 LEU Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain L residue 5 ASP Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 115 ARG Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 260 LYS Chi-restraints excluded: chain L residue 402 ARG Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 24 MET Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 292 ILE Chi-restraints excluded: chain M residue 324 MET Chi-restraints excluded: chain M residue 327 LYS Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 392 LEU Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain N residue 376 THR Chi-restraints excluded: chain N residue 392 LEU Chi-restraints excluded: chain N residue 410 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: [416, 354, 481, 553, 223, 3, 252, 62, 188, 243, 6] chunk 416 optimal weight: 3.9990 chunk 354 optimal weight: 2.9990 chunk 481 optimal weight: 0.9980 chunk 553 optimal weight: 0.7980 chunk 223 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 252 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 243 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 GLN B 272 GLN C 169 GLN C 321 GLN C 350 ASN C 354 GLN D 7 GLN D 16 GLN D 169 GLN D 272 GLN D 321 GLN D 352 ASN E 315 ASN F 329 ASN F 352 ASN F 354 GLN G 169 GLN G 354 GLN H 84 GLN H 101 GLN I 169 GLN I 272 GLN ** I 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 GLN K 169 GLN K 272 GLN K 335 GLN L 169 GLN L 329 ASN L 352 ASN M 84 GLN M 169 GLN M 329 ASN N 169 GLN N 354 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.190432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.163956 restraints weight = 55514.709| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 1.86 r_work: 0.4104 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 43582 Z= 0.171 Angle : 0.696 13.455 58870 Z= 0.348 Chirality : 0.047 0.187 7098 Planarity : 0.004 0.049 7588 Dihedral : 4.960 43.604 5943 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.36 % Favored : 95.39 % Rotamer: Outliers : 3.84 % Allowed : 27.36 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.11), residues: 5572 helix: -0.83 (0.15), residues: 1036 sheet: 0.10 (0.10), residues: 2436 loop : -2.00 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 396 TYR 0.008 0.001 TYR C 96 PHE 0.038 0.002 PHE F 82 TRP 0.010 0.001 TRP K 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (43568) covalent geometry : angle 0.69301 / 0.35 (58842) SS BOND : bond 0.00290 / 0.17 ( 14) SS BOND : angle 2.96867 / 2.01 ( 28) hydrogen bonds : bond 0.03530 / 2.39 ( 1290) hydrogen bonds : angle 5.58244 / 3.86 ( 3651) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1591 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 1407 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.8191 (ptm-80) cc_final: 0.7893 (ptm-80) REVERT: A 335 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8245 (mm110) REVERT: A 370 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7727 (mt-10) REVERT: A 403 ARG cc_start: 0.8000 (ttp-110) cc_final: 0.7722 (ttp-110) REVERT: B 10 GLU cc_start: 0.5853 (OUTLIER) cc_final: 0.5554 (mp0) REVERT: B 241 ARG cc_start: 0.8077 (ttt90) cc_final: 0.7842 (ttt90) REVERT: B 402 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7564 (ttp80) REVERT: C 24 MET cc_start: 0.3750 (tmt) cc_final: 0.2834 (tmt) REVERT: C 115 ARG cc_start: 0.7977 (mmm-85) cc_final: 0.7633 (mtm-85) REVERT: D 24 MET cc_start: 0.2590 (tmt) cc_final: 0.0816 (tmt) REVERT: D 115 ARG cc_start: 0.8061 (mmm-85) cc_final: 0.7714 (mtm-85) REVERT: D 154 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7220 (mm-30) REVERT: E 84 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7223 (tm-30) REVERT: E 154 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7247 (tm-30) REVERT: G 84 GLN cc_start: 0.7451 (mm-40) cc_final: 0.7114 (tm-30) REVERT: I 24 MET cc_start: 0.2471 (OUTLIER) cc_final: 0.1845 (tmt) REVERT: I 154 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7124 (mm-30) REVERT: I 302 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.6055 (tm-30) REVERT: I 304 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8238 (mmtp) REVERT: I 391 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7567 (m110) REVERT: J 53 MET cc_start: 0.4479 (mmt) cc_final: 0.4243 (tpt) REVERT: J 164 ASP cc_start: 0.8138 (t0) cc_final: 0.7929 (t0) REVERT: J 302 GLU cc_start: 0.5908 (OUTLIER) cc_final: 0.5568 (pm20) REVERT: J 396 ARG cc_start: 0.8305 (mtp85) cc_final: 0.7929 (mtp180) REVERT: K 10 GLU cc_start: 0.5526 (mp0) cc_final: 0.5216 (mp0) REVERT: K 60 MET cc_start: 0.5941 (tmm) cc_final: 0.5039 (tmm) REVERT: K 69 ILE cc_start: 0.7935 (mp) cc_final: 0.7621 (mm) REVERT: K 84 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7230 (tm130) REVERT: K 154 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7083 (mm-30) REVERT: K 191 PHE cc_start: 0.8029 (t80) cc_final: 0.7770 (t80) REVERT: L 24 MET cc_start: 0.2137 (tmt) cc_final: 0.1589 (tmt) REVERT: L 60 MET cc_start: 0.4509 (tmm) cc_final: 0.3918 (tmm) REVERT: L 154 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7201 (mm-30) REVERT: L 185 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7853 (ttp80) REVERT: M 10 GLU cc_start: 0.5981 (OUTLIER) cc_final: 0.5644 (pm20) REVERT: M 24 MET cc_start: 0.1317 (OUTLIER) cc_final: 0.1014 (tmt) REVERT: M 53 MET cc_start: 0.4969 (OUTLIER) cc_final: 0.4315 (tpt) REVERT: M 69 ILE cc_start: 0.7046 (mp) cc_final: 0.6836 (mm) REVERT: N 11 ILE cc_start: 0.6869 (OUTLIER) cc_final: 0.6639 (mp) REVERT: N 26 ILE cc_start: 0.8346 (tp) cc_final: 0.8137 (mp) REVERT: N 154 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7112 (mm-30) outliers start: 184 outliers final: 115 residues processed: 1511 average time/residue: 0.7255 time to fit residues: 1299.1553 Evaluate side-chains 1494 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 1369 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 262 LYS Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 278 LYS Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 382 LEU Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 358 GLU Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain I residue 153 ILE Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 382 LEU Chi-restraints excluded: chain I residue 391 ASN Chi-restraints excluded: chain I residue 409 ILE Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain J residue 56 ARG Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 302 GLU Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain K residue 53 MET Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 372 ASP Chi-restraints excluded: chain K residue 382 LEU Chi-restraints excluded: chain K residue 392 LEU Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 145 ILE Chi-restraints excluded: chain L residue 260 LYS Chi-restraints excluded: chain L residue 352 ASN Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 24 MET Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 292 ILE Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 392 LEU Chi-restraints excluded: chain M residue 402 ARG Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 198 LYS Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 392 LEU Chi-restraints excluded: chain N residue 410 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: [23, 375, 151, 373, 328, 443, 379, 475, 50, 8, 349] chunk 23 optimal weight: 0.0980 chunk 375 optimal weight: 0.3980 chunk 151 optimal weight: 2.9990 chunk 373 optimal weight: 2.9990 chunk 328 optimal weight: 0.6980 chunk 443 optimal weight: 8.9990 chunk 379 optimal weight: 4.9990 chunk 475 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 349 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN A 352 ASN A 354 GLN B 101 GLN B 169 GLN B 272 GLN C 169 GLN C 350 ASN C 354 GLN D 272 GLN D 321 GLN D 352 ASN E 315 ASN E 354 GLN F 84 GLN F 169 GLN F 329 ASN F 352 ASN F 354 GLN G 354 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN H 329 ASN H 352 ASN H 354 GLN I 169 GLN I 272 GLN I 352 ASN J 169 GLN J 350 ASN J 352 ASN J 354 GLN K 101 GLN L 169 GLN L 329 ASN L 352 ASN M 169 GLN M 329 ASN M 352 ASN M 354 GLN N 169 GLN N 340 ASN N 354 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.189397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.163826 restraints weight = 55487.419| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 1.84 r_work: 0.4095 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3973 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 43582 Z= 0.193 Angle : 0.720 12.253 58870 Z= 0.357 Chirality : 0.047 0.190 7098 Planarity : 0.004 0.056 7588 Dihedral : 4.962 44.861 5943 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.51 % Favored : 94.24 % Rotamer: Outliers : 3.93 % Allowed : 28.05 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.11), residues: 5572 helix: -0.78 (0.15), residues: 1036 sheet: 0.01 (0.10), residues: 2464 loop : -1.97 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 12 TYR 0.013 0.001 TYR J 96 PHE 0.057 0.002 PHE C 82 TRP 0.012 0.001 TRP G 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (43568) covalent geometry : angle 0.71712 / 0.36 (58842) SS BOND : bond 0.00500 / 0.34 ( 14) SS BOND : angle 2.95477 / 1.99 ( 28) hydrogen bonds : bond 0.03610 / 2.45 ( 1290) hydrogen bonds : angle 5.61650 / 3.89 ( 3651) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1575 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 1387 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.8251 (ptm-80) cc_final: 0.8041 (ptm-80) REVERT: A 335 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8235 (mm110) REVERT: A 370 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 402 ARG cc_start: 0.8106 (mtm-85) cc_final: 0.7871 (ttp80) REVERT: A 403 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7705 (ttp-110) REVERT: B 10 GLU cc_start: 0.5979 (OUTLIER) cc_final: 0.5679 (mp0) REVERT: B 241 ARG cc_start: 0.8049 (ttt90) cc_final: 0.7811 (ttt90) REVERT: B 402 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7511 (ttp80) REVERT: C 24 MET cc_start: 0.3659 (tmt) cc_final: 0.2743 (tmt) REVERT: C 115 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7657 (mtm-85) REVERT: D 24 MET cc_start: 0.2464 (tmt) cc_final: 0.0660 (tmt) REVERT: D 115 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.7688 (mtm-85) REVERT: D 154 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7185 (mm-30) REVERT: D 305 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7923 (ttpp) REVERT: E 84 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7229 (tm-30) REVERT: F 53 MET cc_start: 0.4928 (tpp) cc_final: 0.4344 (tmt) REVERT: G 84 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7139 (tm-30) REVERT: I 24 MET cc_start: 0.2442 (tmt) cc_final: 0.1822 (tmt) REVERT: I 154 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7050 (mm-30) REVERT: I 304 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8322 (mmtp) REVERT: I 391 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7527 (m110) REVERT: J 53 MET cc_start: 0.4503 (mmt) cc_final: 0.4096 (tpt) REVERT: J 164 ASP cc_start: 0.8122 (t0) cc_final: 0.7918 (t0) REVERT: J 302 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5675 (pm20) REVERT: J 396 ARG cc_start: 0.8279 (mtp85) cc_final: 0.7894 (mtp180) REVERT: K 60 MET cc_start: 0.5763 (tmm) cc_final: 0.4921 (tmm) REVERT: K 69 ILE cc_start: 0.7895 (mp) cc_final: 0.7613 (mm) REVERT: K 84 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7200 (tm130) REVERT: K 154 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7067 (mm-30) REVERT: K 191 PHE cc_start: 0.8024 (t80) cc_final: 0.7755 (t80) REVERT: L 24 MET cc_start: 0.2162 (tmt) cc_final: 0.1660 (tmt) REVERT: L 60 MET cc_start: 0.4395 (tmm) cc_final: 0.3823 (tmm) REVERT: L 154 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7263 (mm-30) REVERT: L 185 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7803 (ttp80) REVERT: M 10 GLU cc_start: 0.5901 (OUTLIER) cc_final: 0.5566 (pm20) REVERT: M 24 MET cc_start: 0.1058 (OUTLIER) cc_final: 0.0820 (tmt) REVERT: M 185 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7737 (ttp80) REVERT: M 412 ARG cc_start: 0.7530 (mtm-85) cc_final: 0.7292 (mtm-85) REVERT: N 154 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7018 (mm-30) outliers start: 188 outliers final: 127 residues processed: 1494 average time/residue: 0.5685 time to fit residues: 1009.7563 Evaluate side-chains 1500 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1366 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 262 LYS Chi-restraints excluded: chain F residue 352 ASN Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain G residue 278 LYS Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 382 LEU Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 352 ASN Chi-restraints excluded: chain H residue 358 GLU Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain I residue 153 ILE Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 352 ASN Chi-restraints excluded: chain I residue 382 LEU Chi-restraints excluded: chain I residue 391 ASN Chi-restraints excluded: chain I residue 409 ILE Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 302 GLU Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain K residue 53 MET Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 372 ASP Chi-restraints excluded: chain K residue 392 LEU Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 145 ILE Chi-restraints excluded: chain L residue 399 LYS Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 24 MET Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 292 ILE Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 392 LEU Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 198 LYS Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 392 LEU Chi-restraints excluded: chain N residue 410 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: [369, 26, 215, 90, 405, 186, 116, 40, 208, 347, 507] chunk 369 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 405 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 208 optimal weight: 0.0870 chunk 347 optimal weight: 0.9990 chunk 507 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN A 329 ASN A 352 ASN B 101 GLN C 169 GLN C 354 GLN D 101 GLN D 272 GLN D 352 ASN E 169 GLN E 315 ASN E 354 GLN F 169 GLN F 352 ASN F 354 GLN G 354 GLN H 101 GLN H 352 ASN H 354 GLN I 169 GLN I 272 GLN I 352 ASN J 350 ASN J 352 ASN J 354 GLN K 329 ASN L 169 GLN L 329 ASN L 354 GLN M 169 GLN M 329 ASN ** M 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 354 GLN N 169 GLN N 354 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.190962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.164613 restraints weight = 55495.625| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 1.88 r_work: 0.4111 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 43582 Z= 0.156 Angle : 0.712 12.598 58870 Z= 0.354 Chirality : 0.047 0.216 7098 Planarity : 0.004 0.055 7588 Dihedral : 4.842 46.934 5943 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.50 % Favored : 95.24 % Rotamer: Outliers : 3.07 % Allowed : 29.05 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.11), residues: 5572 helix: -0.73 (0.15), residues: 1050 sheet: 0.02 (0.10), residues: 2464 loop : -1.99 (0.12), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 396 TYR 0.010 0.001 TYR I 96 PHE 0.058 0.002 PHE C 82 TRP 0.009 0.001 TRP K 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (43568) covalent geometry : angle 0.70934 / 0.35 (58842) SS BOND : bond 0.00398 / 0.27 ( 14) SS BOND : angle 2.63560 / 1.74 ( 28) hydrogen bonds : bond 0.03517 / 2.39 ( 1290) hydrogen bonds : angle 5.55718 / 3.85 ( 3651) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1516 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1369 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.8196 (ptm-80) cc_final: 0.7916 (ptm-80) REVERT: A 335 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8153 (mm110) REVERT: A 370 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 402 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7802 (ttp80) REVERT: A 403 ARG cc_start: 0.7973 (ttp-110) cc_final: 0.7695 (ttp-110) REVERT: B 10 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5495 (pm20) REVERT: B 241 ARG cc_start: 0.8070 (ttt90) cc_final: 0.7841 (ttt90) REVERT: B 402 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7494 (ttp80) REVERT: C 24 MET cc_start: 0.3380 (tmt) cc_final: 0.2502 (tmt) REVERT: C 115 ARG cc_start: 0.7950 (mmm-85) cc_final: 0.7614 (mtm-85) REVERT: D 115 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7678 (mtm-85) REVERT: D 154 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7184 (mm-30) REVERT: D 305 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7906 (ttpp) REVERT: E 154 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7196 (tm-30) REVERT: F 53 MET cc_start: 0.4611 (tpp) cc_final: 0.4030 (tmt) REVERT: G 84 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7135 (tm-30) REVERT: I 24 MET cc_start: 0.2510 (tmt) cc_final: 0.1815 (tmt) REVERT: I 154 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7061 (mm-30) REVERT: I 304 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8296 (mmtp) REVERT: I 391 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7525 (m110) REVERT: J 164 ASP cc_start: 0.8088 (t0) cc_final: 0.7881 (t0) REVERT: J 237 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7879 (mt) REVERT: J 302 GLU cc_start: 0.5875 (OUTLIER) cc_final: 0.5563 (pm20) REVERT: J 396 ARG cc_start: 0.8282 (mtp85) cc_final: 0.7894 (mtp180) REVERT: K 10 GLU cc_start: 0.5685 (mp0) cc_final: 0.5350 (mp0) REVERT: K 60 MET cc_start: 0.6110 (OUTLIER) cc_final: 0.5251 (tmm) REVERT: K 69 ILE cc_start: 0.7891 (mp) cc_final: 0.7630 (mm) REVERT: K 84 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7222 (tm130) REVERT: K 154 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7071 (mm-30) REVERT: K 191 PHE cc_start: 0.8021 (t80) cc_final: 0.7729 (t80) REVERT: L 60 MET cc_start: 0.4344 (tmm) cc_final: 0.3731 (tmm) REVERT: L 154 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7200 (mm-30) REVERT: L 185 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7862 (ttp80) REVERT: M 10 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5718 (pm20) REVERT: M 24 MET cc_start: 0.1120 (OUTLIER) cc_final: 0.0899 (tmt) REVERT: M 185 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7746 (ttp80) REVERT: M 412 ARG cc_start: 0.7551 (mtm-85) cc_final: 0.7336 (mtm-85) REVERT: N 154 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7054 (mm-30) outliers start: 147 outliers final: 114 residues processed: 1456 average time/residue: 0.5352 time to fit residues: 924.6888 Evaluate side-chains 1484 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1361 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 175 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 262 LYS Chi-restraints excluded: chain F residue 352 ASN Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain G residue 278 LYS Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 352 ASN Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 148 ASP Chi-restraints excluded: chain I residue 153 ILE Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain I residue 198 LYS Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 382 LEU Chi-restraints excluded: chain I residue 391 ASN Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 302 GLU Chi-restraints excluded: chain J residue 354 GLN Chi-restraints excluded: chain J residue 392 LEU Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain K residue 53 MET Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 372 ASP Chi-restraints excluded: chain K residue 392 LEU Chi-restraints excluded: chain K residue 409 ILE Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 145 ILE Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 24 MET Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 292 ILE Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 392 LEU Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 198 LYS Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 410 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: [54, 481, 238, 182, 0, 67, 526, 498, 334, 1, 6] chunk 54 optimal weight: 0.6980 chunk 481 optimal weight: 0.8980 chunk 238 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 526 optimal weight: 1.9990 chunk 498 optimal weight: 4.9990 chunk 334 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN A 352 ASN B 101 GLN B 272 GLN C 169 GLN C 350 ASN C 354 GLN D 272 GLN D 321 GLN D 352 ASN E 315 ASN F 7 GLN F 169 GLN F 352 ASN F 354 GLN G 354 GLN H 101 GLN H 329 ASN H 350 ASN H 352 ASN H 354 GLN I 168 GLN I 169 GLN I 272 GLN J 350 ASN J 352 ASN J 354 GLN K 329 ASN L 169 GLN L 329 ASN L 354 GLN M 169 GLN ** M 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 354 GLN N 169 GLN N 329 ASN N 354 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.190882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.164430 restraints weight = 55668.251| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 1.88 r_work: 0.4112 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3986 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 43582 Z= 0.161 Angle : 0.714 12.723 58870 Z= 0.354 Chirality : 0.047 0.207 7098 Planarity : 0.004 0.086 7588 Dihedral : 4.840 48.610 5943 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.97 % Favored : 94.78 % Rotamer: Outliers : 3.05 % Allowed : 29.51 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.11), residues: 5572 helix: -0.70 (0.15), residues: 1050 sheet: 0.02 (0.10), residues: 2464 loop : -1.97 (0.12), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 396 TYR 0.011 0.001 TYR J 96 PHE 0.062 0.002 PHE C 82 TRP 0.009 0.001 TRP C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (43568) covalent geometry : angle 0.71158 / 0.35 (58842) SS BOND : bond 0.00427 / 0.28 ( 14) SS BOND : angle 2.59691 / 1.73 ( 28) hydrogen bonds : bond 0.03526 / 2.39 ( 1290) hydrogen bonds : angle 5.56716 / 3.85 ( 3651) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27953.84 seconds wall clock time: 472 minutes 1.11 seconds (28321.11 seconds total)