Starting phenix.real_space_refine on Mon Sep 14 22:29:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tr8_26082/09_2026/7tr8_26082.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tr8_26082/09_2026/7tr8_26082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tr8_26082/09_2026/7tr8_26082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tr8_26082/09_2026/7tr8_26082.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tr8_26082/09_2026/7tr8_26082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tr8_26082/09_2026/7tr8_26082.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tr8_26082/09_2026/7tr8_26082.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tr8_26082/09_2026/7tr8_26082.cif" } resolution = 3.6 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= -0.000 sd= 0.024 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: 6 Type Number sf(0) Gaussians Ni 2 6.56 5 P 44 5.49 5 S 80 5.16 5 C 21341 2.51 5 N 5740 2.21 5 O 6374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33581 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4307 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 548} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2662 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "E" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "G" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "H" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "I" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2597 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 321} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2603 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2596 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2494 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2134 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1936 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 16, 'TRANS': 223} Chain breaks: 2 Chain: "Q" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1823 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain: "R" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 949 Classifications: {'RNAv2': 45} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 13, 'rna3p_pyr': 13} Link IDs: {'rna2p': 18, 'rna3p': 26} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.94, per 1000 atoms: 0.24 Number of scatterers: 33581 At special positions: 0 Unit cell: (117.619, 153.558, 218.902, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ni 2 28.00 S 80 16.00 P 44 15.00 O 6374 8.00 N 5740 7.00 C 21341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS Q 65 " 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: 3.80 Conformation dependent library (CDL) restraints added in 1.8 seconds 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7808 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 45 sheets defined 39.8% alpha, 11.2% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 removed outlier: 4.079A pdb=" N ARG A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 29' Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 78 through 95 Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 133 through 140 Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.639A pdb=" N ALA A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 243 through 255 removed outlier: 4.511A pdb=" N ASP A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 280 removed outlier: 3.616A pdb=" N ASN A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 340 through 347 removed outlier: 3.566A pdb=" N GLN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.733A pdb=" N ALA A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 403 removed outlier: 4.024A pdb=" N THR A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.886A pdb=" N GLY A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 423 removed outlier: 3.764A pdb=" N ILE A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 581 through 587 removed outlier: 3.679A pdb=" N ALA A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 624 removed outlier: 3.588A pdb=" N ALA A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'C' and resid 13 through 30 removed outlier: 4.260A pdb=" N VAL C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 71 removed outlier: 3.634A pdb=" N ALA C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 116 removed outlier: 3.708A pdb=" N TRP C 100 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP C 101 " --> pdb=" O ASN C 97 " (cutoff:3.500A) Proline residue: C 104 - end of helix removed outlier: 3.525A pdb=" N LYS C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 167 Processing helix chain 'C' and resid 194 through 202 Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.960A pdb=" N LEU C 218 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE C 219 " --> pdb=" O ASP C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 219' Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.937A pdb=" N HIS C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'C' and resid 282 through 296 removed outlier: 3.946A pdb=" N LYS C 287 " --> pdb=" O TYR C 283 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 288 " --> pdb=" O HIS C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 310 Processing helix chain 'C' and resid 311 through 326 removed outlier: 4.346A pdb=" N PHE C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 342 removed outlier: 3.611A pdb=" N VAL C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 13 Processing helix chain 'D' and resid 14 through 16 No H-bonds generated for 'chain 'D' and resid 14 through 16' Processing helix chain 'D' and resid 25 through 33 Processing helix chain 'D' and resid 36 through 50 removed outlier: 3.891A pdb=" N LEU D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 73 through 82 removed outlier: 3.749A pdb=" N GLU D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 100 removed outlier: 3.971A pdb=" N LYS D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU D 93 " --> pdb=" O ASP D 89 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER D 96 " --> pdb=" O LYS D 92 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'E' and resid 3 through 14 removed outlier: 3.840A pdb=" N ASN E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR E 14 " --> pdb=" O ARG E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 33 removed outlier: 4.028A pdb=" N VAL E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 49 Processing helix chain 'E' and resid 50 through 59 removed outlier: 3.962A pdb=" N LYS E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU E 59 " --> pdb=" O LYS E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 70 through 83 Processing helix chain 'E' and resid 86 through 100 removed outlier: 3.849A pdb=" N LYS E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 13 removed outlier: 3.606A pdb=" N TYR F 11 " --> pdb=" O ASN F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 24 through 34 removed outlier: 4.340A pdb=" N VAL F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 49 Processing helix chain 'F' and resid 50 through 59 removed outlier: 4.186A pdb=" N GLU F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 82 removed outlier: 3.663A pdb=" N ILE F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 100 removed outlier: 3.518A pdb=" N LEU F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 93 " --> pdb=" O ASP F 89 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TRP F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'G' and resid 5 through 14 removed outlier: 3.803A pdb=" N TYR G 11 " --> pdb=" O ASN G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 33 removed outlier: 3.899A pdb=" N VAL G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 50 removed outlier: 3.703A pdb=" N LEU G 50 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 57 removed outlier: 3.784A pdb=" N LEU G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS G 57 " --> pdb=" O LYS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.742A pdb=" N GLY G 62 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 83 removed outlier: 4.098A pdb=" N ILE G 74 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU G 75 " --> pdb=" O PRO G 71 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 98 removed outlier: 3.563A pdb=" N ALA G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 14 Processing helix chain 'H' and resid 24 through 33 removed outlier: 4.339A pdb=" N VAL H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA H 32 " --> pdb=" O VAL H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 removed outlier: 3.675A pdb=" N LEU H 41 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 59 removed outlier: 4.147A pdb=" N GLU H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 4.041A pdb=" N GLU H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU H 79 " --> pdb=" O GLU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 102 removed outlier: 3.510A pdb=" N LEU H 90 " --> pdb=" O ASN H 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG H 91 " --> pdb=" O PRO H 87 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU H 93 " --> pdb=" O ASP H 89 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 101 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 70 removed outlier: 3.793A pdb=" N LEU I 55 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS I 68 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR I 69 " --> pdb=" O ASP I 65 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR I 70 " --> pdb=" O TYR I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 75 removed outlier: 4.326A pdb=" N VAL I 74 " --> pdb=" O PRO I 71 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN I 75 " --> pdb=" O TYR I 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 71 through 75' Processing helix chain 'I' and resid 77 through 82 removed outlier: 3.782A pdb=" N LEU I 81 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG I 82 " --> pdb=" O GLU I 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 77 through 82' Processing helix chain 'I' and resid 107 through 115 Processing helix chain 'I' and resid 116 through 122 Processing helix chain 'I' and resid 144 through 152 Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 227 through 241 Processing helix chain 'I' and resid 285 through 300 Processing helix chain 'I' and resid 324 through 333 Processing helix chain 'J' and resid 51 through 69 removed outlier: 3.786A pdb=" N LEU J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 75 removed outlier: 4.419A pdb=" N VAL J 74 " --> pdb=" O PRO J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 82 removed outlier: 3.510A pdb=" N LEU J 81 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG J 82 " --> pdb=" O GLU J 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 77 through 82' Processing helix chain 'J' and resid 107 through 115 Processing helix chain 'J' and resid 116 through 121 Processing helix chain 'J' and resid 144 through 152 Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 227 through 241 Processing helix chain 'J' and resid 242 through 243 No H-bonds generated for 'chain 'J' and resid 242 through 243' Processing helix chain 'J' and resid 244 through 248 removed outlier: 3.640A pdb=" N SER J 247 " --> pdb=" O PRO J 244 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY J 248 " --> pdb=" O MET J 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 244 through 248' Processing helix chain 'J' and resid 285 through 300 removed outlier: 3.558A pdb=" N ALA J 289 " --> pdb=" O ASP J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 335 removed outlier: 3.634A pdb=" N MET J 335 " --> pdb=" O ASN J 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 69 removed outlier: 3.679A pdb=" N LEU K 55 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR K 69 " --> pdb=" O ASP K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 75 removed outlier: 4.232A pdb=" N VAL K 74 " --> pdb=" O PRO K 71 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN K 75 " --> pdb=" O TYR K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 Processing helix chain 'K' and resid 107 through 115 Processing helix chain 'K' and resid 115 through 122 Processing helix chain 'K' and resid 144 through 152 Processing helix chain 'K' and resid 227 through 241 Processing helix chain 'K' and resid 286 through 300 Processing helix chain 'K' and resid 324 through 335 Processing helix chain 'L' and resid 51 through 69 removed outlier: 3.617A pdb=" N LYS L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR L 69 " --> pdb=" O ASP L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 82 removed outlier: 3.635A pdb=" N LEU L 81 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG L 82 " --> pdb=" O GLU L 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 77 through 82' Processing helix chain 'L' and resid 107 through 115 Processing helix chain 'L' and resid 115 through 122 Processing helix chain 'L' and resid 144 through 152 removed outlier: 3.565A pdb=" N GLU L 152 " --> pdb=" O ILE L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 241 Processing helix chain 'L' and resid 241 through 246 removed outlier: 3.618A pdb=" N MET L 245 " --> pdb=" O ALA L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 299 removed outlier: 3.742A pdb=" N ALA L 289 " --> pdb=" O ASP L 285 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA L 299 " --> pdb=" O LYS L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 333 removed outlier: 3.631A pdb=" N LEU L 328 " --> pdb=" O SER L 324 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL L 329 " --> pdb=" O VAL L 325 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 336 No H-bonds generated for 'chain 'L' and resid 334 through 336' Processing helix chain 'M' and resid 20 through 24 removed outlier: 3.621A pdb=" N THR M 24 " --> pdb=" O GLY M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 69 removed outlier: 3.936A pdb=" N THR M 69 " --> pdb=" O ASP M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 75 removed outlier: 4.023A pdb=" N VAL M 74 " --> pdb=" O PRO M 71 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN M 75 " --> pdb=" O TYR M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 82 removed outlier: 3.556A pdb=" N LEU M 81 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG M 82 " --> pdb=" O GLU M 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 77 through 82' Processing helix chain 'M' and resid 107 through 115 removed outlier: 3.548A pdb=" N LYS M 113 " --> pdb=" O ALA M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 122 removed outlier: 3.531A pdb=" N ASP M 119 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 151 Processing helix chain 'M' and resid 203 through 205 No H-bonds generated for 'chain 'M' and resid 203 through 205' Processing helix chain 'M' and resid 227 through 241 Processing helix chain 'M' and resid 242 through 246 removed outlier: 3.778A pdb=" N LEU M 246 " --> pdb=" O ILE M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 285 through 300 removed outlier: 3.805A pdb=" N ALA M 289 " --> pdb=" O ASP M 285 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA M 297 " --> pdb=" O ILE M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 334 Processing helix chain 'N' and resid 51 through 70 removed outlier: 3.727A pdb=" N LEU N 55 " --> pdb=" O THR N 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS N 68 " --> pdb=" O VAL N 64 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR N 69 " --> pdb=" O ASP N 65 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR N 70 " --> pdb=" O TYR N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 Processing helix chain 'N' and resid 107 through 115 removed outlier: 3.531A pdb=" N ILE N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 122 removed outlier: 4.192A pdb=" N VAL N 120 " --> pdb=" O ALA N 116 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS N 121 " --> pdb=" O ASP N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 150 removed outlier: 3.708A pdb=" N GLU N 150 " --> pdb=" O ASP N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 155 No H-bonds generated for 'chain 'N' and resid 153 through 155' Processing helix chain 'N' and resid 227 through 241 Processing helix chain 'N' and resid 285 through 301 removed outlier: 3.608A pdb=" N ALA N 297 " --> pdb=" O ILE N 293 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY N 301 " --> pdb=" O ALA N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 335 removed outlier: 3.647A pdb=" N LEU N 328 " --> pdb=" O SER N 324 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 69 removed outlier: 3.732A pdb=" N LEU O 55 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR O 69 " --> pdb=" O ASP O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 Processing helix chain 'O' and resid 107 through 113 removed outlier: 3.534A pdb=" N LYS O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 121 removed outlier: 3.583A pdb=" N VAL O 120 " --> pdb=" O ALA O 116 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS O 121 " --> pdb=" O ASP O 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 116 through 121' Processing helix chain 'O' and resid 144 through 150 removed outlier: 3.629A pdb=" N GLU O 150 " --> pdb=" O ASP O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 227 through 241 Processing helix chain 'O' and resid 285 through 299 removed outlier: 3.544A pdb=" N ALA O 289 " --> pdb=" O ASP O 285 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA O 297 " --> pdb=" O ILE O 293 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA O 299 " --> pdb=" O LYS O 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 324 through 335 removed outlier: 4.008A pdb=" N MET O 335 " --> pdb=" O ASN O 331 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 46 Processing helix chain 'P' and resid 54 through 69 Processing helix chain 'P' and resid 129 through 141 removed outlier: 3.601A pdb=" N ASN P 134 " --> pdb=" O GLN P 130 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU P 135 " --> pdb=" O GLU P 131 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET P 141 " --> pdb=" O LEU P 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 182 removed outlier: 3.857A pdb=" N SER P 181 " --> pdb=" O GLU P 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 24 removed outlier: 3.944A pdb=" N ILE Q 24 " --> pdb=" O ALA Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 38 Proline residue: Q 31 - end of helix removed outlier: 3.544A pdb=" N ARG Q 35 " --> pdb=" O PRO Q 31 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL Q 36 " --> pdb=" O SER Q 32 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET Q 37 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS Q 38 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 59 Processing helix chain 'Q' and resid 62 through 66 removed outlier: 3.500A pdb=" N CYS Q 65 " --> pdb=" O VAL Q 62 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER Q 66 " --> pdb=" O GLY Q 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 62 through 66' Processing helix chain 'Q' and resid 68 through 73 Processing helix chain 'Q' and resid 84 through 101 removed outlier: 3.756A pdb=" N SER Q 88 " --> pdb=" O HIS Q 84 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA Q 89 " --> pdb=" O GLU Q 85 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR Q 90 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS Q 97 " --> pdb=" O TYR Q 93 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP Q 98 " --> pdb=" O ASN Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 116 removed outlier: 3.935A pdb=" N ALA Q 106 " --> pdb=" O ASP Q 102 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS Q 116 " --> pdb=" O VAL Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 143 removed outlier: 3.598A pdb=" N VAL Q 138 " --> pdb=" O THR Q 134 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP Q 140 " --> pdb=" O GLU Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 158 removed outlier: 4.300A pdb=" N GLU Q 153 " --> pdb=" O MET Q 149 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER Q 154 " --> pdb=" O GLU Q 150 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS Q 157 " --> pdb=" O GLU Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 164 removed outlier: 3.554A pdb=" N LYS Q 163 " --> pdb=" O MET Q 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 192 removed outlier: 4.079A pdb=" N VAL Q 178 " --> pdb=" O THR Q 174 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU Q 179 " --> pdb=" O GLN Q 175 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG Q 192 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 210 removed outlier: 3.659A pdb=" N LEU Q 198 " --> pdb=" O ASP Q 194 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG Q 199 " --> pdb=" O SER Q 195 " (cutoff:3.500A) Proline residue: Q 208 - end of helix Processing helix chain 'Q' and resid 211 through 216 removed outlier: 4.011A pdb=" N GLY Q 215 " --> pdb=" O CYS Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 227 removed outlier: 3.909A pdb=" N ALA Q 226 " --> pdb=" O ALA Q 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.527A pdb=" N VAL A 162 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N MET A 198 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE A 164 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL A 70 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP A 165 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 72 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 238 removed outlier: 3.621A pdb=" N ILE A 361 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 363 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N THR A 334 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 260 " --> pdb=" O ALA A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 44 through 46 removed outlier: 3.602A pdb=" N VAL C 192 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AA6, first strand: chain 'C' and resid 170 through 173 Processing sheet with id=AA7, first strand: chain 'I' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 2 through 12 current: chain 'I' and resid 193 through 201 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 193 through 201 current: chain 'I' and resid 305 through 309 Processing sheet with id=AA8, first strand: chain 'I' and resid 26 through 27 removed outlier: 3.728A pdb=" N GLU I 188 " --> pdb=" O ILE I 27 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 32 through 37 Processing sheet with id=AB1, first strand: chain 'I' and resid 94 through 96 Processing sheet with id=AB2, first strand: chain 'I' and resid 123 through 125 removed outlier: 4.600A pdb=" N ALA I 125 " --> pdb=" O ARG I 130 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG I 130 " --> pdb=" O ALA I 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 2 through 14 current: chain 'J' and resid 184 through 201 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 184 through 201 current: chain 'J' and resid 305 through 309 removed outlier: 6.971A pdb=" N VAL J 306 " --> pdb=" O THR J 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 31 through 36 Processing sheet with id=AB5, first strand: chain 'J' and resid 94 through 96 Processing sheet with id=AB6, first strand: chain 'J' and resid 123 through 124 Processing sheet with id=AB7, first strand: chain 'K' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 2 through 14 current: chain 'K' and resid 183 through 201 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 183 through 201 current: chain 'K' and resid 304 through 309 removed outlier: 9.027A pdb=" N THR K 320 " --> pdb=" O ILE K 304 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL K 306 " --> pdb=" O THR K 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'K' and resid 31 through 36 Processing sheet with id=AB9, first strand: chain 'K' and resid 94 through 96 Processing sheet with id=AC1, first strand: chain 'K' and resid 123 through 125 Processing sheet with id=AC2, first strand: chain 'L' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 2 through 14 current: chain 'L' and resid 26 through 29 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 26 through 29 current: chain 'L' and resid 186 through 201 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 186 through 201 current: chain 'L' and resid 305 through 309 removed outlier: 6.962A pdb=" N VAL L 306 " --> pdb=" O THR L 320 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL L 322 " --> pdb=" O VAL L 306 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR L 308 " --> pdb=" O VAL L 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'L' and resid 31 through 36 Processing sheet with id=AC4, first strand: chain 'L' and resid 94 through 96 Processing sheet with id=AC5, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AC6, first strand: chain 'M' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 2 through 14 current: chain 'M' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 190 through 196 current: chain 'M' and resid 306 through 309 removed outlier: 6.913A pdb=" N VAL M 306 " --> pdb=" O THR M 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'M' and resid 26 through 27 Processing sheet with id=AC8, first strand: chain 'M' and resid 31 through 36 Processing sheet with id=AC9, first strand: chain 'M' and resid 94 through 96 Processing sheet with id=AD1, first strand: chain 'M' and resid 123 through 124 removed outlier: 3.590A pdb=" N PHE M 123 " --> pdb=" O ARG M 132 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG M 132 " --> pdb=" O PHE M 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'M' and resid 213 through 215 Processing sheet with id=AD3, first strand: chain 'N' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 2 through 12 current: chain 'N' and resid 193 through 201 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 193 through 201 current: chain 'N' and resid 305 through 309 removed outlier: 6.550A pdb=" N VAL N 306 " --> pdb=" O THR N 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'N' and resid 26 through 27 Processing sheet with id=AD5, first strand: chain 'N' and resid 31 through 36 Processing sheet with id=AD6, first strand: chain 'N' and resid 94 through 96 Processing sheet with id=AD7, first strand: chain 'N' and resid 123 through 125 Processing sheet with id=AD8, first strand: chain 'O' and resid 136 through 138 removed outlier: 3.813A pdb=" N GLU O 265 " --> pdb=" O ARG O 8 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG O 10 " --> pdb=" O VAL O 263 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL O 263 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 32 through 35 removed outlier: 3.772A pdb=" N THR O 32 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL O 47 " --> pdb=" O THR O 32 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 94 through 96 removed outlier: 3.640A pdb=" N ALA O 95 " --> pdb=" O VAL O 103 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 123 through 125 Processing sheet with id=AE3, first strand: chain 'P' and resid 77 through 80 removed outlier: 4.478A pdb=" N TRP P 157 " --> pdb=" O CYS P 7 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 85 through 87 removed outlier: 3.788A pdb=" N ILE P 85 " --> pdb=" O PHE P 115 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN P 87 " --> pdb=" O TYR P 113 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 90 through 94 Processing sheet with id=AE6, first strand: chain 'P' and resid 145 through 146 removed outlier: 4.482A pdb=" N SER P 151 " --> pdb=" O ILE P 146 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 168 through 169 Processing sheet with id=AE8, first strand: chain 'P' and resid 174 through 175 removed outlier: 3.502A pdb=" N ALA P 174 " --> pdb=" O TYR P 218 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 243 through 246 1054 hydrogen bonds defined for protein. 3042 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 7.15 Time building geometry restraints manager: 4.77 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: 10665 1.34 - 1.46: 5623 1.46 - 1.58: 17801 1.58 - 1.70: 88 1.70 - 1.82: 144 Bond restraints: 34321 Sorted by residual: bond pdb=" N ALA A 611 " pdb=" CA ALA A 611 " ideal model delta sigma weight residual 1.463 1.489 -0.026 1.24e-02 6.50e+03 4.34e+00 bond pdb=" C TYR A 450 " pdb=" N PRO A 451 " ideal model delta sigma weight residual 1.336 1.353 -0.017 9.80e-03 1.04e+04 2.90e+00 bond pdb=" CB PRO A 453 " pdb=" CG PRO A 453 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.34e+00 bond pdb=" CA GLY N 153 " pdb=" C GLY N 153 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.04e-02 9.25e+03 2.15e+00 bond pdb=" C LEU A 610 " pdb=" N ALA A 611 " ideal model delta sigma weight residual 1.332 1.350 -0.018 1.31e-02 5.83e+03 1.88e+00 ... (remaining 34316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 45763 1.79 - 3.58: 777 3.58 - 5.38: 169 5.38 - 7.17: 9 7.17 - 8.96: 6 Bond angle restraints: 46724 Sorted by residual: angle pdb=" N GLY N 153 " pdb=" CA GLY N 153 " pdb=" C GLY N 153 " ideal model delta sigma weight residual 111.67 116.36 -4.69 9.20e-01 1.18e+00 2.60e+01 angle pdb=" N ILE A 59 " pdb=" CA ILE A 59 " pdb=" C ILE A 59 " ideal model delta sigma weight residual 111.77 107.11 4.66 1.04e+00 9.25e-01 2.01e+01 angle pdb=" C ARG A 426 " pdb=" N VAL A 427 " pdb=" CA VAL A 427 " ideal model delta sigma weight residual 121.97 129.51 -7.54 1.80e+00 3.09e-01 1.76e+01 angle pdb=" C ALA P 75 " pdb=" N VAL P 76 " pdb=" CA VAL P 76 " ideal model delta sigma weight residual 120.49 125.89 -5.40 1.38e+00 5.25e-01 1.53e+01 angle pdb=" N ALA A 587 " pdb=" CA ALA A 587 " pdb=" C ALA A 587 " ideal model delta sigma weight residual 108.23 113.39 -5.16 1.38e+00 5.25e-01 1.40e+01 ... (remaining 46719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.06: 19945 31.06 - 62.12: 648 62.12 - 93.18: 66 93.18 - 124.23: 0 124.23 - 155.29: 2 Dihedral angle restraints: 20661 sinusoidal: 8524 harmonic: 12137 Sorted by residual: dihedral pdb=" C4' U R 44 " pdb=" C3' U R 44 " pdb=" C2' U R 44 " pdb=" C1' U R 44 " ideal model delta sinusoidal sigma weight residual 36.35 -36.25 72.60 1 3.10e+00 1.04e-01 7.00e+02 dihedral pdb=" C4' G R 42 " pdb=" C3' G R 42 " pdb=" C2' G R 42 " pdb=" C1' G R 42 " ideal model delta sinusoidal sigma weight residual 36.35 -36.03 72.37 1 3.10e+00 1.04e-01 6.96e+02 dihedral pdb=" C4' C R 13 " pdb=" C3' C R 13 " pdb=" C2' C R 13 " pdb=" C1' C R 13 " ideal model delta sinusoidal sigma weight residual 36.34 -35.78 72.12 1 3.10e+00 1.04e-01 6.92e+02 ... (remaining 20658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4604 0.061 - 0.122: 664 0.122 - 0.183: 32 0.183 - 0.244: 57 0.244 - 0.305: 28 Chirality restraints: 5385 Sorted by residual: chirality pdb=" P C R 19 " pdb=" OP1 C R 19 " pdb=" OP2 C R 19 " pdb=" O5' C R 19 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" P U R 15 " pdb=" OP1 U R 15 " pdb=" OP2 U R 15 " pdb=" O5' U R 15 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" P U R 2 " pdb=" OP1 U R 2 " pdb=" OP2 U R 2 " pdb=" O5' U R 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 5382 not shown) Planarity restraints: 5826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 452 " -0.064 5.00e-02 4.00e+02 9.73e-02 1.51e+01 pdb=" N PRO A 453 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 610 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.38e+00 pdb=" C LEU A 610 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU A 610 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A 611 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 337 " 0.044 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO A 338 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " 0.037 5.00e-02 4.00e+02 ... (remaining 5823 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 406 2.61 - 3.18: 30101 3.18 - 3.75: 54124 3.75 - 4.33: 72549 4.33 - 4.90: 118829 Nonbonded interactions: 276009 Sorted by model distance: nonbonded pdb=" NE2 HIS Q 14 " pdb="NI NI Q 302 " model vdw 2.037 2.260 nonbonded pdb=" OG SER P 14 " pdb=" OD1 ASP P 148 " model vdw 2.114 3.040 nonbonded pdb=" OG SER P 52 " pdb=" O SER P 54 " model vdw 2.140 3.040 nonbonded pdb=" OG1 THR Q 10 " pdb=" OE1 GLU Q 13 " model vdw 2.166 3.040 nonbonded pdb=" O ALA A 44 " pdb=" OG1 THR A 48 " model vdw 2.168 3.040 ... (remaining 276004 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and resid 3 through 109) selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 144 or (resid 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 through 164 or resid 180 th \ rough 335)) selection = (chain 'J' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 164 or resid 180 through 335)) selection = (chain 'K' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'L' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'M' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'N' and resid 1 through 335) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 37.350 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4633 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 0.077 34327 Z= 0.112 Angle : 0.584 8.961 46736 Z= 0.304 Chirality : 0.050 0.305 5385 Planarity : 0.004 0.097 5826 Dihedral : 14.899 155.293 12835 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.46 % Favored : 92.16 % Rotamer: Outliers : 0.03 % Allowed : 0.50 % Favored : 99.48 % 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: -1.00 (0.13), residues: 4144 helix: 0.66 (0.15), residues: 1432 sheet: -0.55 (0.21), residues: 673 loop : -1.70 (0.14), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 295 TYR 0.025 0.001 TYR C 20 PHE 0.015 0.001 PHE A 296 TRP 0.016 0.001 TRP H 105 HIS 0.005 0.001 HIS Q 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (34321) covalent geometry : angle 0.58402 / 0.30 (46724) SS BOND : bond 0.00155 / 0.08 ( 6) SS BOND : angle 0.51660 / 0.30 ( 12) hydrogen bonds : bond 0.14175 / 9.16 ( 1054) hydrogen bonds : angle 5.66737 / 4.07 ( 3042) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 887 time to evaluate : 1.292 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 ILE cc_start: 0.5978 (mm) cc_final: 0.5683 (mm) REVERT: A 418 VAL cc_start: 0.8396 (t) cc_final: 0.8186 (t) REVERT: A 420 ASP cc_start: 0.7973 (m-30) cc_final: 0.7679 (m-30) REVERT: C 129 THR cc_start: 0.6251 (m) cc_final: 0.5666 (p) REVERT: C 271 MET cc_start: 0.8890 (tpt) cc_final: 0.8683 (tpt) REVERT: C 297 THR cc_start: 0.7477 (m) cc_final: 0.7097 (p) REVERT: C 308 MET cc_start: 0.8085 (mmp) cc_final: 0.7550 (mmt) REVERT: D 16 VAL cc_start: 0.8658 (t) cc_final: 0.8256 (p) REVERT: D 33 LYS cc_start: 0.9232 (mttp) cc_final: 0.8786 (ptpp) REVERT: D 38 GLU cc_start: 0.8022 (mp0) cc_final: 0.7740 (pm20) REVERT: D 40 LEU cc_start: 0.8011 (tp) cc_final: 0.7389 (pp) REVERT: D 53 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8663 (tptm) REVERT: D 75 GLU cc_start: 0.8599 (pm20) cc_final: 0.8335 (pm20) REVERT: E 75 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7852 (mm-30) REVERT: E 89 ASP cc_start: 0.8767 (p0) cc_final: 0.8343 (p0) REVERT: F 12 LEU cc_start: 0.8313 (mt) cc_final: 0.8077 (mt) REVERT: F 86 ASN cc_start: 0.7796 (p0) cc_final: 0.7445 (p0) REVERT: F 92 LYS cc_start: 0.8149 (ptpp) cc_final: 0.7399 (tttt) REVERT: F 95 VAL cc_start: 0.7619 (p) cc_final: 0.6652 (t) REVERT: I 42 TRP cc_start: 0.4952 (m100) cc_final: 0.4593 (m100) REVERT: I 51 THR cc_start: 0.6533 (p) cc_final: 0.4961 (p) REVERT: I 140 PHE cc_start: 0.4870 (m-10) cc_final: 0.4333 (m-10) REVERT: I 160 ILE cc_start: 0.4425 (mt) cc_final: 0.4168 (mm) REVERT: I 185 PHE cc_start: 0.8551 (p90) cc_final: 0.7614 (p90) REVERT: I 300 LEU cc_start: 0.8189 (mt) cc_final: 0.7894 (tp) REVERT: I 320 THR cc_start: 0.6497 (m) cc_final: 0.6069 (m) REVERT: J 10 ARG cc_start: 0.6902 (mtp180) cc_final: 0.6464 (ttt180) REVERT: J 107 ASP cc_start: 0.7479 (t70) cc_final: 0.7273 (t70) REVERT: J 218 ASN cc_start: 0.8601 (m-40) cc_final: 0.8243 (t0) REVERT: J 219 GLN cc_start: 0.8740 (pt0) cc_final: 0.8266 (pm20) REVERT: J 305 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7784 (mp0) REVERT: J 312 ASP cc_start: 0.8632 (p0) cc_final: 0.7487 (t0) REVERT: J 328 LEU cc_start: 0.7533 (tt) cc_final: 0.7303 (mt) REVERT: J 332 LEU cc_start: 0.7605 (mt) cc_final: 0.7202 (mp) REVERT: K 2 TYR cc_start: 0.5912 (m-10) cc_final: 0.5711 (m-10) REVERT: K 65 ASP cc_start: 0.7567 (m-30) cc_final: 0.7056 (m-30) REVERT: K 77 THR cc_start: 0.6267 (m) cc_final: 0.5982 (m) REVERT: K 218 ASN cc_start: 0.8491 (m-40) cc_final: 0.8263 (m-40) REVERT: K 275 ILE cc_start: 0.5698 (pt) cc_final: 0.5332 (pt) REVERT: K 335 MET cc_start: 0.8393 (ptp) cc_final: 0.7963 (ppp) REVERT: L 61 VAL cc_start: 0.8549 (t) cc_final: 0.8099 (t) REVERT: L 88 PHE cc_start: 0.7554 (m-80) cc_final: 0.7017 (t80) REVERT: L 160 ILE cc_start: 0.2947 (mt) cc_final: 0.2333 (mp) REVERT: L 219 GLN cc_start: 0.8396 (mp10) cc_final: 0.8064 (mp10) REVERT: L 334 LYS cc_start: 0.8217 (mmpt) cc_final: 0.7982 (mmtm) REVERT: M 30 THR cc_start: 0.2933 (t) cc_final: 0.2423 (p) REVERT: M 54 MET cc_start: 0.4943 (tpp) cc_final: 0.4515 (tpp) REVERT: M 63 PHE cc_start: 0.3707 (t80) cc_final: 0.2821 (t80) REVERT: N 9 ILE cc_start: 0.4470 (pt) cc_final: 0.4253 (pt) REVERT: N 213 VAL cc_start: 0.2968 (m) cc_final: 0.2423 (p) REVERT: N 239 LEU cc_start: 0.7944 (mt) cc_final: 0.7429 (mt) REVERT: N 279 VAL cc_start: 0.4896 (p) cc_final: 0.4304 (m) REVERT: N 304 ILE cc_start: 0.1473 (mt) cc_final: 0.0849 (tt) REVERT: O 219 GLN cc_start: 0.6024 (mp10) cc_final: 0.5575 (pp30) REVERT: O 244 PRO cc_start: 0.0212 (Cg_exo) cc_final: -0.0992 (Cg_endo) REVERT: O 287 ILE cc_start: 0.8398 (mp) cc_final: 0.8192 (tp) REVERT: P 230 VAL cc_start: 0.7587 (m) cc_final: 0.6188 (m) REVERT: Q 122 MET cc_start: 0.7810 (ptp) cc_final: 0.7453 (pmm) REVERT: Q 129 ASP cc_start: 0.8010 (t0) cc_final: 0.7553 (t0) REVERT: Q 159 MET cc_start: 0.5876 (mmp) cc_final: 0.5486 (mmp) REVERT: Q 207 ILE cc_start: 0.8633 (mm) cc_final: 0.8419 (mm) outliers start: 1 outliers final: 0 residues processed: 888 average time/residue: 0.2495 time to fit residues: 343.7024 Evaluate side-chains 471 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 0.0270 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 overall best weight: 2.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 490 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 HIS E 83 GLN ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 HIS ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN K 163 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 57 HIS M 59 HIS M 162 HIS ** M 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN N 53 ASN ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 9 GLN Q 70 GLN ** Q 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.139786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.120513 restraints weight = 148644.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.123296 restraints weight = 93842.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.125195 restraints weight = 65370.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.126504 restraints weight = 49387.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.127420 restraints weight = 39771.318| |-----------------------------------------------------------------------------| r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 34327 Z= 0.232 Angle : 0.932 21.018 46736 Z= 0.438 Chirality : 0.065 0.963 5385 Planarity : 0.006 0.139 5826 Dihedral : 9.458 155.844 5085 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.16 % Favored : 91.51 % Rotamer: Outliers : 2.54 % Allowed : 13.06 % Favored : 84.40 % 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 (0.13), residues: 4144 helix: 0.20 (0.14), residues: 1408 sheet: -0.30 (0.22), residues: 555 loop : -1.77 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 130 TYR 0.034 0.002 TYR J 26 PHE 0.034 0.003 PHE J 67 TRP 0.020 0.002 TRP J 42 HIS 0.014 0.002 HIS K 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.23 (34321) covalent geometry : angle 0.93196 / 0.44 (46724) SS BOND : bond 0.00103 / 0.05 ( 6) SS BOND : angle 0.73832 / 0.41 ( 12) hydrogen bonds : bond 0.04219 / 2.76 ( 1054) hydrogen bonds : angle 4.89867 / 3.46 ( 3042) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 533 time to evaluate : 1.356 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 THR cc_start: 0.5654 (OUTLIER) cc_final: 0.5435 (m) REVERT: A 318 GLN cc_start: 0.6146 (mp10) cc_final: 0.5783 (mp10) REVERT: A 324 LEU cc_start: 0.8632 (mp) cc_final: 0.8244 (mp) REVERT: A 326 LEU cc_start: 0.8716 (tp) cc_final: 0.8499 (tp) REVERT: A 420 ASP cc_start: 0.8775 (m-30) cc_final: 0.8311 (m-30) REVERT: C 55 ARG cc_start: 0.7659 (ttt180) cc_final: 0.7266 (ttt180) REVERT: C 308 MET cc_start: 0.8165 (mmp) cc_final: 0.7738 (mmm) REVERT: D 16 VAL cc_start: 0.8944 (t) cc_final: 0.8717 (p) REVERT: D 33 LYS cc_start: 0.9113 (mttp) cc_final: 0.8824 (ptpp) REVERT: D 54 LEU cc_start: 0.9271 (mm) cc_final: 0.8872 (mm) REVERT: D 91 ARG cc_start: 0.8504 (mmm-85) cc_final: 0.8243 (mmm-85) REVERT: E 29 ASP cc_start: 0.7745 (m-30) cc_final: 0.7371 (p0) REVERT: E 67 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7865 (mmm160) REVERT: E 92 LYS cc_start: 0.8661 (pttm) cc_final: 0.8447 (pptt) REVERT: F 92 LYS cc_start: 0.8734 (ptpp) cc_final: 0.8495 (ptmt) REVERT: I 42 TRP cc_start: 0.5983 (m100) cc_final: 0.4801 (m100) REVERT: I 300 LEU cc_start: 0.8237 (mt) cc_final: 0.7893 (tp) REVERT: J 119 ASP cc_start: 0.5326 (t0) cc_final: 0.5078 (t70) REVERT: J 183 MET cc_start: 0.2565 (tmm) cc_final: 0.1963 (tmm) REVERT: J 218 ASN cc_start: 0.7252 (m-40) cc_final: 0.6928 (m-40) REVERT: J 235 ILE cc_start: 0.8294 (mt) cc_final: 0.8068 (pt) REVERT: K 254 LEU cc_start: 0.8067 (pt) cc_final: 0.7822 (mp) REVERT: L 1 MET cc_start: 0.3589 (tpp) cc_final: 0.2893 (tpp) REVERT: L 288 GLU cc_start: 0.8464 (mp0) cc_final: 0.8214 (pm20) REVERT: M 163 ASN cc_start: 0.7144 (p0) cc_final: 0.6808 (p0) REVERT: M 209 GLN cc_start: 0.7086 (mt0) cc_final: 0.6809 (mt0) REVERT: M 336 VAL cc_start: 0.3498 (OUTLIER) cc_final: 0.2983 (p) REVERT: N 54 MET cc_start: 0.1675 (mtt) cc_final: 0.0808 (mtm) REVERT: N 105 LEU cc_start: 0.6500 (mp) cc_final: 0.6210 (mp) REVERT: O 315 GLU cc_start: 0.7690 (mp0) cc_final: 0.7218 (mp0) REVERT: P 89 PHE cc_start: 0.6733 (OUTLIER) cc_final: 0.5972 (t80) REVERT: P 112 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: Q 18 MET cc_start: 0.7410 (tpt) cc_final: 0.6925 (tpt) REVERT: Q 114 MET cc_start: 0.8708 (tmm) cc_final: 0.8093 (tmm) REVERT: Q 115 MET cc_start: 0.7926 (mmm) cc_final: 0.7317 (mmm) REVERT: Q 122 MET cc_start: 0.8607 (ptp) cc_final: 0.7682 (pmm) REVERT: Q 129 ASP cc_start: 0.7925 (t0) cc_final: 0.7588 (t0) REVERT: Q 159 MET cc_start: 0.7728 (mmp) cc_final: 0.7489 (mmm) REVERT: Q 207 ILE cc_start: 0.8915 (mm) cc_final: 0.8711 (mm) outliers start: 87 outliers final: 50 residues processed: 589 average time/residue: 0.2357 time to fit residues: 222.2526 Evaluate side-chains 453 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 399 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain G residue 4 TRP Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 308 THR Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 335 MET Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 66 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 283 TYR Chi-restraints excluded: chain M residue 286 TYR Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 225 VAL Chi-restraints excluded: chain N residue 303 ASN Chi-restraints excluded: chain O residue 66 TYR Chi-restraints excluded: chain O residue 87 ARG Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 89 PHE Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain P residue 112 GLU Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 167 LYS Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 218 TYR Chi-restraints excluded: chain P residue 221 ILE Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 134 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 268 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 234 optimal weight: 0.0870 chunk 67 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 399 optimal weight: 2.9990 chunk 374 optimal weight: 0.0980 chunk 154 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN J 162 HIS K 163 ASN K 209 GLN K 219 GLN ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 310 ASN ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 162 HIS M 296 ASN ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 21 GLN Q 70 GLN ** Q 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.138248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.119124 restraints weight = 147282.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.121988 restraints weight = 91848.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.123995 restraints weight = 63482.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.125327 restraints weight = 46982.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.126290 restraints weight = 37436.702| |-----------------------------------------------------------------------------| r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5637 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 34327 Z= 0.144 Angle : 0.755 17.717 46736 Z= 0.360 Chirality : 0.054 0.539 5385 Planarity : 0.005 0.131 5826 Dihedral : 9.336 148.749 5085 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.67 % Favored : 92.08 % Rotamer: Outliers : 2.54 % Allowed : 16.82 % Favored : 80.64 % 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: -1.30 (0.13), residues: 4144 helix: 0.20 (0.14), residues: 1406 sheet: -0.29 (0.22), residues: 552 loop : -1.77 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG J 37 TYR 0.026 0.002 TYR K 26 PHE 0.046 0.002 PHE A 124 TRP 0.025 0.002 TRP J 42 HIS 0.014 0.001 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (34321) covalent geometry : angle 0.75534 / 0.36 (46724) SS BOND : bond 0.00048 / 0.02 ( 6) SS BOND : angle 0.50746 / 0.28 ( 12) hydrogen bonds : bond 0.03563 / 2.38 ( 1054) hydrogen bonds : angle 4.68392 / 3.31 ( 3042) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 448 time to evaluate : 1.363 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: 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: 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: symmetry clash REVERT: A 53 MET cc_start: 0.3207 (ttt) cc_final: 0.2853 (ppp) REVERT: A 175 MET cc_start: 0.8641 (mmm) cc_final: 0.7868 (mmt) REVERT: A 318 GLN cc_start: 0.6191 (mp10) cc_final: 0.5974 (mp10) REVERT: A 420 ASP cc_start: 0.8749 (m-30) cc_final: 0.8294 (m-30) REVERT: A 439 ASP cc_start: 0.8604 (m-30) cc_final: 0.8242 (m-30) REVERT: A 484 TYR cc_start: 0.7716 (m-80) cc_final: 0.7345 (m-80) REVERT: C 129 THR cc_start: 0.6960 (m) cc_final: 0.6402 (p) REVERT: C 193 ASP cc_start: 0.8824 (p0) cc_final: 0.8420 (p0) REVERT: C 308 MET cc_start: 0.8522 (mmp) cc_final: 0.8138 (mmm) REVERT: D 16 VAL cc_start: 0.8972 (t) cc_final: 0.8751 (p) REVERT: D 33 LYS cc_start: 0.9086 (mttp) cc_final: 0.8761 (ptpp) REVERT: D 38 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6591 (pm20) REVERT: D 54 LEU cc_start: 0.9274 (mm) cc_final: 0.8885 (mm) REVERT: D 91 ARG cc_start: 0.8540 (mmm-85) cc_final: 0.8195 (mmm-85) REVERT: E 67 ARG cc_start: 0.8256 (mmm160) cc_final: 0.8008 (mmm160) REVERT: F 92 LYS cc_start: 0.8854 (ptpp) cc_final: 0.8306 (ptmt) REVERT: I 42 TRP cc_start: 0.5912 (m100) cc_final: 0.4728 (m100) REVERT: I 218 ASN cc_start: 0.9011 (m110) cc_final: 0.8738 (p0) REVERT: I 300 LEU cc_start: 0.8212 (mt) cc_final: 0.7899 (tt) REVERT: J 5 ILE cc_start: 0.6171 (OUTLIER) cc_final: 0.5879 (tp) REVERT: J 19 GLN cc_start: 0.8231 (pt0) cc_final: 0.7812 (pm20) REVERT: J 183 MET cc_start: 0.2199 (tmm) cc_final: 0.1968 (tmm) REVERT: J 218 ASN cc_start: 0.7482 (m-40) cc_final: 0.7193 (m-40) REVERT: K 183 MET cc_start: 0.5054 (tmm) cc_final: 0.4327 (tmm) REVERT: K 185 PHE cc_start: 0.7189 (p90) cc_final: 0.6988 (p90) REVERT: K 253 ASN cc_start: 0.5157 (t0) cc_final: 0.4462 (t0) REVERT: K 254 LEU cc_start: 0.8392 (pt) cc_final: 0.8155 (mp) REVERT: L 72 TYR cc_start: 0.6311 (OUTLIER) cc_final: 0.5660 (t80) REVERT: L 278 LEU cc_start: 0.3290 (OUTLIER) cc_final: 0.2887 (pp) REVERT: L 288 GLU cc_start: 0.8392 (mp0) cc_final: 0.8110 (pm20) REVERT: L 315 GLU cc_start: 0.6652 (tp30) cc_final: 0.6431 (mm-30) REVERT: M 54 MET cc_start: 0.5661 (tpt) cc_final: 0.4766 (tpp) REVERT: M 163 ASN cc_start: 0.6934 (p0) cc_final: 0.6681 (p0) REVERT: M 209 GLN cc_start: 0.6839 (mt0) cc_final: 0.6614 (mt0) REVERT: N 54 MET cc_start: 0.1318 (mtt) cc_final: 0.0754 (mtm) REVERT: N 105 LEU cc_start: 0.6480 (mp) cc_final: 0.6140 (mp) REVERT: O 124 LEU cc_start: 0.2966 (tp) cc_final: 0.2707 (tp) REVERT: O 287 ILE cc_start: 0.8996 (mm) cc_final: 0.8651 (tp) REVERT: P 89 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.5408 (t80) REVERT: Q 69 TYR cc_start: 0.7944 (t80) cc_final: 0.7586 (t80) REVERT: Q 111 LEU cc_start: 0.9391 (mt) cc_final: 0.9133 (mt) REVERT: Q 115 MET cc_start: 0.7879 (mmm) cc_final: 0.7408 (mmm) REVERT: Q 122 MET cc_start: 0.8622 (ptp) cc_final: 0.7753 (pmm) REVERT: Q 159 MET cc_start: 0.7712 (mmp) cc_final: 0.7474 (mmm) REVERT: Q 198 LEU cc_start: 0.9329 (mt) cc_final: 0.9126 (mt) outliers start: 87 outliers final: 49 residues processed: 506 average time/residue: 0.2132 time to fit residues: 177.9711 Evaluate side-chains 428 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 374 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain G residue 4 TRP Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 335 MET Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 283 TYR Chi-restraints excluded: chain M residue 287 ILE Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 303 ASN Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain O residue 87 ARG Chi-restraints excluded: chain P residue 89 PHE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain P residue 167 LYS Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 218 TYR Chi-restraints excluded: chain P residue 221 ILE Chi-restraints excluded: chain Q residue 4 LYS Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 134 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 224 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 chunk 324 optimal weight: 0.4980 chunk 98 optimal weight: 0.0020 chunk 336 optimal weight: 1.9990 chunk 316 optimal weight: 0.7980 chunk 200 optimal weight: 0.0980 chunk 295 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 313 optimal weight: 9.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 GLN J 162 HIS L 53 ASN ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 162 HIS ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 HIS ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.137569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.118658 restraints weight = 147435.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.121535 restraints weight = 92096.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.123489 restraints weight = 63417.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.124793 restraints weight = 47173.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.125727 restraints weight = 37565.138| |-----------------------------------------------------------------------------| r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 34327 Z= 0.128 Angle : 0.724 18.965 46736 Z= 0.345 Chirality : 0.051 0.387 5385 Planarity : 0.005 0.101 5826 Dihedral : 9.369 149.166 5085 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.77 % Favored : 91.99 % Rotamer: Outliers : 2.59 % Allowed : 18.57 % Favored : 78.83 % 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: -1.40 (0.13), residues: 4144 helix: 0.08 (0.14), residues: 1428 sheet: -0.48 (0.22), residues: 573 loop : -1.79 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 37 TYR 0.021 0.001 TYR A 400 PHE 0.047 0.002 PHE A 124 TRP 0.025 0.002 TRP N 58 HIS 0.010 0.001 HIS J 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (34321) covalent geometry : angle 0.72434 / 0.34 (46724) SS BOND : bond 0.00055 / 0.03 ( 6) SS BOND : angle 0.47542 / 0.26 ( 12) hydrogen bonds : bond 0.03258 / 2.17 ( 1054) hydrogen bonds : angle 4.59372 / 3.25 ( 3042) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 422 time to evaluate : 1.333 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: 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: 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 53 MET cc_start: 0.3677 (ttt) cc_final: 0.2938 (ppp) REVERT: A 165 ASP cc_start: 0.6306 (t70) cc_final: 0.5867 (p0) REVERT: A 318 GLN cc_start: 0.6168 (mp10) cc_final: 0.5939 (mp10) REVERT: A 420 ASP cc_start: 0.8724 (m-30) cc_final: 0.8292 (m-30) REVERT: A 422 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8091 (p0) REVERT: C 20 TYR cc_start: 0.8862 (t80) cc_final: 0.8525 (t80) REVERT: C 65 MET cc_start: 0.8036 (mmm) cc_final: 0.7754 (mmt) REVERT: C 129 THR cc_start: 0.6952 (m) cc_final: 0.6388 (p) REVERT: C 193 ASP cc_start: 0.8764 (p0) cc_final: 0.8379 (p0) REVERT: C 308 MET cc_start: 0.8539 (mmp) cc_final: 0.7969 (mmm) REVERT: D 16 VAL cc_start: 0.8973 (t) cc_final: 0.8738 (p) REVERT: D 33 LYS cc_start: 0.9080 (mttp) cc_final: 0.8764 (ptpp) REVERT: D 38 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6681 (pm20) REVERT: D 53 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8734 (mmmm) REVERT: D 54 LEU cc_start: 0.9243 (mm) cc_final: 0.8816 (mm) REVERT: D 84 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6196 (tp) REVERT: D 91 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.8231 (mmm-85) REVERT: F 92 LYS cc_start: 0.8763 (ptpp) cc_final: 0.8221 (ptmt) REVERT: I 42 TRP cc_start: 0.5942 (m100) cc_final: 0.4744 (m100) REVERT: I 142 LEU cc_start: 0.8326 (mm) cc_final: 0.7956 (mp) REVERT: I 218 ASN cc_start: 0.9010 (m110) cc_final: 0.8745 (p0) REVERT: J 5 ILE cc_start: 0.6192 (OUTLIER) cc_final: 0.5936 (tp) REVERT: J 19 GLN cc_start: 0.8350 (pt0) cc_final: 0.7617 (pm20) REVERT: J 26 TYR cc_start: 0.6044 (OUTLIER) cc_final: 0.4070 (m-10) REVERT: J 183 MET cc_start: 0.3449 (tmm) cc_final: 0.3088 (tmm) REVERT: J 211 LEU cc_start: 0.7463 (mp) cc_final: 0.6971 (tp) REVERT: J 218 ASN cc_start: 0.7567 (m-40) cc_final: 0.7318 (m-40) REVERT: K 24 THR cc_start: 0.2564 (OUTLIER) cc_final: 0.2340 (p) REVERT: K 26 TYR cc_start: 0.6549 (m-80) cc_final: 0.6339 (m-80) REVERT: K 253 ASN cc_start: 0.5321 (t0) cc_final: 0.4596 (t0) REVERT: L 278 LEU cc_start: 0.3825 (OUTLIER) cc_final: 0.3466 (pp) REVERT: L 288 GLU cc_start: 0.8417 (mp0) cc_final: 0.8159 (pm20) REVERT: L 315 GLU cc_start: 0.6676 (tp30) cc_final: 0.6473 (mm-30) REVERT: M 54 MET cc_start: 0.6460 (tpt) cc_final: 0.5851 (tpp) REVERT: M 103 VAL cc_start: 0.5413 (t) cc_final: 0.5132 (m) REVERT: M 209 GLN cc_start: 0.6666 (mt0) cc_final: 0.6460 (mt0) REVERT: N 54 MET cc_start: 0.1266 (mtt) cc_final: 0.0584 (mtm) REVERT: N 105 LEU cc_start: 0.6480 (mp) cc_final: 0.6114 (mp) REVERT: N 154 GLU cc_start: 0.2021 (OUTLIER) cc_final: 0.1207 (pp20) REVERT: N 245 MET cc_start: 0.2924 (OUTLIER) cc_final: 0.2376 (mmp) REVERT: O 124 LEU cc_start: 0.2961 (tp) cc_final: 0.2726 (tp) REVERT: O 287 ILE cc_start: 0.8892 (mm) cc_final: 0.8556 (tp) REVERT: P 89 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.5225 (t80) REVERT: P 109 MET cc_start: 0.6483 (OUTLIER) cc_final: 0.6255 (mmm) REVERT: Q 18 MET cc_start: 0.5931 (tpt) cc_final: 0.5659 (tpt) REVERT: Q 56 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8794 (mt) REVERT: Q 122 MET cc_start: 0.8598 (ptp) cc_final: 0.7823 (pmm) REVERT: Q 159 MET cc_start: 0.7677 (mmp) cc_final: 0.7348 (mmm) REVERT: Q 198 LEU cc_start: 0.9196 (mt) cc_final: 0.8995 (mt) outliers start: 89 outliers final: 58 residues processed: 485 average time/residue: 0.2095 time to fit residues: 166.8918 Evaluate side-chains 451 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 381 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain G residue 4 TRP Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 26 TYR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 335 MET Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 283 TYR Chi-restraints excluded: chain M residue 287 ILE Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 303 ASN Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain O residue 87 ARG Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 89 PHE Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain P residue 109 MET Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 167 LYS Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 218 TYR Chi-restraints excluded: chain P residue 221 ILE Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain Q residue 142 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 366 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 352 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 321 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 299 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN C 141 HIS C 209 HIS C 246 HIS G 86 ASN I 19 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 HIS ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 ASN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 GLN O 53 ASN ** O 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 223 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 130 GLN ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.118643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.099147 restraints weight = 149286.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.101825 restraints weight = 90668.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.103622 restraints weight = 61767.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.104841 restraints weight = 46002.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.105647 restraints weight = 36807.502| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.7768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 34327 Z= 0.289 Angle : 0.995 14.807 46736 Z= 0.498 Chirality : 0.059 0.573 5385 Planarity : 0.007 0.137 5826 Dihedral : 10.363 149.459 5085 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 26.23 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.80 % Favored : 89.94 % Rotamer: Outliers : 3.91 % Allowed : 20.47 % Favored : 75.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.32 (0.12), residues: 4144 helix: -0.86 (0.13), residues: 1441 sheet: -1.11 (0.21), residues: 586 loop : -2.18 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG C 118 TYR 0.037 0.003 TYR M 2 PHE 0.041 0.004 PHE A 124 TRP 0.052 0.004 TRP N 58 HIS 0.049 0.004 HIS J 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.29 (34321) covalent geometry : angle 0.99469 / 0.50 (46724) SS BOND : bond 0.00206 / 0.11 ( 6) SS BOND : angle 0.90567 / 0.51 ( 12) hydrogen bonds : bond 0.04557 / 3.00 ( 1054) hydrogen bonds : angle 5.32361 / 3.75 ( 3042) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 489 time to evaluate : 1.342 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: 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: symmetry clash REVERT: A 53 MET cc_start: 0.3930 (ttt) cc_final: 0.3203 (ppp) REVERT: A 165 ASP cc_start: 0.6898 (t70) cc_final: 0.6350 (p0) REVERT: A 175 MET cc_start: 0.8902 (mmm) cc_final: 0.8225 (mmt) REVERT: A 318 GLN cc_start: 0.6265 (mp10) cc_final: 0.5916 (mp10) REVERT: C 20 TYR cc_start: 0.8795 (t80) cc_final: 0.8290 (t80) REVERT: C 108 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8226 (pt0) REVERT: C 112 LYS cc_start: 0.9071 (ptmm) cc_final: 0.8268 (ptpt) REVERT: C 117 LYS cc_start: 0.7609 (tppt) cc_final: 0.7289 (tppt) REVERT: C 118 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7577 (ptt-90) REVERT: C 193 ASP cc_start: 0.8696 (p0) cc_final: 0.8309 (p0) REVERT: C 206 HIS cc_start: 0.8936 (m-70) cc_final: 0.8561 (m90) REVERT: D 33 LYS cc_start: 0.9296 (mttp) cc_final: 0.9019 (ptpp) REVERT: D 53 LYS cc_start: 0.9268 (mmmm) cc_final: 0.9048 (mmmm) REVERT: D 88 LYS cc_start: 0.7789 (tptt) cc_final: 0.7439 (tppt) REVERT: D 91 ARG cc_start: 0.8763 (mmm-85) cc_final: 0.8428 (mmm-85) REVERT: F 92 LYS cc_start: 0.8839 (ptpp) cc_final: 0.8107 (ptmt) REVERT: F 96 SER cc_start: 0.9368 (OUTLIER) cc_final: 0.8841 (p) REVERT: I 1 MET cc_start: 0.7890 (mmm) cc_final: 0.7545 (mmm) REVERT: I 119 ASP cc_start: 0.6487 (t70) cc_final: 0.5922 (t0) REVERT: I 142 LEU cc_start: 0.8525 (mm) cc_final: 0.8063 (mp) REVERT: I 199 VAL cc_start: 0.8273 (t) cc_final: 0.8030 (t) REVERT: J 19 GLN cc_start: 0.9089 (pt0) cc_final: 0.8814 (pt0) REVERT: J 26 TYR cc_start: 0.6702 (OUTLIER) cc_final: 0.5105 (m-10) REVERT: J 59 HIS cc_start: 0.8671 (t-90) cc_final: 0.8344 (t70) REVERT: J 183 MET cc_start: 0.2860 (tmm) cc_final: 0.2298 (tmm) REVERT: J 218 ASN cc_start: 0.7844 (m-40) cc_final: 0.7582 (m-40) REVERT: K 1 MET cc_start: 0.6428 (ppp) cc_final: 0.5841 (ttp) REVERT: K 24 THR cc_start: 0.4017 (OUTLIER) cc_final: 0.3699 (p) REVERT: K 26 TYR cc_start: 0.6700 (m-80) cc_final: 0.6404 (m-80) REVERT: K 183 MET cc_start: 0.4778 (tmm) cc_final: 0.4145 (tmm) REVERT: K 245 MET cc_start: 0.7141 (mmm) cc_final: 0.6865 (mmp) REVERT: L 14 HIS cc_start: 0.5267 (p-80) cc_final: 0.4991 (p-80) REVERT: L 19 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7306 (tm-30) REVERT: L 27 ILE cc_start: 0.5562 (OUTLIER) cc_final: 0.5126 (pt) REVERT: L 54 MET cc_start: 0.9030 (tpt) cc_final: 0.8681 (tpt) REVERT: L 66 TYR cc_start: 0.8464 (m-80) cc_final: 0.7781 (m-10) REVERT: L 288 GLU cc_start: 0.8590 (mp0) cc_final: 0.8257 (pm20) REVERT: L 308 THR cc_start: 0.7134 (p) cc_final: 0.6906 (p) REVERT: M 87 ARG cc_start: 0.4327 (OUTLIER) cc_final: 0.3794 (tpp80) REVERT: M 263 VAL cc_start: 0.0418 (OUTLIER) cc_final: -0.0462 (t) REVERT: M 291 ARG cc_start: 0.8342 (tpt90) cc_final: 0.8101 (ttp80) REVERT: N 54 MET cc_start: 0.2457 (mtt) cc_final: 0.1400 (mtm) REVERT: N 105 LEU cc_start: 0.7460 (mp) cc_final: 0.6908 (mp) REVERT: N 154 GLU cc_start: 0.2310 (OUTLIER) cc_final: 0.0952 (pp20) REVERT: N 219 GLN cc_start: 0.4310 (pm20) cc_final: 0.3585 (pp30) REVERT: N 263 VAL cc_start: 0.1960 (OUTLIER) cc_final: 0.1746 (m) REVERT: N 278 LEU cc_start: 0.3081 (OUTLIER) cc_final: 0.2792 (tt) REVERT: O 211 LEU cc_start: 0.6714 (tp) cc_final: 0.5898 (pt) REVERT: P 89 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7117 (t80) REVERT: P 144 ASP cc_start: 0.7612 (m-30) cc_final: 0.7331 (m-30) REVERT: P 223 GLU cc_start: 0.7044 (tp30) cc_final: 0.6817 (tp30) REVERT: Q 18 MET cc_start: 0.6315 (tpt) cc_final: 0.5868 (tpt) REVERT: Q 46 GLU cc_start: 0.9387 (mt-10) cc_final: 0.8841 (pm20) REVERT: Q 85 GLU cc_start: 0.8094 (pt0) cc_final: 0.7400 (pm20) REVERT: Q 118 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8564 (tp30) REVERT: Q 122 MET cc_start: 0.8674 (ptp) cc_final: 0.8398 (ptp) outliers start: 134 outliers final: 70 residues processed: 596 average time/residue: 0.2098 time to fit residues: 205.7729 Evaluate side-chains 470 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 389 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 4 TRP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 88 PHE Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 308 THR Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 26 TYR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 88 PHE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 335 MET Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 207 ILE Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 87 ARG Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain N residue 130 ARG Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 278 LEU Chi-restraints excluded: chain N residue 303 ASN Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 89 PHE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain P residue 151 SER Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 167 LYS Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 218 TYR Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain Q residue 105 ILE Chi-restraints excluded: chain Q residue 127 SER Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain Q residue 142 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 349 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 375 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 278 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 HIS K 209 GLN ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 HIS ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 HIS ** O 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.122994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.102846 restraints weight = 146081.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.105542 restraints weight = 88615.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.107352 restraints weight = 60772.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.108572 restraints weight = 45523.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.109403 restraints weight = 36750.317| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.8062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 34327 Z= 0.151 Angle : 0.770 14.605 46736 Z= 0.370 Chirality : 0.052 0.411 5385 Planarity : 0.005 0.101 5826 Dihedral : 9.729 143.409 5085 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.01 % Favored : 91.77 % Rotamer: Outliers : 3.18 % Allowed : 24.34 % Favored : 72.48 % 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: -1.98 (0.13), residues: 4144 helix: -0.46 (0.13), residues: 1442 sheet: -0.91 (0.22), residues: 572 loop : -2.06 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG N 231 TYR 0.032 0.002 TYR N 283 PHE 0.026 0.002 PHE M 261 TRP 0.035 0.002 TRP J 42 HIS 0.006 0.001 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (34321) covalent geometry : angle 0.77003 / 0.37 (46724) SS BOND : bond 0.00113 / 0.06 ( 6) SS BOND : angle 0.63748 / 0.35 ( 12) hydrogen bonds : bond 0.03378 / 2.25 ( 1054) hydrogen bonds : angle 4.85953 / 3.43 ( 3042) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 443 time to evaluate : 1.290 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.3881 (ttt) cc_final: 0.3318 (ppp) REVERT: A 165 ASP cc_start: 0.6712 (t70) cc_final: 0.6042 (p0) REVERT: A 300 ASP cc_start: 0.9017 (m-30) cc_final: 0.8626 (p0) REVERT: A 318 GLN cc_start: 0.6251 (mp10) cc_final: 0.5934 (mp10) REVERT: A 439 ASP cc_start: 0.8478 (m-30) cc_final: 0.8185 (m-30) REVERT: C 20 TYR cc_start: 0.8907 (t80) cc_final: 0.8134 (t80) REVERT: C 52 GLU cc_start: 0.9156 (mp0) cc_final: 0.8025 (mm-30) REVERT: C 108 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8253 (pt0) REVERT: C 112 LYS cc_start: 0.8895 (ptmm) cc_final: 0.8688 (ptpt) REVERT: C 131 MET cc_start: 0.8684 (tmm) cc_final: 0.8263 (tmm) REVERT: C 193 ASP cc_start: 0.8759 (p0) cc_final: 0.8488 (p0) REVERT: C 206 HIS cc_start: 0.8888 (m-70) cc_final: 0.8653 (m90) REVERT: D 33 LYS cc_start: 0.9239 (mttp) cc_final: 0.8973 (ptpp) REVERT: D 38 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: D 53 LYS cc_start: 0.9355 (mmmm) cc_final: 0.9139 (mmmm) REVERT: D 88 LYS cc_start: 0.7802 (tptt) cc_final: 0.7433 (tppt) REVERT: D 91 ARG cc_start: 0.8723 (mmm-85) cc_final: 0.8388 (mmm-85) REVERT: E 91 ARG cc_start: 0.7913 (mmm160) cc_final: 0.7619 (mmm160) REVERT: F 92 LYS cc_start: 0.8787 (ptpp) cc_final: 0.7969 (ptmt) REVERT: F 96 SER cc_start: 0.9408 (t) cc_final: 0.8937 (p) REVERT: I 1 MET cc_start: 0.8043 (mmm) cc_final: 0.7633 (mmm) REVERT: I 199 VAL cc_start: 0.8304 (t) cc_final: 0.8078 (t) REVERT: I 218 ASN cc_start: 0.9133 (m110) cc_final: 0.8841 (p0) REVERT: J 19 GLN cc_start: 0.9124 (pt0) cc_final: 0.8809 (pt0) REVERT: J 26 TYR cc_start: 0.6489 (OUTLIER) cc_final: 0.4596 (m-10) REVERT: J 218 ASN cc_start: 0.7917 (m-40) cc_final: 0.7669 (m-40) REVERT: K 1 MET cc_start: 0.6864 (ppp) cc_final: 0.6436 (ttp) REVERT: K 17 ASN cc_start: 0.7030 (t0) cc_final: 0.6810 (t0) REVERT: K 26 TYR cc_start: 0.6734 (m-80) cc_final: 0.6320 (m-80) REVERT: K 183 MET cc_start: 0.4978 (tmm) cc_final: 0.4448 (tmm) REVERT: L 65 ASP cc_start: 0.8387 (t0) cc_final: 0.7579 (m-30) REVERT: L 288 GLU cc_start: 0.8765 (mp0) cc_final: 0.8386 (pm20) REVERT: L 304 ILE cc_start: 0.7391 (mm) cc_final: 0.6973 (mm) REVERT: L 315 GLU cc_start: 0.6259 (mm-30) cc_final: 0.6000 (mm-30) REVERT: M 209 GLN cc_start: 0.7326 (mt0) cc_final: 0.7035 (mt0) REVERT: M 291 ARG cc_start: 0.8040 (tpt90) cc_final: 0.7547 (ttp80) REVERT: N 54 MET cc_start: 0.1739 (mtt) cc_final: 0.1459 (mtm) REVERT: N 105 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6853 (mp) REVERT: N 154 GLU cc_start: 0.2078 (OUTLIER) cc_final: 0.0803 (pp20) REVERT: N 219 GLN cc_start: 0.5073 (pm20) cc_final: 0.4485 (pp30) REVERT: N 263 VAL cc_start: 0.2721 (OUTLIER) cc_final: 0.2444 (m) REVERT: O 211 LEU cc_start: 0.7282 (tp) cc_final: 0.6511 (pt) REVERT: P 1 MET cc_start: 0.4899 (mtp) cc_final: 0.4546 (ptp) REVERT: P 89 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.6427 (t80) REVERT: P 144 ASP cc_start: 0.7366 (m-30) cc_final: 0.7099 (m-30) REVERT: P 223 GLU cc_start: 0.7435 (tp30) cc_final: 0.6997 (tp30) REVERT: Q 13 GLU cc_start: 0.8649 (pp20) cc_final: 0.8387 (pp20) REVERT: Q 46 GLU cc_start: 0.9394 (mt-10) cc_final: 0.8800 (pm20) REVERT: Q 69 TYR cc_start: 0.7808 (t80) cc_final: 0.7416 (t80) REVERT: Q 85 GLU cc_start: 0.8151 (pt0) cc_final: 0.7528 (pm20) REVERT: Q 96 LEU cc_start: 0.8795 (mt) cc_final: 0.8386 (tt) REVERT: Q 105 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9094 (tt) REVERT: Q 122 MET cc_start: 0.8702 (ptp) cc_final: 0.8177 (pmm) REVERT: Q 198 LEU cc_start: 0.9094 (mt) cc_final: 0.8804 (mt) outliers start: 109 outliers final: 65 residues processed: 524 average time/residue: 0.2026 time to fit residues: 175.9720 Evaluate side-chains 453 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 381 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain G residue 4 TRP Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain J residue 26 TYR Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 131 ARG Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 317 ILE Chi-restraints excluded: chain J residue 335 MET Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 262 LYS Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 265 GLU Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 105 LEU Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain N residue 194 TYR Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 303 ASN Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 89 PHE Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 167 LYS Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 218 TYR Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 105 ILE Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 166 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 385 optimal weight: 0.6980 chunk 182 optimal weight: 8.9990 chunk 198 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 259 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 280 optimal weight: 6.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS C 106 ASN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN J 163 ASN ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN N 331 ASN ** O 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.111948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.091759 restraints weight = 149964.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.094299 restraints weight = 90492.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.095973 restraints weight = 62064.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.097126 restraints weight = 46882.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.097899 restraints weight = 38024.107| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.9800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 34327 Z= 0.242 Angle : 0.877 11.855 46736 Z= 0.437 Chirality : 0.055 0.403 5385 Planarity : 0.007 0.166 5826 Dihedral : 9.942 147.003 5085 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.70 % Favored : 89.99 % Rotamer: Outliers : 3.70 % Allowed : 24.43 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.23 (0.13), residues: 4144 helix: -0.68 (0.13), residues: 1435 sheet: -1.22 (0.21), residues: 594 loop : -2.15 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG M 231 TYR 0.036 0.002 TYR F 14 PHE 0.033 0.003 PHE M 261 TRP 0.029 0.002 TRP J 42 HIS 0.014 0.002 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (34321) covalent geometry : angle 0.87678 / 0.44 (46724) SS BOND : bond 0.00183 / 0.10 ( 6) SS BOND : angle 0.68526 / 0.39 ( 12) hydrogen bonds : bond 0.03888 / 2.59 ( 1054) hydrogen bonds : angle 5.20305 / 3.66 ( 3042) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 423 time to evaluate : 1.201 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: 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 165 ASP cc_start: 0.6855 (t70) cc_final: 0.6238 (p0) REVERT: A 300 ASP cc_start: 0.9056 (m-30) cc_final: 0.8529 (p0) REVERT: A 318 GLN cc_start: 0.6381 (mp10) cc_final: 0.6029 (mp10) REVERT: A 428 LEU cc_start: 0.8090 (mt) cc_final: 0.7231 (mp) REVERT: A 602 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6908 (p0) REVERT: C 52 GLU cc_start: 0.9126 (mp0) cc_final: 0.8396 (mm-30) REVERT: C 111 MET cc_start: 0.8338 (mmm) cc_final: 0.7989 (mmm) REVERT: C 131 MET cc_start: 0.8752 (tmm) cc_final: 0.8370 (tmm) REVERT: C 193 ASP cc_start: 0.8879 (p0) cc_final: 0.8539 (p0) REVERT: C 301 LEU cc_start: 0.9524 (mt) cc_final: 0.9284 (pp) REVERT: C 308 MET cc_start: 0.8784 (mmm) cc_final: 0.8276 (mmm) REVERT: D 33 LYS cc_start: 0.9363 (mttp) cc_final: 0.9117 (ptpp) REVERT: D 84 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6812 (tp) REVERT: D 88 LYS cc_start: 0.8137 (tptt) cc_final: 0.7843 (tppt) REVERT: D 91 ARG cc_start: 0.8910 (mmm-85) cc_final: 0.8446 (mmm-85) REVERT: F 92 LYS cc_start: 0.8990 (ptpp) cc_final: 0.8466 (ptpt) REVERT: F 96 SER cc_start: 0.9460 (t) cc_final: 0.9143 (p) REVERT: G 92 LYS cc_start: 0.7413 (ttpp) cc_final: 0.7015 (tptm) REVERT: H 10 ARG cc_start: 0.7352 (ttp80) cc_final: 0.7152 (tmm160) REVERT: I 199 VAL cc_start: 0.8606 (t) cc_final: 0.8350 (t) REVERT: I 201 ASP cc_start: 0.8295 (m-30) cc_final: 0.7275 (t0) REVERT: J 26 TYR cc_start: 0.6006 (OUTLIER) cc_final: 0.4266 (m-10) REVERT: J 33 LYS cc_start: 0.8067 (mttt) cc_final: 0.7473 (mmtp) REVERT: J 54 MET cc_start: 0.9056 (tpp) cc_final: 0.8687 (tpp) REVERT: J 183 MET cc_start: 0.3032 (tmm) cc_final: 0.2736 (tmm) REVERT: J 218 ASN cc_start: 0.8262 (m-40) cc_final: 0.8004 (m-40) REVERT: J 335 MET cc_start: 0.7102 (ptt) cc_final: 0.6605 (ppp) REVERT: K 1 MET cc_start: 0.7102 (ppp) cc_final: 0.6477 (ppp) REVERT: K 11 LEU cc_start: 0.6757 (mm) cc_final: 0.6266 (mm) REVERT: K 26 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: K 183 MET cc_start: 0.5338 (tmm) cc_final: 0.4651 (tmm) REVERT: L 1 MET cc_start: 0.6453 (tpt) cc_final: 0.6053 (tpp) REVERT: L 27 ILE cc_start: 0.6299 (OUTLIER) cc_final: 0.6088 (pt) REVERT: L 119 ASP cc_start: 0.7587 (t0) cc_final: 0.7167 (t70) REVERT: L 197 SER cc_start: 0.8375 (t) cc_final: 0.8110 (t) REVERT: M 1 MET cc_start: 0.7779 (mmm) cc_final: 0.6749 (mmp) REVERT: M 61 VAL cc_start: 0.8290 (t) cc_final: 0.8062 (t) REVERT: M 209 GLN cc_start: 0.7712 (mt0) cc_final: 0.7465 (mt0) REVERT: M 291 ARG cc_start: 0.8505 (tpt90) cc_final: 0.8174 (ttp80) REVERT: M 326 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6847 (pt0) REVERT: N 90 GLN cc_start: 0.8192 (tp40) cc_final: 0.7887 (tp40) REVERT: N 105 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7981 (mp) REVERT: N 112 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.6316 (mm) REVERT: N 130 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6766 (tpp80) REVERT: N 154 GLU cc_start: 0.2721 (OUTLIER) cc_final: 0.1207 (pp20) REVERT: N 263 VAL cc_start: 0.2733 (OUTLIER) cc_final: 0.2480 (m) REVERT: P 21 GLN cc_start: 0.7691 (tp40) cc_final: 0.7483 (tp40) REVERT: P 42 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6876 (mt) REVERT: P 89 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7003 (t80) REVERT: P 109 MET cc_start: 0.8181 (mmm) cc_final: 0.7678 (mmm) REVERT: P 144 ASP cc_start: 0.7888 (m-30) cc_final: 0.7543 (m-30) REVERT: P 223 GLU cc_start: 0.7394 (tp30) cc_final: 0.6748 (tp30) REVERT: Q 18 MET cc_start: 0.7266 (tpt) cc_final: 0.6932 (tpt) REVERT: Q 46 GLU cc_start: 0.9437 (mt-10) cc_final: 0.8993 (pm20) REVERT: Q 57 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8541 (tp) REVERT: Q 69 TYR cc_start: 0.8333 (t80) cc_final: 0.7856 (t80) REVERT: Q 85 GLU cc_start: 0.8163 (pt0) cc_final: 0.7803 (pm20) REVERT: Q 96 LEU cc_start: 0.9108 (mt) cc_final: 0.8580 (tt) REVERT: Q 105 ILE cc_start: 0.9505 (tt) cc_final: 0.9058 (tt) REVERT: Q 129 ASP cc_start: 0.7122 (t0) cc_final: 0.6894 (t0) outliers start: 127 outliers final: 74 residues processed: 516 average time/residue: 0.2080 time to fit residues: 177.7982 Evaluate side-chains 451 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 364 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain G residue 4 TRP Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 88 PHE Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 26 TYR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 88 PHE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 261 PHE Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 317 ILE Chi-restraints excluded: chain K residue 26 TYR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 262 LYS Chi-restraints excluded: chain M residue 14 HIS Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 9 ILE Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 105 LEU Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 130 ARG Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 194 TYR Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 283 TYR Chi-restraints excluded: chain N residue 303 ASN Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 89 PHE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 167 LYS Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 218 TYR Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain Q residue 142 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 286 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 263 optimal weight: 0.6980 chunk 56 optimal weight: 20.0000 chunk 318 optimal weight: 10.0000 chunk 376 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 371 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 GLN J 331 ASN ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN K 296 ASN ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN N 331 ASN ** O 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.113211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.092950 restraints weight = 147154.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.095575 restraints weight = 88158.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.097304 restraints weight = 59888.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.098490 restraints weight = 44847.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.099283 restraints weight = 36104.987| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 1.0118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 34327 Z= 0.148 Angle : 0.777 13.553 46736 Z= 0.373 Chirality : 0.051 0.358 5385 Planarity : 0.005 0.101 5826 Dihedral : 9.701 143.411 5085 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.89 % Favored : 91.82 % Rotamer: Outliers : 2.94 % Allowed : 26.12 % Favored : 70.93 % 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: -1.97 (0.13), residues: 4144 helix: -0.39 (0.14), residues: 1451 sheet: -1.02 (0.21), residues: 582 loop : -2.08 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 155 TYR 0.021 0.002 TYR A 400 PHE 0.024 0.002 PHE I 261 TRP 0.023 0.002 TRP K 42 HIS 0.021 0.002 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (34321) covalent geometry : angle 0.77676 / 0.37 (46724) SS BOND : bond 0.00100 / 0.06 ( 6) SS BOND : angle 0.55627 / 0.31 ( 12) hydrogen bonds : bond 0.03292 / 2.20 ( 1054) hydrogen bonds : angle 4.89933 / 3.46 ( 3042) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 399 time to evaluate : 1.339 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7410 (pmm) cc_final: 0.7156 (pmm) REVERT: A 53 MET cc_start: 0.5029 (ttt) cc_final: 0.4183 (tmm) REVERT: A 73 LEU cc_start: 0.9247 (mm) cc_final: 0.8763 (mt) REVERT: A 165 ASP cc_start: 0.6991 (t70) cc_final: 0.6328 (p0) REVERT: A 175 MET cc_start: 0.8828 (mmm) cc_final: 0.8119 (mmt) REVERT: A 300 ASP cc_start: 0.9070 (m-30) cc_final: 0.8494 (p0) REVERT: A 318 GLN cc_start: 0.6365 (mp10) cc_final: 0.6033 (mp10) REVERT: A 428 LEU cc_start: 0.8056 (mt) cc_final: 0.7068 (mp) REVERT: C 52 GLU cc_start: 0.9065 (mp0) cc_final: 0.8477 (mm-30) REVERT: C 116 LYS cc_start: 0.8606 (pttt) cc_final: 0.8076 (pptt) REVERT: C 131 MET cc_start: 0.8767 (tmm) cc_final: 0.8304 (tmm) REVERT: C 193 ASP cc_start: 0.9092 (p0) cc_final: 0.8823 (p0) REVERT: C 308 MET cc_start: 0.8777 (mmm) cc_final: 0.8337 (mmm) REVERT: D 33 LYS cc_start: 0.9348 (mttp) cc_final: 0.9097 (ptpp) REVERT: D 84 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6799 (tp) REVERT: D 91 ARG cc_start: 0.8805 (mmm-85) cc_final: 0.8435 (mmm-85) REVERT: F 92 LYS cc_start: 0.8932 (ptpp) cc_final: 0.8373 (ptpt) REVERT: F 96 SER cc_start: 0.9398 (t) cc_final: 0.9008 (p) REVERT: G 92 LYS cc_start: 0.7410 (ttpp) cc_final: 0.7076 (tptm) REVERT: H 10 ARG cc_start: 0.7139 (ttp80) cc_final: 0.6881 (tmm160) REVERT: I 55 LEU cc_start: 0.8931 (mm) cc_final: 0.8677 (mt) REVERT: I 199 VAL cc_start: 0.8666 (t) cc_final: 0.8393 (t) REVERT: I 201 ASP cc_start: 0.8449 (m-30) cc_final: 0.7409 (t0) REVERT: J 1 MET cc_start: 0.8275 (tmm) cc_final: 0.8009 (tmm) REVERT: J 19 GLN cc_start: 0.9258 (pt0) cc_final: 0.8808 (pt0) REVERT: J 26 TYR cc_start: 0.6029 (OUTLIER) cc_final: 0.4359 (m-10) REVERT: J 35 THR cc_start: 0.7387 (m) cc_final: 0.7172 (m) REVERT: J 54 MET cc_start: 0.8899 (tpp) cc_final: 0.8679 (tpp) REVERT: J 218 ASN cc_start: 0.8432 (m-40) cc_final: 0.8217 (m-40) REVERT: J 335 MET cc_start: 0.7363 (ptt) cc_final: 0.7134 (ppp) REVERT: K 1 MET cc_start: 0.7062 (ppp) cc_final: 0.6783 (ttp) REVERT: K 11 LEU cc_start: 0.6787 (mm) cc_final: 0.6299 (mm) REVERT: K 26 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6235 (m-80) REVERT: K 183 MET cc_start: 0.4815 (tmm) cc_final: 0.4490 (tmm) REVERT: K 237 SER cc_start: 0.9336 (m) cc_final: 0.9118 (p) REVERT: L 1 MET cc_start: 0.6757 (tpt) cc_final: 0.6381 (tpp) REVERT: L 119 ASP cc_start: 0.7619 (t0) cc_final: 0.7325 (t0) REVERT: L 197 SER cc_start: 0.8251 (t) cc_final: 0.7992 (t) REVERT: L 312 ASP cc_start: 0.6656 (t70) cc_final: 0.6260 (t70) REVERT: M 1 MET cc_start: 0.7452 (mmm) cc_final: 0.6525 (mmp) REVERT: M 236 GLU cc_start: 0.7286 (tt0) cc_final: 0.6550 (mm-30) REVERT: M 291 ARG cc_start: 0.8336 (tpt90) cc_final: 0.8005 (ttp80) REVERT: N 90 GLN cc_start: 0.8174 (tp40) cc_final: 0.7809 (tp40) REVERT: N 105 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8026 (mp) REVERT: N 154 GLU cc_start: 0.2619 (OUTLIER) cc_final: 0.1119 (pp20) REVERT: N 318 GLU cc_start: 0.0112 (OUTLIER) cc_final: -0.0790 (pp20) REVERT: P 1 MET cc_start: 0.6219 (mtt) cc_final: 0.5660 (ptp) REVERT: P 21 GLN cc_start: 0.7567 (tp40) cc_final: 0.7312 (tp40) REVERT: P 89 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7283 (t80) REVERT: P 110 ARG cc_start: 0.6718 (mmt180) cc_final: 0.5927 (mmt-90) REVERT: P 144 ASP cc_start: 0.7892 (m-30) cc_final: 0.7497 (m-30) REVERT: P 199 LYS cc_start: 0.8155 (mttp) cc_final: 0.7935 (mppt) REVERT: P 223 GLU cc_start: 0.7385 (tp30) cc_final: 0.6740 (tp30) REVERT: Q 18 MET cc_start: 0.6789 (tpt) cc_final: 0.6365 (tpt) REVERT: Q 46 GLU cc_start: 0.9459 (mt-10) cc_final: 0.8972 (pm20) REVERT: Q 69 TYR cc_start: 0.8287 (t80) cc_final: 0.7754 (t80) REVERT: Q 85 GLU cc_start: 0.8273 (pt0) cc_final: 0.7909 (pm20) REVERT: Q 96 LEU cc_start: 0.9055 (mt) cc_final: 0.8539 (tt) REVERT: Q 105 ILE cc_start: 0.9514 (tt) cc_final: 0.9113 (tt) REVERT: Q 129 ASP cc_start: 0.7166 (t0) cc_final: 0.6897 (t0) REVERT: Q 149 MET cc_start: 0.7125 (mmp) cc_final: 0.6566 (mmp) REVERT: Q 159 MET cc_start: 0.7979 (mmm) cc_final: 0.7750 (mmm) outliers start: 101 outliers final: 62 residues processed: 472 average time/residue: 0.2103 time to fit residues: 164.5422 Evaluate side-chains 426 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 357 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain G residue 4 TRP Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 26 TYR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 317 ILE Chi-restraints excluded: chain K residue 26 TYR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 166 ASP Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 265 GLU Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 105 LEU Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain N residue 303 ASN Chi-restraints excluded: chain N residue 318 GLU Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 54 MET Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 89 PHE Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 167 LYS Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 218 TYR Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain Q residue 142 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 395 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 376 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 234 optimal weight: 0.4980 chunk 412 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 HIS ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 57 HIS ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 296 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.112764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.092549 restraints weight = 146527.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.095132 restraints weight = 88089.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.096872 restraints weight = 60185.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.098053 restraints weight = 45125.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.098811 restraints weight = 36373.954| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 1.0345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 34327 Z= 0.145 Angle : 0.776 13.455 46736 Z= 0.373 Chirality : 0.051 0.371 5385 Planarity : 0.005 0.102 5826 Dihedral : 9.630 143.400 5085 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.57 % Favored : 91.14 % Rotamer: Outliers : 2.59 % Allowed : 26.73 % Favored : 70.67 % 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: -1.92 (0.13), residues: 4144 helix: -0.30 (0.14), residues: 1445 sheet: -1.01 (0.21), residues: 595 loop : -2.08 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 55 TYR 0.021 0.001 TYR A 400 PHE 0.024 0.002 PHE M 282 TRP 0.028 0.002 TRP J 42 HIS 0.019 0.001 HIS J 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (34321) covalent geometry : angle 0.77578 / 0.37 (46724) SS BOND : bond 0.00101 / 0.06 ( 6) SS BOND : angle 0.52959 / 0.30 ( 12) hydrogen bonds : bond 0.03213 / 2.15 ( 1054) hydrogen bonds : angle 4.82546 / 3.41 ( 3042) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 379 time to evaluate : 1.306 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: symmetry clash REVERT: A 31 MET cc_start: 0.7432 (pmm) cc_final: 0.7169 (pmm) REVERT: A 53 MET cc_start: 0.4763 (ttt) cc_final: 0.4196 (tmm) REVERT: A 73 LEU cc_start: 0.9276 (mm) cc_final: 0.8822 (mt) REVERT: A 165 ASP cc_start: 0.6806 (t70) cc_final: 0.6236 (p0) REVERT: A 175 MET cc_start: 0.8840 (mmm) cc_final: 0.8283 (mmt) REVERT: A 300 ASP cc_start: 0.9037 (m-30) cc_final: 0.8506 (p0) REVERT: A 318 GLN cc_start: 0.6546 (mp10) cc_final: 0.6205 (mp10) REVERT: A 428 LEU cc_start: 0.8121 (mt) cc_final: 0.7227 (mp) REVERT: C 52 GLU cc_start: 0.9140 (mp0) cc_final: 0.8698 (mm-30) REVERT: C 55 ARG cc_start: 0.8133 (ttt180) cc_final: 0.7303 (tpt-90) REVERT: C 111 MET cc_start: 0.7897 (mmm) cc_final: 0.7557 (tpt) REVERT: C 131 MET cc_start: 0.8806 (tmm) cc_final: 0.8488 (tmm) REVERT: C 193 ASP cc_start: 0.9058 (p0) cc_final: 0.8738 (p0) REVERT: C 308 MET cc_start: 0.8803 (mmm) cc_final: 0.8382 (mmm) REVERT: D 33 LYS cc_start: 0.9336 (mttp) cc_final: 0.9091 (ptpp) REVERT: D 53 LYS cc_start: 0.9222 (mmmm) cc_final: 0.8569 (mptt) REVERT: D 84 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6825 (tp) REVERT: D 91 ARG cc_start: 0.8827 (mmm-85) cc_final: 0.8491 (mmm-85) REVERT: E 95 VAL cc_start: 0.8393 (t) cc_final: 0.8182 (p) REVERT: F 92 LYS cc_start: 0.8875 (ptpp) cc_final: 0.8425 (ptpt) REVERT: F 96 SER cc_start: 0.9496 (t) cc_final: 0.9104 (p) REVERT: G 92 LYS cc_start: 0.7792 (ttpp) cc_final: 0.7361 (tptp) REVERT: H 10 ARG cc_start: 0.7162 (ttp80) cc_final: 0.6915 (tmm160) REVERT: I 199 VAL cc_start: 0.8724 (t) cc_final: 0.8453 (t) REVERT: I 201 ASP cc_start: 0.8498 (m-30) cc_final: 0.7304 (t0) REVERT: J 1 MET cc_start: 0.8156 (tmm) cc_final: 0.7888 (tmm) REVERT: J 19 GLN cc_start: 0.9274 (pt0) cc_final: 0.8819 (pt0) REVERT: J 26 TYR cc_start: 0.6036 (OUTLIER) cc_final: 0.4181 (m-10) REVERT: J 35 THR cc_start: 0.7459 (m) cc_final: 0.7223 (m) REVERT: J 218 ASN cc_start: 0.8529 (m-40) cc_final: 0.8292 (m-40) REVERT: J 335 MET cc_start: 0.7417 (ptt) cc_final: 0.7216 (ppp) REVERT: K 11 LEU cc_start: 0.6808 (mm) cc_final: 0.6325 (mm) REVERT: K 26 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6179 (m-80) REVERT: K 119 ASP cc_start: 0.8221 (t0) cc_final: 0.7835 (t0) REVERT: K 183 MET cc_start: 0.5065 (tmm) cc_final: 0.4740 (tmm) REVERT: K 207 ILE cc_start: 0.8085 (tt) cc_final: 0.7684 (mm) REVERT: K 237 SER cc_start: 0.9335 (m) cc_final: 0.9094 (p) REVERT: K 245 MET cc_start: 0.8240 (mmp) cc_final: 0.7419 (mmp) REVERT: L 1 MET cc_start: 0.6757 (tpt) cc_final: 0.6525 (tpp) REVERT: L 119 ASP cc_start: 0.7645 (t0) cc_final: 0.7413 (t70) REVERT: L 197 SER cc_start: 0.8078 (t) cc_final: 0.7835 (t) REVERT: L 312 ASP cc_start: 0.6716 (t70) cc_final: 0.6325 (t70) REVERT: M 1 MET cc_start: 0.7491 (mmm) cc_final: 0.6640 (mmp) REVERT: M 236 GLU cc_start: 0.7342 (tt0) cc_final: 0.6586 (mm-30) REVERT: M 291 ARG cc_start: 0.8371 (tpt90) cc_final: 0.8014 (ttp80) REVERT: N 54 MET cc_start: 0.1991 (ptm) cc_final: 0.1492 (mmm) REVERT: N 90 GLN cc_start: 0.8216 (tp40) cc_final: 0.7838 (tp40) REVERT: N 105 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8011 (mp) REVERT: N 154 GLU cc_start: 0.2607 (OUTLIER) cc_final: 0.1147 (pp20) REVERT: N 318 GLU cc_start: -0.0040 (OUTLIER) cc_final: -0.0918 (pp20) REVERT: P 1 MET cc_start: 0.6201 (mtt) cc_final: 0.5511 (ptp) REVERT: P 89 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7175 (t80) REVERT: P 110 ARG cc_start: 0.6757 (mmt180) cc_final: 0.6210 (mmt-90) REVERT: P 143 ILE cc_start: 0.7683 (mm) cc_final: 0.7462 (tp) REVERT: P 144 ASP cc_start: 0.7976 (m-30) cc_final: 0.7611 (m-30) REVERT: P 199 LYS cc_start: 0.8237 (mttp) cc_final: 0.7674 (mppt) REVERT: P 223 GLU cc_start: 0.7426 (tp30) cc_final: 0.6731 (tp30) REVERT: Q 18 MET cc_start: 0.6777 (tpt) cc_final: 0.6367 (tpt) REVERT: Q 46 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9017 (pm20) REVERT: Q 85 GLU cc_start: 0.8108 (pt0) cc_final: 0.7811 (pm20) REVERT: Q 96 LEU cc_start: 0.9074 (mt) cc_final: 0.8553 (tt) REVERT: Q 105 ILE cc_start: 0.9525 (tt) cc_final: 0.9114 (tt) REVERT: Q 149 MET cc_start: 0.7099 (mmp) cc_final: 0.6569 (mmp) REVERT: Q 198 LEU cc_start: 0.9096 (mt) cc_final: 0.8758 (mt) outliers start: 89 outliers final: 61 residues processed: 446 average time/residue: 0.2079 time to fit residues: 154.3632 Evaluate side-chains 419 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 351 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain G residue 4 TRP Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain J residue 26 TYR Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 317 ILE Chi-restraints excluded: chain K residue 26 TYR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain M residue 14 HIS Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 72 TYR Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 105 LEU Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain N residue 303 ASN Chi-restraints excluded: chain N residue 318 GLU Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 54 MET Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 89 PHE Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 167 LYS Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 218 TYR Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain Q residue 142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 403 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 371 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 256 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 197 optimal weight: 0.0170 chunk 288 optimal weight: 0.9980 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.112763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.092507 restraints weight = 147485.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.095146 restraints weight = 87785.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.096905 restraints weight = 59628.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.098067 restraints weight = 44502.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.098820 restraints weight = 35972.694| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 1.0558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 34327 Z= 0.139 Angle : 0.785 15.512 46736 Z= 0.377 Chirality : 0.051 0.376 5385 Planarity : 0.005 0.103 5826 Dihedral : 9.566 143.496 5085 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.52 % Favored : 91.22 % Rotamer: Outliers : 2.04 % Allowed : 27.32 % Favored : 70.64 % Cbeta Deviations : 0.03 % 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: -1.85 (0.13), residues: 4144 helix: -0.21 (0.14), residues: 1434 sheet: -0.97 (0.21), residues: 595 loop : -2.06 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 231 TYR 0.030 0.001 TYR C 283 PHE 0.021 0.002 PHE M 282 TRP 0.033 0.002 TRP J 42 HIS 0.013 0.001 HIS J 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (34321) covalent geometry : angle 0.78457 / 0.38 (46724) SS BOND : bond 0.00105 / 0.06 ( 6) SS BOND : angle 0.54128 / 0.30 ( 12) hydrogen bonds : bond 0.03133 / 2.10 ( 1054) hydrogen bonds : angle 4.80142 / 3.40 ( 3042) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 374 time to evaluate : 1.299 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7453 (pmm) cc_final: 0.7213 (pmm) REVERT: A 53 MET cc_start: 0.4756 (ttt) cc_final: 0.4282 (tmm) REVERT: A 73 LEU cc_start: 0.9277 (mm) cc_final: 0.8949 (tp) REVERT: A 165 ASP cc_start: 0.6780 (t70) cc_final: 0.6261 (p0) REVERT: A 175 MET cc_start: 0.8863 (mmm) cc_final: 0.8229 (mmt) REVERT: A 300 ASP cc_start: 0.8884 (m-30) cc_final: 0.8219 (p0) REVERT: A 318 GLN cc_start: 0.6507 (mp10) cc_final: 0.6171 (mp10) REVERT: A 428 LEU cc_start: 0.8041 (mt) cc_final: 0.7839 (mt) REVERT: A 486 PHE cc_start: 0.4184 (t80) cc_final: 0.3918 (t80) REVERT: C 55 ARG cc_start: 0.8070 (ttt180) cc_final: 0.7569 (tpt-90) REVERT: C 131 MET cc_start: 0.8803 (tmm) cc_final: 0.7626 (tmm) REVERT: C 193 ASP cc_start: 0.8998 (p0) cc_final: 0.8692 (p0) REVERT: D 33 LYS cc_start: 0.9303 (mttp) cc_final: 0.9102 (ptpp) REVERT: D 84 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6775 (tp) REVERT: D 91 ARG cc_start: 0.8651 (mmm-85) cc_final: 0.8347 (mmm-85) REVERT: E 91 ARG cc_start: 0.8379 (mmm160) cc_final: 0.7181 (mmp80) REVERT: E 92 LYS cc_start: 0.9308 (pptt) cc_final: 0.8937 (pptt) REVERT: E 95 VAL cc_start: 0.8374 (t) cc_final: 0.8159 (p) REVERT: F 92 LYS cc_start: 0.8857 (ptpp) cc_final: 0.8411 (ptpt) REVERT: F 96 SER cc_start: 0.9517 (t) cc_final: 0.9155 (p) REVERT: G 92 LYS cc_start: 0.7671 (ttpp) cc_final: 0.7221 (tptp) REVERT: H 10 ARG cc_start: 0.7163 (ttp80) cc_final: 0.6902 (tmm160) REVERT: I 199 VAL cc_start: 0.8743 (t) cc_final: 0.8434 (t) REVERT: I 201 ASP cc_start: 0.8480 (m-30) cc_final: 0.7292 (t0) REVERT: I 205 VAL cc_start: 0.8124 (t) cc_final: 0.7888 (t) REVERT: I 250 ILE cc_start: 0.8908 (pt) cc_final: 0.8661 (mm) REVERT: J 1 MET cc_start: 0.8151 (tmm) cc_final: 0.7597 (tmm) REVERT: J 19 GLN cc_start: 0.9254 (pt0) cc_final: 0.8815 (pt0) REVERT: J 26 TYR cc_start: 0.5918 (OUTLIER) cc_final: 0.4428 (m-10) REVERT: J 35 THR cc_start: 0.7772 (m) cc_final: 0.7558 (m) REVERT: J 218 ASN cc_start: 0.8510 (m-40) cc_final: 0.8272 (m-40) REVERT: K 11 LEU cc_start: 0.6802 (mm) cc_final: 0.6280 (mm) REVERT: K 26 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6151 (m-80) REVERT: K 183 MET cc_start: 0.5048 (tmm) cc_final: 0.4707 (tmm) REVERT: K 207 ILE cc_start: 0.7966 (tt) cc_final: 0.7630 (mm) REVERT: K 245 MET cc_start: 0.8247 (mmp) cc_final: 0.7391 (mmp) REVERT: L 55 LEU cc_start: 0.9195 (tp) cc_final: 0.8970 (tp) REVERT: L 119 ASP cc_start: 0.7589 (t0) cc_final: 0.7370 (t70) REVERT: L 197 SER cc_start: 0.8091 (t) cc_final: 0.7850 (t) REVERT: L 245 MET cc_start: 0.9058 (mmm) cc_final: 0.8491 (mtp) REVERT: L 312 ASP cc_start: 0.6598 (t70) cc_final: 0.6190 (t70) REVERT: M 1 MET cc_start: 0.7453 (mmm) cc_final: 0.6793 (mmp) REVERT: M 236 GLU cc_start: 0.7541 (tt0) cc_final: 0.6806 (mm-30) REVERT: M 291 ARG cc_start: 0.8364 (tpt90) cc_final: 0.8026 (ttp80) REVERT: N 54 MET cc_start: 0.2056 (ptm) cc_final: 0.1637 (mmm) REVERT: N 90 GLN cc_start: 0.8210 (tp40) cc_final: 0.7803 (tp40) REVERT: N 105 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8186 (mp) REVERT: N 154 GLU cc_start: 0.2574 (OUTLIER) cc_final: 0.1140 (pp20) REVERT: N 318 GLU cc_start: -0.0021 (OUTLIER) cc_final: -0.1215 (pp20) REVERT: O 104 GLN cc_start: 0.8947 (tt0) cc_final: 0.8689 (tp-100) REVERT: P 1 MET cc_start: 0.6221 (mtt) cc_final: 0.5156 (ptm) REVERT: P 89 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.7296 (t80) REVERT: P 110 ARG cc_start: 0.6742 (mmt180) cc_final: 0.6192 (mmt-90) REVERT: P 143 ILE cc_start: 0.7633 (mm) cc_final: 0.7416 (tp) REVERT: P 144 ASP cc_start: 0.7750 (m-30) cc_final: 0.7475 (m-30) REVERT: P 199 LYS cc_start: 0.7794 (mttp) cc_final: 0.7541 (mppt) REVERT: P 223 GLU cc_start: 0.7268 (tp30) cc_final: 0.6478 (tp30) REVERT: Q 18 MET cc_start: 0.6730 (tpt) cc_final: 0.6331 (tpt) REVERT: Q 46 GLU cc_start: 0.9449 (mt-10) cc_final: 0.9020 (pm20) REVERT: Q 85 GLU cc_start: 0.8087 (pt0) cc_final: 0.7824 (pm20) REVERT: Q 96 LEU cc_start: 0.9069 (mt) cc_final: 0.8574 (tt) REVERT: Q 105 ILE cc_start: 0.9516 (tt) cc_final: 0.9092 (tt) REVERT: Q 149 MET cc_start: 0.7043 (mmp) cc_final: 0.6477 (mmp) REVERT: Q 198 LEU cc_start: 0.9065 (mt) cc_final: 0.8739 (mt) outliers start: 70 outliers final: 56 residues processed: 425 average time/residue: 0.2107 time to fit residues: 148.9679 Evaluate side-chains 414 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 351 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 283 TYR Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain G residue 4 TRP Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain J residue 26 TYR Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 227 ASP Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 317 ILE Chi-restraints excluded: chain K residue 26 TYR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 265 GLU Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 105 LEU Chi-restraints excluded: chain N residue 154 GLU Chi-restraints excluded: chain N residue 303 ASN Chi-restraints excluded: chain N residue 318 GLU Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 89 PHE Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 167 LYS Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 218 TYR Chi-restraints excluded: chain Q residue 91 TYR Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain Q residue 142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 319 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 356 optimal weight: 4.9990 chunk 55 optimal weight: 0.2980 chunk 257 optimal weight: 1.9990 chunk 305 optimal weight: 6.9990 chunk 276 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 355 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 HIS ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.112344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.092086 restraints weight = 147322.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.094682 restraints weight = 88050.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.096389 restraints weight = 60041.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.097554 restraints weight = 45200.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.098318 restraints weight = 36630.388| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 1.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 34327 Z= 0.137 Angle : 0.771 13.727 46736 Z= 0.370 Chirality : 0.050 0.355 5385 Planarity : 0.005 0.103 5826 Dihedral : 9.509 143.565 5085 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.57 % Favored : 91.17 % Rotamer: Outliers : 1.90 % Allowed : 27.76 % Favored : 70.35 % 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: -1.82 (0.13), residues: 4144 helix: -0.17 (0.14), residues: 1444 sheet: -1.01 (0.21), residues: 598 loop : -2.04 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 155 TYR 0.021 0.001 TYR K 249 PHE 0.042 0.002 PHE K 261 TRP 0.041 0.002 TRP K 42 HIS 0.029 0.002 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (34321) covalent geometry : angle 0.77152 / 0.37 (46724) SS BOND : bond 0.00113 / 0.06 ( 6) SS BOND : angle 0.48496 / 0.27 ( 12) hydrogen bonds : bond 0.03088 / 2.06 ( 1054) hydrogen bonds : angle 4.78285 / 3.37 ( 3042) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7573.02 seconds wall clock time: 131 minutes 25.26 seconds (7885.26 seconds total)