Starting phenix.real_space_refine on Tue Sep 15 02:45:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5xte_6774/09_2026/5xte_6774.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xte_6774/09_2026/5xte_6774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5xte_6774/09_2026/5xte_6774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xte_6774/09_2026/5xte_6774.map" model { file = "/net/cci-nas-00/data/ceres_data/5xte_6774/09_2026/5xte_6774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xte_6774/09_2026/5xte_6774.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5xte_6774/09_2026/5xte_6774.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5xte_6774/09_2026/5xte_6774.cif" } resolution = 3.4 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= 0.005 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 Fe 10 7.16 5 P 27 5.49 5 S 160 5.16 5 C 22222 2.51 5 N 5724 2.21 5 O 6349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s 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: 34492 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 694 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "B" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 413 Classifications: {'peptide': 57} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 48} Chain: "C" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1521 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "D" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 509 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "E" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 580 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 921 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "G" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "H" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1924 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 219} Chain: "J" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3009 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 354} Chain: "K" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3159 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 404} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3453 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 426} Chain: "N" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 687 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 75} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "O" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 409 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 48} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1521 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "Q" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 509 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "R" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 580 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8} Unresolved non-hydrogen planarities: 32 Chain: "S" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 921 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "T" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "U" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1924 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 219} Chain: "V" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3009 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 354} Chain: "W" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3162 Classifications: {'peptide': 419} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 404} Chain: "Y" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3453 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 426} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "H" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'CDL': 1, 'HEC': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "J" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 263 Unusual residues: {'CDL': 2, 'HEM': 2, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 74 Chain: "L" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 165 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "N" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'CDL': 1, 'HEC': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Chain: "V" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'HEM': 2, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "Y" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18936 SG CYS P 236 76.516 48.096 24.127 1.00 35.05 S Time building chain proxies: 7.45, per 1000 atoms: 0.22 Number of scatterers: 34492 At special positions: 0 Unit cell: (150.537, 142.956, 177.612, 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) Fe 10 26.01 S 160 16.00 P 27 15.00 O 6349 8.00 N 5724 7.00 C 22222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 222 " - pdb=" SG CYS C 238 " distance=2.03 Simple disulfide: pdb=" SG CYS P 222 " - pdb=" SG CYS P 238 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C 301 " pdb="FE2 FES C 301 " - pdb=" ND1 HIS C 219 " pdb="FE2 FES C 301 " - pdb=" ND1 HIS C 239 " pdb="FE1 FES C 301 " - pdb=" SG CYS C 217 " pdb="FE1 FES C 301 " - pdb=" SG CYS C 236 " pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 239 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 219 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 236 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 217 " Number of angles added : 6 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7888 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 20 sheets defined 58.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.549A pdb=" N GLN A 24 " --> pdb=" O PRO A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 72 removed outlier: 4.417A pdb=" N ILE A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) Proline residue: A 36 - end of helix removed outlier: 4.724A pdb=" N PHE A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Proline residue: A 51 - end of helix Processing helix chain 'A' and resid 73 through 82 removed outlier: 4.124A pdb=" N ALA A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 7 removed outlier: 3.656A pdb=" N SER B 6 " --> pdb=" O SER B 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 103 through 142 removed outlier: 3.901A pdb=" N GLU C 108 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 116 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 180 through 190 removed outlier: 3.591A pdb=" N VAL C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'D' and resid 5 through 14 removed outlier: 3.848A pdb=" N LYS D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 48 removed outlier: 4.014A pdb=" N ARG D 34 " --> pdb=" O MET D 30 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN D 48 " --> pdb=" O TYR D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'E' and resid 19 through 27 removed outlier: 3.865A pdb=" N GLU E 23 " --> pdb=" O GLU E 19 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 removed outlier: 4.249A pdb=" N THR E 32 " --> pdb=" O ASP E 28 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU E 40 " --> pdb=" O GLN E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 59 Processing helix chain 'E' and resid 67 through 84 removed outlier: 4.117A pdb=" N ALA E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS E 84 " --> pdb=" O HIS E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 25 removed outlier: 3.605A pdb=" N GLY F 16 " --> pdb=" O LYS F 12 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE F 17 " --> pdb=" O TRP F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 33 through 38 removed outlier: 3.695A pdb=" N THR F 37 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE F 38 " --> pdb=" O ARG F 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 33 through 38' Processing helix chain 'F' and resid 41 through 51 removed outlier: 3.676A pdb=" N ARG F 50 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 73 removed outlier: 3.589A pdb=" N ASP F 58 " --> pdb=" O ASN F 54 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 removed outlier: 3.642A pdb=" N TRP F 81 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 110 Processing helix chain 'F' and resid 111 through 111 No H-bonds generated for 'chain 'F' and resid 111 through 111' Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 7 through 36 removed outlier: 3.993A pdb=" N GLU G 12 " --> pdb=" O PRO G 8 " (cutoff:3.500A) Proline residue: G 19 - end of helix Processing helix chain 'G' and resid 38 through 43 removed outlier: 3.672A pdb=" N LEU G 42 " --> pdb=" O TRP G 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.941A pdb=" N GLY H 100 " --> pdb=" O SER H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 118 Processing helix chain 'H' and resid 134 through 139 removed outlier: 3.742A pdb=" N VAL H 138 " --> pdb=" O HIS H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 150 removed outlier: 3.641A pdb=" N ALA H 150 " --> pdb=" O LYS H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 188 Processing helix chain 'H' and resid 199 through 204 removed outlier: 3.610A pdb=" N ARG H 204 " --> pdb=" O ILE H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 217 removed outlier: 3.823A pdb=" N VAL H 211 " --> pdb=" O GLY H 207 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER H 213 " --> pdb=" O ASP H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 279 Processing helix chain 'H' and resid 281 through 316 removed outlier: 3.584A pdb=" N ARG H 287 " --> pdb=" O ASP H 283 " (cutoff:3.500A) Proline residue: H 301 - end of helix removed outlier: 5.091A pdb=" N VAL H 313 " --> pdb=" O HIS H 309 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU H 314 " --> pdb=" O LYS H 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 8 removed outlier: 3.671A pdb=" N THR J 7 " --> pdb=" O PRO J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 18 removed outlier: 4.000A pdb=" N LEU J 13 " --> pdb=" O PRO J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 31 through 53 removed outlier: 4.397A pdb=" N SER J 35 " --> pdb=" O TRP J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 71 removed outlier: 4.471A pdb=" N SER J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 104 removed outlier: 3.553A pdb=" N ILE J 79 " --> pdb=" O TYR J 75 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER J 88 " --> pdb=" O ALA J 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY J 101 " --> pdb=" O HIS J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 108 removed outlier: 3.666A pdb=" N LEU J 108 " --> pdb=" O GLY J 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 105 through 108' Processing helix chain 'J' and resid 109 through 132 removed outlier: 3.611A pdb=" N VAL J 132 " --> pdb=" O PHE J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 149 removed outlier: 3.722A pdb=" N TRP J 141 " --> pdb=" O GLN J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 153 Processing helix chain 'J' and resid 156 through 166 Processing helix chain 'J' and resid 171 through 201 Proline residue: J 186 - end of helix removed outlier: 3.699A pdb=" N ALA J 191 " --> pdb=" O PHE J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 215 No H-bonds generated for 'chain 'J' and resid 213 through 215' Processing helix chain 'J' and resid 220 through 245 removed outlier: 4.444A pdb=" N ILE J 226 " --> pdb=" O PRO J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 284 removed outlier: 3.971A pdb=" N PHE J 276 " --> pdb=" O TRP J 272 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ALA J 277 " --> pdb=" O TYR J 273 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR J 278 " --> pdb=" O PHE J 274 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR J 279 " --> pdb=" O LEU J 275 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE J 280 " --> pdb=" O PHE J 276 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL J 284 " --> pdb=" O ILE J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 304 removed outlier: 3.952A pdb=" N ILE J 298 " --> pdb=" O LEU J 294 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU J 301 " --> pdb=" O SER J 297 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA J 302 " --> pdb=" O ILE J 298 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET J 303 " --> pdb=" O LEU J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 305 through 308 Processing helix chain 'J' and resid 314 through 317 removed outlier: 3.915A pdb=" N PHE J 317 " --> pdb=" O SER J 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 314 through 317' Processing helix chain 'J' and resid 318 through 340 removed outlier: 3.541A pdb=" N LEU J 324 " --> pdb=" O LEU J 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 364 removed outlier: 3.577A pdb=" N ILE J 350 " --> pdb=" O PRO J 346 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE J 362 " --> pdb=" O TYR J 358 " (cutoff:3.500A) Processing helix chain 'J' and resid 364 through 377 removed outlier: 3.821A pdb=" N THR J 368 " --> pdb=" O ILE J 364 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU J 377 " --> pdb=" O GLU J 373 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 72 removed outlier: 3.900A pdb=" N GLU K 72 " --> pdb=" O SER K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 84 Processing helix chain 'K' and resid 85 through 89 removed outlier: 4.102A pdb=" N SER K 88 " --> pdb=" O LEU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 107 Processing helix chain 'K' and resid 129 through 143 removed outlier: 3.523A pdb=" N GLU K 135 " --> pdb=" O ASP K 131 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN K 139 " --> pdb=" O GLU K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 155 Processing helix chain 'K' and resid 156 through 166 removed outlier: 3.828A pdb=" N ILE K 160 " --> pdb=" O PRO K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 182 removed outlier: 3.826A pdb=" N HIS K 172 " --> pdb=" O ASN K 168 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN K 176 " --> pdb=" O HIS K 172 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA K 179 " --> pdb=" O GLU K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 188 Processing helix chain 'K' and resid 193 through 197 Processing helix chain 'K' and resid 201 through 213 Processing helix chain 'K' and resid 226 through 234 removed outlier: 3.853A pdb=" N GLN K 232 " --> pdb=" O PRO K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 239 removed outlier: 3.962A pdb=" N ASN K 239 " --> pdb=" O GLN K 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 293 removed outlier: 3.519A pdb=" N LEU K 293 " --> pdb=" O LEU K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 315 removed outlier: 3.675A pdb=" N GLN K 311 " --> pdb=" O SER K 307 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS K 315 " --> pdb=" O GLN K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 363 removed outlier: 3.669A pdb=" N LYS K 352 " --> pdb=" O GLY K 348 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE K 361 " --> pdb=" O GLN K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 388 removed outlier: 4.019A pdb=" N VAL K 371 " --> pdb=" O SER K 367 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN K 372 " --> pdb=" O ASN K 368 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER K 388 " --> pdb=" O MET K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 403 removed outlier: 3.557A pdb=" N VAL K 402 " --> pdb=" O SER K 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 419 removed outlier: 3.760A pdb=" N VAL K 419 " --> pdb=" O GLN K 415 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 434 removed outlier: 3.511A pdb=" N ILE K 424 " --> pdb=" O ALA K 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 45 removed outlier: 3.935A pdb=" N GLN L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL L 45 " --> pdb=" O ALA L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 87 removed outlier: 4.024A pdb=" N ASN L 87 " --> pdb=" O GLU L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 96 Processing helix chain 'L' and resid 105 through 117 Processing helix chain 'L' and resid 139 through 151 removed outlier: 3.653A pdb=" N LEU L 146 " --> pdb=" O LYS L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 176 removed outlier: 3.701A pdb=" N ASP L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN L 173 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP L 176 " --> pdb=" O MET L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 193 Processing helix chain 'L' and resid 195 through 199 removed outlier: 3.766A pdb=" N GLN L 199 " --> pdb=" O PRO L 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 209 removed outlier: 3.893A pdb=" N ARG L 209 " --> pdb=" O SER L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 223 Processing helix chain 'L' and resid 238 through 251 removed outlier: 3.530A pdb=" N HIS L 249 " --> pdb=" O LEU L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 261 removed outlier: 3.629A pdb=" N ASP L 260 " --> pdb=" O TYR L 257 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 312 removed outlier: 4.097A pdb=" N ALA L 303 " --> pdb=" O PRO L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 333 Processing helix chain 'L' and resid 364 through 381 removed outlier: 3.697A pdb=" N MET L 369 " --> pdb=" O ILE L 365 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 402 Processing helix chain 'L' and resid 405 through 420 removed outlier: 3.855A pdb=" N VAL L 409 " --> pdb=" O GLY L 405 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR L 419 " --> pdb=" O ARG L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 425 through 435 removed outlier: 3.662A pdb=" N GLU L 435 " --> pdb=" O SER L 431 " (cutoff:3.500A) Processing helix chain 'L' and resid 437 through 449 Processing helix chain 'L' and resid 467 through 473 Processing helix chain 'L' and resid 474 through 476 No H-bonds generated for 'chain 'L' and resid 474 through 476' Processing helix chain 'N' and resid 4 through 8 removed outlier: 3.661A pdb=" N LEU N 8 " --> pdb=" O PHE N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 24 Processing helix chain 'N' and resid 29 through 82 removed outlier: 5.054A pdb=" N ILE N 35 " --> pdb=" O PHE N 31 " (cutoff:3.500A) Proline residue: N 36 - end of helix removed outlier: 5.046A pdb=" N PHE N 47 " --> pdb=" O ARG N 43 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG N 48 " --> pdb=" O GLU N 44 " (cutoff:3.500A) Proline residue: N 51 - end of helix Proline residue: N 75 - end of helix Processing helix chain 'O' and resid 30 through 34 removed outlier: 3.568A pdb=" N VAL O 34 " --> pdb=" O GLN O 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 97 removed outlier: 3.605A pdb=" N LEU P 97 " --> pdb=" O LEU P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 140 removed outlier: 4.601A pdb=" N SER P 106 " --> pdb=" O SER P 102 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU P 108 " --> pdb=" O ARG P 104 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA P 109 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER P 114 " --> pdb=" O ARG P 110 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET P 140 " --> pdb=" O PHE P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 150 Processing helix chain 'P' and resid 180 through 190 removed outlier: 3.522A pdb=" N ILE P 184 " --> pdb=" O THR P 180 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL P 190 " --> pdb=" O GLN P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 200 through 205 removed outlier: 3.893A pdb=" N VAL P 205 " --> pdb=" O ASP P 201 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 13 removed outlier: 3.715A pdb=" N LEU Q 13 " --> pdb=" O LYS Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 48 removed outlier: 4.510A pdb=" N ARG Q 34 " --> pdb=" O MET Q 30 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN Q 48 " --> pdb=" O TYR Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 60 removed outlier: 3.979A pdb=" N LYS Q 57 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS Q 58 " --> pdb=" O HIS Q 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 27 Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 40 through 60 Processing helix chain 'R' and resid 67 through 90 removed outlier: 4.071A pdb=" N ALA R 77 " --> pdb=" O ASP R 73 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N PHE R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASN R 88 " --> pdb=" O HIS R 84 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN R 89 " --> pdb=" O LYS R 85 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU R 90 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 25 Processing helix chain 'S' and resid 26 through 31 Processing helix chain 'S' and resid 33 through 37 Processing helix chain 'S' and resid 41 through 50 Processing helix chain 'S' and resid 52 through 72 removed outlier: 3.607A pdb=" N LYS S 72 " --> pdb=" O ASP S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 81 Processing helix chain 'S' and resid 91 through 110 Processing helix chain 'T' and resid 2 through 6 Processing helix chain 'T' and resid 7 through 37 Proline residue: T 19 - end of helix Processing helix chain 'T' and resid 38 through 43 Processing helix chain 'U' and resid 106 through 118 Processing helix chain 'U' and resid 134 through 139 removed outlier: 3.854A pdb=" N VAL U 138 " --> pdb=" O HIS U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 141 through 152 removed outlier: 3.676A pdb=" N ALA U 150 " --> pdb=" O LYS U 146 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU U 151 " --> pdb=" O GLU U 147 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL U 152 " --> pdb=" O LEU U 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 181 through 188 Processing helix chain 'U' and resid 199 through 204 removed outlier: 3.550A pdb=" N ARG U 204 " --> pdb=" O ILE U 200 " (cutoff:3.500A) Processing helix chain 'U' and resid 207 through 217 removed outlier: 3.642A pdb=" N VAL U 211 " --> pdb=" O GLY U 207 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER U 213 " --> pdb=" O ASP U 209 " (cutoff:3.500A) Processing helix chain 'U' and resid 262 through 279 Processing helix chain 'U' and resid 281 through 317 Proline residue: U 301 - end of helix removed outlier: 4.694A pdb=" N VAL U 313 " --> pdb=" O HIS U 309 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU U 314 " --> pdb=" O LYS U 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 7 Processing helix chain 'V' and resid 8 through 18 Processing helix chain 'V' and resid 31 through 50 removed outlier: 3.884A pdb=" N SER V 35 " --> pdb=" O TRP V 31 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE V 42 " --> pdb=" O GLY V 38 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY V 48 " --> pdb=" O GLN V 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 71 removed outlier: 3.529A pdb=" N ILE V 66 " --> pdb=" O ALA V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 104 removed outlier: 3.903A pdb=" N ILE V 79 " --> pdb=" O TYR V 75 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER V 88 " --> pdb=" O ALA V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 105 through 108 removed outlier: 3.704A pdb=" N LEU V 108 " --> pdb=" O GLY V 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 105 through 108' Processing helix chain 'V' and resid 109 through 133 Processing helix chain 'V' and resid 136 through 151 removed outlier: 3.768A pdb=" N LEU V 149 " --> pdb=" O VAL V 145 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU V 150 " --> pdb=" O ILE V 146 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER V 151 " --> pdb=" O THR V 147 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 166 removed outlier: 3.751A pdb=" N LEU V 160 " --> pdb=" O ILE V 156 " (cutoff:3.500A) Processing helix chain 'V' and resid 171 through 201 Proline residue: V 186 - end of helix Processing helix chain 'V' and resid 213 through 215 No H-bonds generated for 'chain 'V' and resid 213 through 215' Processing helix chain 'V' and resid 223 through 245 removed outlier: 3.523A pdb=" N PHE V 245 " --> pdb=" O THR V 241 " (cutoff:3.500A) Processing helix chain 'V' and resid 271 through 273 No H-bonds generated for 'chain 'V' and resid 271 through 273' Processing helix chain 'V' and resid 274 through 284 Processing helix chain 'V' and resid 286 through 300 removed outlier: 3.757A pdb=" N ILE V 298 " --> pdb=" O LEU V 294 " (cutoff:3.500A) Processing helix chain 'V' and resid 303 through 308 Processing helix chain 'V' and resid 314 through 317 removed outlier: 3.980A pdb=" N PHE V 317 " --> pdb=" O SER V 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 314 through 317' Processing helix chain 'V' and resid 318 through 339 Processing helix chain 'V' and resid 344 through 364 removed outlier: 3.594A pdb=" N ILE V 349 " --> pdb=" O TYR V 345 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE V 362 " --> pdb=" O TYR V 358 " (cutoff:3.500A) Processing helix chain 'V' and resid 364 through 377 Processing helix chain 'W' and resid 68 through 72 Processing helix chain 'W' and resid 78 through 84 removed outlier: 3.721A pdb=" N LEU W 82 " --> pdb=" O GLY W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 89 removed outlier: 4.414A pdb=" N SER W 88 " --> pdb=" O LEU W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 107 Processing helix chain 'W' and resid 129 through 142 removed outlier: 4.248A pdb=" N GLU W 135 " --> pdb=" O ASP W 131 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR W 142 " --> pdb=" O LEU W 138 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 155 Processing helix chain 'W' and resid 156 through 166 removed outlier: 4.036A pdb=" N ILE W 160 " --> pdb=" O PRO W 156 " (cutoff:3.500A) Processing helix chain 'W' and resid 168 through 182 removed outlier: 3.769A pdb=" N HIS W 172 " --> pdb=" O ASN W 168 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL W 173 " --> pdb=" O PRO W 169 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN W 176 " --> pdb=" O HIS W 172 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 188 Processing helix chain 'W' and resid 193 through 197 Processing helix chain 'W' and resid 201 through 213 removed outlier: 3.598A pdb=" N ASN W 211 " --> pdb=" O TYR W 207 " (cutoff:3.500A) Processing helix chain 'W' and resid 226 through 239 removed outlier: 3.523A pdb=" N LEU W 230 " --> pdb=" O SER W 226 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN W 239 " --> pdb=" O GLU W 235 " (cutoff:3.500A) Processing helix chain 'W' and resid 280 through 293 removed outlier: 3.562A pdb=" N ASN W 284 " --> pdb=" O SER W 280 " (cutoff:3.500A) Processing helix chain 'W' and resid 307 through 317 removed outlier: 4.092A pdb=" N LYS W 315 " --> pdb=" O GLN W 311 " (cutoff:3.500A) Processing helix chain 'W' and resid 346 through 363 removed outlier: 3.850A pdb=" N LYS W 352 " --> pdb=" O GLY W 348 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA W 353 " --> pdb=" O ASP W 349 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR W 355 " --> pdb=" O ILE W 351 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN W 356 " --> pdb=" O LYS W 352 " (cutoff:3.500A) Processing helix chain 'W' and resid 367 through 388 removed outlier: 3.838A pdb=" N VAL W 371 " --> pdb=" O SER W 367 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER W 388 " --> pdb=" O MET W 384 " (cutoff:3.500A) Processing helix chain 'W' and resid 388 through 403 removed outlier: 4.451A pdb=" N LEU W 401 " --> pdb=" O GLY W 397 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL W 402 " --> pdb=" O SER W 398 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA W 403 " --> pdb=" O GLN W 399 " (cutoff:3.500A) Processing helix chain 'W' and resid 408 through 418 Processing helix chain 'W' and resid 420 through 434 Processing helix chain 'Y' and resid 37 through 42 removed outlier: 3.517A pdb=" N LEU Y 42 " --> pdb=" O PHE Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 82 removed outlier: 3.633A pdb=" N GLU Y 82 " --> pdb=" O SER Y 79 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 87 removed outlier: 4.022A pdb=" N ASN Y 87 " --> pdb=" O GLU Y 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 88 through 97 Processing helix chain 'Y' and resid 105 through 116 Processing helix chain 'Y' and resid 139 through 153 removed outlier: 3.507A pdb=" N ALA Y 143 " --> pdb=" O ASP Y 139 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU Y 145 " --> pdb=" O PRO Y 141 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU Y 146 " --> pdb=" O LYS Y 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 157 through 177 removed outlier: 3.978A pdb=" N ASP Y 166 " --> pdb=" O GLU Y 162 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN Y 173 " --> pdb=" O LEU Y 169 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA Y 177 " --> pdb=" O GLN Y 173 " (cutoff:3.500A) Processing helix chain 'Y' and resid 179 through 193 Processing helix chain 'Y' and resid 195 through 199 removed outlier: 3.749A pdb=" N GLN Y 199 " --> pdb=" O PRO Y 196 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 211 removed outlier: 3.730A pdb=" N ARG Y 209 " --> pdb=" O GLU Y 206 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU Y 211 " --> pdb=" O VAL Y 208 " (cutoff:3.500A) Processing helix chain 'Y' and resid 212 through 224 Processing helix chain 'Y' and resid 238 through 248 removed outlier: 3.925A pdb=" N LYS Y 248 " --> pdb=" O ASP Y 244 " (cutoff:3.500A) Processing helix chain 'Y' and resid 249 through 253 removed outlier: 3.711A pdb=" N GLY Y 252 " --> pdb=" O HIS Y 249 " (cutoff:3.500A) Processing helix chain 'Y' and resid 257 through 261 Processing helix chain 'Y' and resid 299 through 312 removed outlier: 4.138A pdb=" N ALA Y 303 " --> pdb=" O PRO Y 299 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 333 removed outlier: 3.726A pdb=" N VAL Y 333 " --> pdb=" O ALA Y 329 " (cutoff:3.500A) Processing helix chain 'Y' and resid 364 through 381 removed outlier: 3.512A pdb=" N LEU Y 372 " --> pdb=" O MET Y 368 " (cutoff:3.500A) Processing helix chain 'Y' and resid 384 through 402 Processing helix chain 'Y' and resid 405 through 421 removed outlier: 3.826A pdb=" N VAL Y 409 " --> pdb=" O GLY Y 405 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU Y 418 " --> pdb=" O GLY Y 414 " (cutoff:3.500A) Processing helix chain 'Y' and resid 425 through 434 Processing helix chain 'Y' and resid 437 through 449 Processing helix chain 'Y' and resid 467 through 474 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 4.090A pdb=" N TYR L 459 " --> pdb=" O HIS L 286 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER L 340 " --> pdb=" O VAL L 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 14 through 16 removed outlier: 3.813A pdb=" N LEU B 15 " --> pdb=" O VAL K 112 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL K 48 " --> pdb=" O LEU K 220 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N GLY K 222 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ALA K 50 " --> pdb=" O GLY K 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AA4, first strand: chain 'C' and resid 232 through 235 removed outlier: 6.304A pdb=" N TYR C 243 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU C 251 " --> pdb=" O HIS C 242 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ASP C 244 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE C 249 " --> pdb=" O ASP C 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 265 removed outlier: 3.783A pdb=" N GLU C 264 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 272 " --> pdb=" O GLU C 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'H' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'J' and resid 22 through 24 Processing sheet with id=AA8, first strand: chain 'K' and resid 257 through 259 removed outlier: 7.213A pdb=" N ILE K 258 " --> pdb=" O ALA K 440 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA K 439 " --> pdb=" O ALA K 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 68 through 69 Processing sheet with id=AB1, first strand: chain 'L' and resid 121 through 124 Processing sheet with id=AB2, first strand: chain 'N' and resid 16 through 18 removed outlier: 3.682A pdb=" N GLU Y 274 " --> pdb=" O SER N 18 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER Y 340 " --> pdb=" O VAL Y 359 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR Y 314 " --> pdb=" O PHE Y 341 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 166 through 169 Processing sheet with id=AB4, first strand: chain 'P' and resid 225 through 226 Processing sheet with id=AB5, first strand: chain 'P' and resid 263 through 265 Processing sheet with id=AB6, first strand: chain 'U' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'V' and resid 22 through 24 Processing sheet with id=AB8, first strand: chain 'W' and resid 41 through 42 removed outlier: 6.760A pdb=" N VAL W 48 " --> pdb=" O LEU W 220 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 257 through 259 removed outlier: 6.690A pdb=" N ILE W 258 " --> pdb=" O ALA W 440 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 51 through 52 removed outlier: 5.960A pdb=" N ARG Y 58 " --> pdb=" O LEU Y 231 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA Y 233 " --> pdb=" O ARG Y 58 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA Y 60 " --> pdb=" O ALA Y 233 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLY Y 235 " --> pdb=" O ALA Y 60 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU Y 62 " --> pdb=" O GLY Y 235 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 68 through 69 1718 hydrogen bonds defined for protein. 4881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.40: 14256 1.40 - 1.60: 20774 1.60 - 1.80: 149 1.80 - 2.00: 122 2.00 - 2.20: 32 Bond restraints: 35333 Sorted by residual: bond pdb=" CB7 CDL H 403 " pdb=" OB8 CDL H 403 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CB7 CDL G 101 " pdb=" OB8 CDL G 101 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL J 405 " pdb=" OA8 CDL J 405 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CB7 CDL U 403 " pdb=" OB8 CDL U 403 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.17e+02 bond pdb=" CB7 CDL Y 501 " pdb=" OB8 CDL Y 501 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 ... (remaining 35328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 46735 3.43 - 6.85: 981 6.85 - 10.28: 122 10.28 - 13.70: 15 13.70 - 17.13: 15 Bond angle restraints: 47868 Sorted by residual: angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 90.52 13.81 1.14e+00 7.69e-01 1.47e+02 angle pdb=" S1 FES C 301 " pdb="FE2 FES C 301 " pdb=" S2 FES C 301 " ideal model delta sigma weight residual 104.33 90.76 13.57 1.14e+00 7.69e-01 1.42e+02 angle pdb="FE1 FES C 301 " pdb=" S2 FES C 301 " pdb="FE2 FES C 301 " ideal model delta sigma weight residual 75.66 89.19 -13.53 1.14e+00 7.69e-01 1.41e+02 angle pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " pdb="FE2 FES P 301 " ideal model delta sigma weight residual 75.66 88.94 -13.28 1.14e+00 7.69e-01 1.36e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 90.53 13.80 1.20e+00 6.94e-01 1.32e+02 ... (remaining 47863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 20451 33.95 - 67.90: 501 67.90 - 101.86: 32 101.86 - 135.81: 7 135.81 - 169.76: 6 Dihedral angle restraints: 20997 sinusoidal: 8740 harmonic: 12257 Sorted by residual: dihedral pdb=" CA GLU V 271 " pdb=" C GLU V 271 " pdb=" N TRP V 272 " pdb=" CA TRP V 272 " ideal model delta harmonic sigma weight residual 180.00 -152.30 -27.70 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" N ASP K 451 " pdb=" C ASP K 451 " pdb=" CA ASP K 451 " pdb=" CB ASP K 451 " ideal model delta harmonic sigma weight residual 122.80 135.43 -12.63 0 2.50e+00 1.60e-01 2.55e+01 dihedral pdb=" CA THR B 37 " pdb=" C THR B 37 " pdb=" N PRO B 38 " pdb=" CA PRO B 38 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 20994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4550 0.078 - 0.156: 558 0.156 - 0.234: 34 0.234 - 0.311: 14 0.311 - 0.389: 6 Chirality restraints: 5162 Sorted by residual: chirality pdb=" CA ASP K 451 " pdb=" N ASP K 451 " pdb=" C ASP K 451 " pdb=" CB ASP K 451 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA TRP V 141 " pdb=" N TRP V 141 " pdb=" C TRP V 141 " pdb=" CB TRP V 141 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA ILE Y 424 " pdb=" N ILE Y 424 " pdb=" C ILE Y 424 " pdb=" CB ILE Y 424 " both_signs ideal model delta sigma weight residual False 2.43 2.11 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 5159 not shown) Planarity restraints: 6010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC H 402 " -0.017 2.00e-02 2.50e+03 4.52e-02 4.61e+01 pdb=" C2C HEC H 402 " 0.124 2.00e-02 2.50e+03 pdb=" C3C HEC H 402 " -0.011 2.00e-02 2.50e+03 pdb=" C4C HEC H 402 " -0.005 2.00e-02 2.50e+03 pdb=" CAC HEC H 402 " -0.028 2.00e-02 2.50e+03 pdb=" CHC HEC H 402 " -0.024 2.00e-02 2.50e+03 pdb=" CHD HEC H 402 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEC H 402 " -0.036 2.00e-02 2.50e+03 pdb=" NC HEC H 402 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN V 341 " 0.057 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO V 342 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO V 342 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO V 342 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 73 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C ASP R 73 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP R 73 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE R 74 " 0.018 2.00e-02 2.50e+03 ... (remaining 6007 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 20 2.11 - 2.80: 10007 2.80 - 3.50: 48725 3.50 - 4.20: 81624 4.20 - 4.90: 144119 Nonbonded interactions: 284495 Sorted by model distance: nonbonded pdb=" OE2 GLU Y 411 " pdb=" NH1 ARG Y 415 " model vdw 1.408 3.120 nonbonded pdb=" OH TYR F 22 " pdb=" OE2 GLU F 87 " model vdw 1.490 3.040 nonbonded pdb=" NE1 TRP Y 296 " pdb=" OG1 THR Y 419 " model vdw 1.641 3.120 nonbonded pdb=" CD1 LEU T 40 " pdb=" CD1 ILE T 41 " model vdw 1.658 3.880 nonbonded pdb=" NE1 TRP Y 296 " pdb=" CG2 THR Y 419 " model vdw 1.726 3.540 ... (remaining 284490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 101)) selection = chain 'N' } ncs_group { reference = (chain 'B' and (resid 1 through 30 or (resid 31 through 32 and (name N or name C \ A or name C or name O or name CB )) or resid 33 through 57)) selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = chain 'D' selection = (chain 'Q' and resid 2 through 63) } ncs_group { reference = chain 'E' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'S' } ncs_group { reference = (chain 'G' and resid 2 through 52) selection = (chain 'T' and resid 2 through 52) } ncs_group { reference = (chain 'H' and (resid 85 through 325 or (resid 401 and (name N or name C1 or nam \ e C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C43 or na \ me C44 or name C45 or name C5 or name O1P or name O2 or name O2P or name O3 or n \ ame O3P or name O4 or name O4P or name O5 or name P )) or resid 402 through 403) \ ) selection = chain 'U' } ncs_group { reference = (chain 'J' and resid 2 through 403) selection = chain 'V' } ncs_group { reference = chain 'K' selection = (chain 'W' and (resid 35 through 452 or (resid 453 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'L' and resid 35 through 480) selection = (chain 'Y' and resid 35 through 480) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 37.500 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.017 1.177 35352 Z= 1.011 Angle : 1.344 53.394 47878 Z= 0.860 Chirality : 0.052 0.389 5162 Planarity : 0.005 0.086 6010 Dihedral : 13.534 169.759 13103 Min Nonbonded Distance : 1.408 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 1.36 % Allowed : 5.03 % Favored : 93.61 % Rotamer: Outliers : 1.49 % Allowed : 1.55 % Favored : 96.96 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 4178 helix: -1.56 (0.09), residues: 2001 sheet: -1.92 (0.27), residues: 318 loop : 1.18 (0.16), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 204 TYR 0.032 0.002 TYR Y 186 PHE 0.021 0.002 PHE E 74 TRP 0.038 0.002 TRP H 96 HIS 0.015 0.002 HIS K 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00842 / 0.55 (35333) covalent geometry : angle 1.29006 / 0.85 (47868) SS BOND : bond 0.00293 / 0.16 ( 2) SS BOND : angle 18.84862 / 8.81 ( 4) hydrogen bonds : bond 0.17085 / 11.52 ( 1718) hydrogen bonds : angle 8.65206 / 6.14 ( 4881) metal coordination : bond 0.75150 / 49.14 ( 8) metal coordination : angle 30.08121 / 16.60 ( 6) Misc. bond : bond 0.57590 / 44.46 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 973 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7495 (tpt170) REVERT: A 43 ARG cc_start: 0.8365 (ttp-110) cc_final: 0.8007 (mtt180) REVERT: A 66 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7844 (tp30) REVERT: E 50 LEU cc_start: 0.8430 (tt) cc_final: 0.8082 (tp) REVERT: E 79 ASP cc_start: 0.7845 (m-30) cc_final: 0.7609 (m-30) REVERT: J 72 ASP cc_start: 0.7185 (m-30) cc_final: 0.6942 (m-30) REVERT: J 150 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8360 (mt) REVERT: N 25 ARG cc_start: 0.7479 (ptt180) cc_final: 0.6141 (tpt-90) REVERT: P 98 ASP cc_start: 0.4258 (p0) cc_final: 0.3853 (p0) REVERT: P 145 ASP cc_start: 0.8379 (p0) cc_final: 0.7850 (p0) REVERT: T 40 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7379 (mp) REVERT: T 41 ILE cc_start: 0.8121 (mp) cc_final: 0.7686 (mm) REVERT: U 115 GLN cc_start: 0.8115 (mt0) cc_final: 0.7664 (mt0) REVERT: U 216 THR cc_start: 0.8926 (m) cc_final: 0.8545 (p) REVERT: V 17 SER cc_start: 0.8261 (p) cc_final: 0.7995 (p) outliers start: 53 outliers final: 29 residues processed: 1008 average time/residue: 0.2379 time to fit residues: 372.5970 Evaluate side-chains 541 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 508 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain J residue 124 MET Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain K residue 365 ASN Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain W residue 254 ARG Chi-restraints excluded: chain W residue 451 ASP Chi-restraints excluded: chain W residue 453 LEU Chi-restraints excluded: chain Y residue 96 LEU Chi-restraints excluded: chain Y residue 422 ARG Chi-restraints excluded: chain Y residue 423 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.4980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 HIS ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 39 GLN F 23 ASN F 70 ASN F 73 HIS F 74 GLN ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 HIS ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN J 206 ASN J 260 ASN ** J 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 HIS K 139 ASN K 155 GLN K 178 HIS K 184 ASN K 206 HIS K 212 HIS K 311 GLN K 319 GLN ** K 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 ASN ** L 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 HIS L 207 ASN L 239 HIS L 301 ASN ** L 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 HIS ** P 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 GLN P 178 HIS P 242 HIS R 39 GLN R 80 HIS R 84 HIS S 28 ASN S 70 ASN ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 282 HIS U 284 HIS V 137 GLN ** V 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 255 ASN V 260 ASN W 81 HIS W 139 ASN W 155 GLN W 157 GLN W 206 HIS W 212 HIS ** W 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 298 HIS W 310 HIS W 414 GLN W 421 ASN Y 87 ASN Y 95 HIS Y 301 ASN Y 339 GLN Y 342 GLN Y 469 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.121858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.099252 restraints weight = 66935.251| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.12 r_work: 0.3198 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.223 35352 Z= 0.191 Angle : 0.795 14.145 47878 Z= 0.400 Chirality : 0.046 0.242 5162 Planarity : 0.005 0.047 6010 Dihedral : 14.883 167.234 5447 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.07 % Favored : 95.62 % Rotamer: Outliers : 2.45 % Allowed : 9.11 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.13), residues: 4178 helix: 0.26 (0.10), residues: 2072 sheet: -1.98 (0.24), residues: 374 loop : 0.41 (0.16), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG N 41 TYR 0.027 0.002 TYR Y 186 PHE 0.035 0.002 PHE Y 98 TRP 0.027 0.002 TRP Y 296 HIS 0.021 0.002 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (35333) covalent geometry : angle 0.79079 / 0.40 (47868) SS BOND : bond 0.00535 / 0.31 ( 2) SS BOND : angle 1.30324 / 0.70 ( 4) hydrogen bonds : bond 0.05295 / 3.53 ( 1718) hydrogen bonds : angle 5.59899 / 3.93 ( 4881) metal coordination : bond 0.05475 / 3.92 ( 8) metal coordination : angle 7.13135 / 3.80 ( 6) Misc. bond : bond 0.09442 / 5.31 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 569 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7180 (tpt170) REVERT: A 43 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7647 (mtt180) REVERT: C 234 TYR cc_start: 0.8040 (m-80) cc_final: 0.7808 (m-80) REVERT: C 235 TYR cc_start: 0.7578 (t80) cc_final: 0.7313 (t80) REVERT: C 239 HIS cc_start: 0.8113 (m90) cc_final: 0.7662 (m90) REVERT: C 242 HIS cc_start: 0.7968 (m-70) cc_final: 0.7340 (m-70) REVERT: D 31 PHE cc_start: 0.8340 (m-10) cc_final: 0.8069 (m-10) REVERT: D 51 LYS cc_start: 0.8852 (mttt) cc_final: 0.8448 (mttp) REVERT: E 68 THR cc_start: 0.8617 (p) cc_final: 0.8399 (t) REVERT: E 79 ASP cc_start: 0.8760 (m-30) cc_final: 0.8397 (m-30) REVERT: F 53 GLU cc_start: 0.8211 (tp30) cc_final: 0.7906 (mm-30) REVERT: F 102 ARG cc_start: 0.9139 (ttp-170) cc_final: 0.8873 (ttp80) REVERT: G 43 ASP cc_start: 0.8371 (m-30) cc_final: 0.8113 (m-30) REVERT: H 102 LEU cc_start: 0.9143 (mt) cc_final: 0.8942 (mt) REVERT: H 244 MET cc_start: 0.8739 (ttp) cc_final: 0.8300 (ttp) REVERT: H 295 MET cc_start: 0.9012 (tpp) cc_final: 0.8806 (mmm) REVERT: J 4 MET cc_start: 0.5882 (mpp) cc_final: 0.5567 (mpp) REVERT: J 150 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9332 (mt) REVERT: J 375 LYS cc_start: 0.8491 (mttp) cc_final: 0.8062 (mttp) REVERT: L 305 GLN cc_start: 0.8743 (mp10) cc_final: 0.8203 (mp10) REVERT: N 25 ARG cc_start: 0.7544 (ptt180) cc_final: 0.5789 (tpt-90) REVERT: N 66 GLU cc_start: 0.7805 (tp30) cc_final: 0.7402 (mp0) REVERT: P 80 HIS cc_start: 0.7045 (p-80) cc_final: 0.6634 (p-80) REVERT: P 272 ILE cc_start: 0.7742 (mm) cc_final: 0.7370 (mt) REVERT: Q 31 PHE cc_start: 0.8245 (m-10) cc_final: 0.8014 (m-10) REVERT: Q 34 ARG cc_start: 0.8260 (mmm160) cc_final: 0.7990 (tpt90) REVERT: T 23 THR cc_start: 0.9241 (m) cc_final: 0.8735 (p) REVERT: V 15 ASN cc_start: 0.8885 (t0) cc_final: 0.8672 (t0) outliers start: 87 outliers final: 48 residues processed: 628 average time/residue: 0.2215 time to fit residues: 221.8016 Evaluate side-chains 522 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 472 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain P residue 149 LEU Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 180 THR Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 316 MET Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 254 ARG Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 422 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 139 optimal weight: 3.9990 chunk 373 optimal weight: 0.7980 chunk 331 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 367 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 308 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 240 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS H 282 HIS J 267 HIS K 184 ASN K 399 GLN ** K 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 305 GLN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN R 39 GLN U 115 GLN U 265 GLN ** V 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 255 ASN W 426 ASN ** Y 357 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 = 0.3710 r_free = 0.3710 target = 0.119855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.096367 restraints weight = 66589.278| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.22 r_work: 0.3151 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.323 35352 Z= 0.178 Angle : 0.712 13.784 47878 Z= 0.356 Chirality : 0.044 0.477 5162 Planarity : 0.005 0.041 6010 Dihedral : 13.810 162.883 5410 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.33 % Rotamer: Outliers : 2.71 % Allowed : 10.88 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.13), residues: 4178 helix: 0.81 (0.11), residues: 2103 sheet: -1.96 (0.24), residues: 400 loop : 0.10 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 56 TYR 0.021 0.002 TYR Q 60 PHE 0.033 0.002 PHE Y 98 TRP 0.018 0.002 TRP V 379 HIS 0.016 0.002 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (35333) covalent geometry : angle 0.71045 / 0.36 (47868) SS BOND : bond 0.01010 / 0.63 ( 2) SS BOND : angle 1.53675 / 0.66 ( 4) hydrogen bonds : bond 0.04743 / 3.16 ( 1718) hydrogen bonds : angle 5.03730 / 3.53 ( 4881) metal coordination : bond 0.01700 / 1.25 ( 8) metal coordination : angle 4.19178 / 2.66 ( 6) Misc. bond : bond 0.12251 / 6.48 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 514 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7260 (tpt170) REVERT: A 43 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.7636 (mtt180) REVERT: C 230 ASP cc_start: 0.7246 (p0) cc_final: 0.7029 (p0) REVERT: C 234 TYR cc_start: 0.8159 (m-80) cc_final: 0.7899 (m-80) REVERT: C 235 TYR cc_start: 0.7380 (t80) cc_final: 0.7132 (t80) REVERT: C 270 MET cc_start: 0.6184 (mmm) cc_final: 0.5760 (mmm) REVERT: D 51 LYS cc_start: 0.8864 (mttt) cc_final: 0.8523 (mttp) REVERT: E 65 GLU cc_start: 0.7483 (tp30) cc_final: 0.7240 (tp30) REVERT: E 68 THR cc_start: 0.8606 (p) cc_final: 0.8373 (t) REVERT: E 69 GLU cc_start: 0.7203 (pt0) cc_final: 0.6906 (pt0) REVERT: E 79 ASP cc_start: 0.8964 (m-30) cc_final: 0.8651 (m-30) REVERT: G 15 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8392 (mttm) REVERT: G 43 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8193 (m-30) REVERT: H 244 MET cc_start: 0.8967 (ttp) cc_final: 0.8419 (ttp) REVERT: J 44 GLN cc_start: 0.9204 (mm110) cc_final: 0.8998 (mm-40) REVERT: J 150 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9325 (mt) REVERT: J 375 LYS cc_start: 0.8473 (mttp) cc_final: 0.8050 (mttp) REVERT: L 305 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8370 (mp10) REVERT: N 25 ARG cc_start: 0.7577 (ptt180) cc_final: 0.5766 (tpt-90) REVERT: N 32 THR cc_start: 0.8772 (p) cc_final: 0.8548 (t) REVERT: N 66 GLU cc_start: 0.7840 (tp30) cc_final: 0.7465 (mm-30) REVERT: P 165 MET cc_start: 0.6876 (pmm) cc_final: 0.6252 (pmm) REVERT: P 272 ILE cc_start: 0.7897 (mm) cc_final: 0.7504 (mt) REVERT: Q 16 ARG cc_start: 0.7797 (ttt90) cc_final: 0.7526 (ttm170) REVERT: Q 34 ARG cc_start: 0.8297 (mmm160) cc_final: 0.8072 (tpt90) REVERT: R 45 LYS cc_start: 0.8686 (pptt) cc_final: 0.8441 (pttt) REVERT: R 69 GLU cc_start: 0.8062 (tt0) cc_final: 0.7851 (tt0) REVERT: S 15 ASP cc_start: 0.8540 (t0) cc_final: 0.8180 (m-30) REVERT: U 190 ASN cc_start: 0.7820 (t0) cc_final: 0.7542 (t0) REVERT: U 244 MET cc_start: 0.8875 (ttp) cc_final: 0.8517 (ttp) REVERT: V 12 LYS cc_start: 0.9152 (mmmm) cc_final: 0.8950 (mtpp) REVERT: V 271 GLU cc_start: 0.7629 (pt0) cc_final: 0.7382 (pt0) REVERT: Y 296 TRP cc_start: 0.8252 (OUTLIER) cc_final: 0.7752 (t-100) outliers start: 96 outliers final: 57 residues processed: 574 average time/residue: 0.2123 time to fit residues: 196.3512 Evaluate side-chains 525 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 462 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 81 CYS Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 260 GLU Chi-restraints excluded: chain K residue 451 ASP Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain L residue 305 GLN Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain P residue 149 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 141 THR Chi-restraints excluded: chain U residue 223 THR Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 202 GLU Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 316 MET Chi-restraints excluded: chain V residue 336 THR Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 11 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 336 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 402 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 chunk 194 optimal weight: 0.0010 chunk 148 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS K 184 ASN ** K 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 ASN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN P 199 GLN R 39 GLN ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 206 ASN V 313 GLN W 178 HIS ** W 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 284 ASN Y 342 GLN ** Y 357 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 = 0.3664 r_free = 0.3664 target = 0.116751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.093053 restraints weight = 66982.391| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.17 r_work: 0.3092 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.384 35352 Z= 0.239 Angle : 0.744 16.127 47878 Z= 0.370 Chirality : 0.046 0.338 5162 Planarity : 0.005 0.073 6010 Dihedral : 13.345 158.397 5396 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.52 % Favored : 95.17 % Rotamer: Outliers : 3.50 % Allowed : 11.81 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.13), residues: 4178 helix: 1.05 (0.11), residues: 2090 sheet: -1.97 (0.24), residues: 408 loop : -0.14 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 100 TYR 0.020 0.002 TYR Y 186 PHE 0.027 0.002 PHE K 237 TRP 0.020 0.002 TRP V 379 HIS 0.014 0.002 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.24 (35333) covalent geometry : angle 0.74195 / 0.37 (47868) SS BOND : bond 0.00208 / 0.12 ( 2) SS BOND : angle 0.74589 / 0.31 ( 4) hydrogen bonds : bond 0.04980 / 3.32 ( 1718) hydrogen bonds : angle 4.87416 / 3.42 ( 4881) metal coordination : bond 0.00877 / 0.60 ( 8) metal coordination : angle 4.79206 / 3.27 ( 6) Misc. bond : bond 0.14983 / 8.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 476 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8877 (ptm-80) cc_final: 0.7301 (tpt170) REVERT: A 43 ARG cc_start: 0.8291 (ttp-110) cc_final: 0.7630 (mtt180) REVERT: A 69 ARG cc_start: 0.8200 (ttp-110) cc_final: 0.7864 (ttm110) REVERT: C 101 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7112 (tttp) REVERT: C 186 GLN cc_start: 0.7670 (pp30) cc_final: 0.7453 (pp30) REVERT: C 234 TYR cc_start: 0.8178 (m-80) cc_final: 0.7730 (m-80) REVERT: D 31 PHE cc_start: 0.8629 (m-10) cc_final: 0.8289 (m-80) REVERT: D 51 LYS cc_start: 0.8923 (mttt) cc_final: 0.8502 (mttp) REVERT: E 28 ASP cc_start: 0.9216 (OUTLIER) cc_final: 0.8949 (t0) REVERT: E 79 ASP cc_start: 0.9035 (m-30) cc_final: 0.8657 (m-30) REVERT: G 15 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8370 (mttm) REVERT: G 43 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8237 (m-30) REVERT: H 228 ARG cc_start: 0.6150 (tmm-80) cc_final: 0.5776 (tmm-80) REVERT: H 244 MET cc_start: 0.9058 (ttp) cc_final: 0.8324 (ttp) REVERT: J 44 GLN cc_start: 0.9187 (mm110) cc_final: 0.8915 (mm-40) REVERT: J 150 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9325 (mt) REVERT: J 375 LYS cc_start: 0.8555 (mttp) cc_final: 0.8155 (mttp) REVERT: L 305 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8596 (mp10) REVERT: L 368 MET cc_start: 0.6599 (mtt) cc_final: 0.6212 (mtt) REVERT: N 25 ARG cc_start: 0.7748 (ptt180) cc_final: 0.5746 (tpt-90) REVERT: N 32 THR cc_start: 0.8743 (p) cc_final: 0.8530 (t) REVERT: R 45 LYS cc_start: 0.8771 (pptt) cc_final: 0.8461 (pttt) REVERT: R 81 CYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7882 (p) REVERT: U 190 ASN cc_start: 0.7986 (t0) cc_final: 0.7637 (t0) REVERT: U 244 MET cc_start: 0.9201 (ttp) cc_final: 0.8961 (ttp) REVERT: V 252 ASP cc_start: 0.8550 (t0) cc_final: 0.8096 (t0) REVERT: W 214 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8348 (p) REVERT: W 235 GLU cc_start: 0.7353 (tp30) cc_final: 0.6884 (mm-30) REVERT: Y 296 TRP cc_start: 0.8276 (OUTLIER) cc_final: 0.7430 (t-100) outliers start: 124 outliers final: 74 residues processed: 561 average time/residue: 0.2070 time to fit residues: 189.7473 Evaluate side-chains 523 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 441 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 81 CYS Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 260 GLU Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain L residue 305 GLN Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 149 LEU Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain R residue 39 GLN Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 141 THR Chi-restraints excluded: chain U residue 253 LEU Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 119 LEU Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 202 GLU Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 316 MET Chi-restraints excluded: chain V residue 336 THR Chi-restraints excluded: chain V residue 343 VAL Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 154 LEU Chi-restraints excluded: chain W residue 214 THR Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 287 optimal weight: 0.4980 chunk 387 optimal weight: 0.6980 chunk 286 optimal weight: 2.9990 chunk 318 optimal weight: 0.5980 chunk 225 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 362 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 184 ASN ** W 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 339 GLN ** Y 357 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 = 0.3691 r_free = 0.3691 target = 0.118613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094865 restraints weight = 66756.633| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.14 r_work: 0.3131 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.331 35352 Z= 0.154 Angle : 0.665 12.766 47878 Z= 0.330 Chirality : 0.043 0.307 5162 Planarity : 0.004 0.043 6010 Dihedral : 12.707 157.305 5388 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.16 % Favored : 95.52 % Rotamer: Outliers : 3.24 % Allowed : 12.80 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.13), residues: 4178 helix: 1.27 (0.11), residues: 2098 sheet: -1.83 (0.25), residues: 404 loop : -0.21 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 100 TYR 0.020 0.002 TYR Y 420 PHE 0.023 0.001 PHE Y 358 TRP 0.021 0.001 TRP V 379 HIS 0.014 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (35333) covalent geometry : angle 0.66286 / 0.33 (47868) SS BOND : bond 0.00192 / 0.11 ( 2) SS BOND : angle 0.51413 / 0.24 ( 4) hydrogen bonds : bond 0.04381 / 2.91 ( 1718) hydrogen bonds : angle 4.65999 / 3.28 ( 4881) metal coordination : bond 0.00539 / 0.39 ( 8) metal coordination : angle 4.82016 / 3.48 ( 6) Misc. bond : bond 0.12968 / 7.09 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 497 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7279 (tpt170) REVERT: A 43 ARG cc_start: 0.8244 (ttp-110) cc_final: 0.7528 (mtt180) REVERT: A 69 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7854 (ttm110) REVERT: C 101 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7155 (tttm) REVERT: C 154 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.6526 (pt) REVERT: C 186 GLN cc_start: 0.7647 (pp30) cc_final: 0.7440 (pp30) REVERT: C 234 TYR cc_start: 0.8117 (m-80) cc_final: 0.7585 (m-80) REVERT: D 31 PHE cc_start: 0.8604 (m-10) cc_final: 0.8283 (m-80) REVERT: D 51 LYS cc_start: 0.8901 (mttt) cc_final: 0.8542 (mtpp) REVERT: E 28 ASP cc_start: 0.9236 (OUTLIER) cc_final: 0.8991 (t0) REVERT: E 35 GLU cc_start: 0.8200 (pp20) cc_final: 0.7726 (pp20) REVERT: E 38 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7564 (mp0) REVERT: E 79 ASP cc_start: 0.9062 (m-30) cc_final: 0.8665 (m-30) REVERT: F 60 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8598 (mmp) REVERT: G 15 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8413 (mmtm) REVERT: G 43 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8236 (m-30) REVERT: H 244 MET cc_start: 0.8974 (ttp) cc_final: 0.8130 (ttp) REVERT: J 44 GLN cc_start: 0.9127 (mm110) cc_final: 0.8825 (mm-40) REVERT: J 124 MET cc_start: 0.9099 (mmm) cc_final: 0.8848 (mtp) REVERT: J 150 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9319 (mt) REVERT: J 282 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.8245 (mtm-85) REVERT: J 375 LYS cc_start: 0.8471 (mttp) cc_final: 0.8121 (mttp) REVERT: K 61 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9044 (pt) REVERT: L 305 GLN cc_start: 0.8849 (mp10) cc_final: 0.8431 (mp10) REVERT: L 368 MET cc_start: 0.6544 (mtm) cc_final: 0.6226 (mtt) REVERT: L 475 MET cc_start: 0.8944 (mmp) cc_final: 0.8697 (mmt) REVERT: N 25 ARG cc_start: 0.7654 (ptt180) cc_final: 0.5679 (tpt-90) REVERT: N 32 THR cc_start: 0.8688 (p) cc_final: 0.8466 (t) REVERT: N 50 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8953 (t) REVERT: R 36 GLN cc_start: 0.8617 (mp10) cc_final: 0.8245 (mp10) REVERT: R 45 LYS cc_start: 0.8739 (pptt) cc_final: 0.8471 (pttt) REVERT: R 69 GLU cc_start: 0.7957 (tt0) cc_final: 0.7692 (tt0) REVERT: R 81 CYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7862 (p) REVERT: S 15 ASP cc_start: 0.8538 (t0) cc_final: 0.8158 (m-30) REVERT: U 190 ASN cc_start: 0.8151 (t0) cc_final: 0.7766 (t0) REVERT: U 199 TYR cc_start: 0.8455 (m-80) cc_final: 0.8173 (m-80) REVERT: V 12 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8988 (mtpp) REVERT: V 252 ASP cc_start: 0.8554 (t0) cc_final: 0.8181 (t0) REVERT: V 278 TYR cc_start: 0.8311 (t80) cc_final: 0.8108 (t80) REVERT: W 214 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8134 (p) REVERT: W 235 GLU cc_start: 0.7422 (tp30) cc_final: 0.7041 (mm-30) REVERT: Y 296 TRP cc_start: 0.8190 (OUTLIER) cc_final: 0.7485 (t-100) outliers start: 115 outliers final: 62 residues processed: 575 average time/residue: 0.2054 time to fit residues: 192.6799 Evaluate side-chains 517 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 443 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 281 LEU Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 260 GLU Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain K residue 451 ASP Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 141 THR Chi-restraints excluded: chain U residue 155 GLN Chi-restraints excluded: chain U residue 253 LEU Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 119 LEU Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 316 MET Chi-restraints excluded: chain V residue 336 THR Chi-restraints excluded: chain V residue 343 VAL Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 214 THR Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 95 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 258 optimal weight: 0.8980 chunk 398 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 334 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 GLN ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 309 HIS V 313 GLN W 176 ASN ** W 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.117261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093713 restraints weight = 66676.892| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.15 r_work: 0.3103 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.328 35352 Z= 0.188 Angle : 0.683 14.015 47878 Z= 0.337 Chirality : 0.044 0.331 5162 Planarity : 0.004 0.045 6010 Dihedral : 12.469 154.907 5386 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.52 % Favored : 95.17 % Rotamer: Outliers : 3.52 % Allowed : 13.34 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.13), residues: 4178 helix: 1.31 (0.11), residues: 2117 sheet: -1.76 (0.25), residues: 404 loop : -0.32 (0.16), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 100 TYR 0.018 0.002 TYR U 232 PHE 0.035 0.002 PHE K 237 TRP 0.022 0.001 TRP V 379 HIS 0.013 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (35333) covalent geometry : angle 0.68012 / 0.34 (47868) SS BOND : bond 0.00203 / 0.11 ( 2) SS BOND : angle 0.47845 / 0.25 ( 4) hydrogen bonds : bond 0.04492 / 2.99 ( 1718) hydrogen bonds : angle 4.62210 / 3.25 ( 4881) metal coordination : bond 0.00631 / 0.44 ( 8) metal coordination : angle 5.28582 / 3.89 ( 6) Misc. bond : bond 0.13337 / 7.39 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 466 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7272 (tpt170) REVERT: A 43 ARG cc_start: 0.8299 (ttp-110) cc_final: 0.7527 (mtt180) REVERT: A 69 ARG cc_start: 0.8177 (ttp-110) cc_final: 0.7829 (ttm110) REVERT: C 101 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7076 (tttp) REVERT: C 234 TYR cc_start: 0.8179 (m-80) cc_final: 0.7640 (m-80) REVERT: C 235 TYR cc_start: 0.7675 (t80) cc_final: 0.7337 (t80) REVERT: D 31 PHE cc_start: 0.8597 (m-10) cc_final: 0.8354 (m-80) REVERT: D 51 LYS cc_start: 0.8903 (mttt) cc_final: 0.8535 (mtpp) REVERT: E 28 ASP cc_start: 0.9246 (OUTLIER) cc_final: 0.9020 (t0) REVERT: E 51 GLU cc_start: 0.8459 (pp20) cc_final: 0.8231 (pp20) REVERT: E 79 ASP cc_start: 0.9073 (m-30) cc_final: 0.8652 (m-30) REVERT: F 60 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8657 (mmp) REVERT: G 15 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8617 (tmtt) REVERT: G 39 ARG cc_start: 0.8867 (tpp80) cc_final: 0.8663 (tpp80) REVERT: G 43 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8323 (m-30) REVERT: H 244 MET cc_start: 0.9008 (ttp) cc_final: 0.8156 (ttp) REVERT: J 44 GLN cc_start: 0.9145 (mm110) cc_final: 0.8850 (mm-40) REVERT: J 124 MET cc_start: 0.9113 (mmm) cc_final: 0.8890 (mtp) REVERT: J 282 ARG cc_start: 0.8593 (mtm-85) cc_final: 0.8357 (mtm-85) REVERT: J 375 LYS cc_start: 0.8534 (mttp) cc_final: 0.8139 (mttp) REVERT: L 305 GLN cc_start: 0.8850 (mp10) cc_final: 0.8390 (mp10) REVERT: N 25 ARG cc_start: 0.7714 (ptt180) cc_final: 0.5665 (tpt-90) REVERT: N 50 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8951 (t) REVERT: N 66 GLU cc_start: 0.7896 (tp30) cc_final: 0.7681 (tp30) REVERT: P 220 LEU cc_start: 0.8591 (mt) cc_final: 0.8215 (mt) REVERT: Q 17 ARG cc_start: 0.8042 (mtm110) cc_final: 0.7811 (mtm110) REVERT: Q 30 MET cc_start: 0.9006 (tpp) cc_final: 0.8750 (ttp) REVERT: R 45 LYS cc_start: 0.8694 (pptt) cc_final: 0.8489 (pttm) REVERT: R 69 GLU cc_start: 0.7984 (tt0) cc_final: 0.7729 (tt0) REVERT: R 81 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7863 (p) REVERT: S 15 ASP cc_start: 0.8527 (t0) cc_final: 0.8132 (m-30) REVERT: U 190 ASN cc_start: 0.8141 (t0) cc_final: 0.7771 (t0) REVERT: U 244 MET cc_start: 0.9022 (ttp) cc_final: 0.8749 (ttp) REVERT: V 252 ASP cc_start: 0.8607 (t0) cc_final: 0.8227 (t0) REVERT: W 135 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8205 (tp30) REVERT: W 214 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8270 (p) REVERT: W 235 GLU cc_start: 0.7385 (tp30) cc_final: 0.6977 (mm-30) REVERT: W 268 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7632 (p-80) REVERT: Y 173 GLN cc_start: 0.5532 (OUTLIER) cc_final: 0.4836 (mp10) REVERT: Y 296 TRP cc_start: 0.8206 (OUTLIER) cc_final: 0.7377 (t-100) outliers start: 125 outliers final: 72 residues processed: 555 average time/residue: 0.2074 time to fit residues: 188.3023 Evaluate side-chains 521 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 438 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 81 CYS Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 379 TRP Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 260 GLU Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 451 ASP Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 141 THR Chi-restraints excluded: chain U residue 155 GLN Chi-restraints excluded: chain U residue 263 MET Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 119 LEU Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 316 MET Chi-restraints excluded: chain V residue 336 THR Chi-restraints excluded: chain V residue 343 VAL Chi-restraints excluded: chain V residue 377 LEU Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 214 THR Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 268 HIS Chi-restraints excluded: chain W residue 329 SER Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 173 GLN Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 314 optimal weight: 0.0050 chunk 319 optimal weight: 0.9990 chunk 371 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 403 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 326 optimal weight: 1.9990 chunk 347 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 52 optimal weight: 0.2980 chunk 402 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 291 HIS K 415 GLN L 305 GLN L 308 ASN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.118507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095052 restraints weight = 66561.374| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.17 r_work: 0.3130 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.298 35352 Z= 0.146 Angle : 0.652 11.985 47878 Z= 0.322 Chirality : 0.042 0.357 5162 Planarity : 0.004 0.045 6010 Dihedral : 12.075 152.875 5382 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.21 % Favored : 95.50 % Rotamer: Outliers : 3.02 % Allowed : 14.29 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.13), residues: 4178 helix: 1.45 (0.11), residues: 2113 sheet: -1.56 (0.26), residues: 404 loop : -0.36 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 100 TYR 0.019 0.001 TYR V 224 PHE 0.022 0.001 PHE Y 358 TRP 0.023 0.001 TRP V 379 HIS 0.013 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (35333) covalent geometry : angle 0.64921 / 0.32 (47868) SS BOND : bond 0.00610 / 0.38 ( 2) SS BOND : angle 0.70507 / 0.31 ( 4) hydrogen bonds : bond 0.04143 / 2.75 ( 1718) hydrogen bonds : angle 4.48544 / 3.15 ( 4881) metal coordination : bond 0.00502 / 0.32 ( 8) metal coordination : angle 5.32548 / 3.96 ( 6) Misc. bond : bond 0.12036 / 6.67 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 481 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7256 (tpt170) REVERT: A 43 ARG cc_start: 0.8231 (ttp-110) cc_final: 0.7493 (mtt180) REVERT: A 48 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7162 (mpt180) REVERT: A 65 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8416 (mm-30) REVERT: A 69 ARG cc_start: 0.8144 (ttp-110) cc_final: 0.7776 (ttm110) REVERT: C 101 LYS cc_start: 0.7970 (mmtt) cc_final: 0.7102 (tttp) REVERT: C 231 PHE cc_start: 0.7464 (m-80) cc_final: 0.7069 (m-80) REVERT: C 239 HIS cc_start: 0.8162 (m90) cc_final: 0.7625 (m90) REVERT: D 31 PHE cc_start: 0.8576 (m-10) cc_final: 0.8302 (m-80) REVERT: D 51 LYS cc_start: 0.8885 (mttt) cc_final: 0.8512 (mtpp) REVERT: E 28 ASP cc_start: 0.9207 (OUTLIER) cc_final: 0.8991 (t0) REVERT: E 35 GLU cc_start: 0.8214 (pp20) cc_final: 0.7701 (pp20) REVERT: E 38 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7416 (mp0) REVERT: E 55 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8690 (mm-30) REVERT: E 79 ASP cc_start: 0.9088 (m-30) cc_final: 0.8663 (m-30) REVERT: G 15 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8634 (tmtt) REVERT: G 39 ARG cc_start: 0.8909 (tpp80) cc_final: 0.8691 (tpp80) REVERT: G 43 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8327 (m-30) REVERT: H 244 MET cc_start: 0.8952 (ttp) cc_final: 0.8103 (ttp) REVERT: J 4 MET cc_start: 0.5158 (mpp) cc_final: 0.4923 (mpp) REVERT: J 44 GLN cc_start: 0.9097 (mm110) cc_final: 0.8780 (mm-40) REVERT: J 375 LYS cc_start: 0.8471 (mttp) cc_final: 0.8063 (mttp) REVERT: K 414 GLN cc_start: 0.8652 (mp10) cc_final: 0.8356 (mp10) REVERT: L 279 ASP cc_start: 0.8326 (t70) cc_final: 0.7936 (t70) REVERT: N 25 ARG cc_start: 0.7731 (ptt180) cc_final: 0.5746 (tpt-90) REVERT: N 50 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8937 (t) REVERT: N 66 GLU cc_start: 0.7888 (tp30) cc_final: 0.7616 (tp30) REVERT: P 220 LEU cc_start: 0.8613 (mt) cc_final: 0.8258 (mt) REVERT: R 66 ASP cc_start: 0.7490 (t0) cc_final: 0.6999 (t70) REVERT: R 69 GLU cc_start: 0.7989 (tt0) cc_final: 0.7732 (tt0) REVERT: R 81 CYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7774 (p) REVERT: S 15 ASP cc_start: 0.8539 (t0) cc_final: 0.8117 (m-30) REVERT: U 190 ASN cc_start: 0.8195 (t0) cc_final: 0.7804 (t0) REVERT: U 244 MET cc_start: 0.8972 (ttp) cc_final: 0.8497 (ttp) REVERT: V 252 ASP cc_start: 0.8637 (t0) cc_final: 0.8190 (t0) REVERT: W 135 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8243 (tp30) REVERT: W 214 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8194 (p) REVERT: W 235 GLU cc_start: 0.7483 (tp30) cc_final: 0.7115 (mm-30) REVERT: W 268 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7689 (p-80) REVERT: W 413 LEU cc_start: 0.9079 (mt) cc_final: 0.8869 (mt) REVERT: Y 42 LEU cc_start: 0.8448 (tt) cc_final: 0.7932 (mt) outliers start: 107 outliers final: 62 residues processed: 553 average time/residue: 0.2108 time to fit residues: 189.6061 Evaluate side-chains 520 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 449 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 81 CYS Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 281 LEU Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 379 TRP Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain L residue 305 GLN Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 141 THR Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 119 LEU Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 316 MET Chi-restraints excluded: chain V residue 343 VAL Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 214 THR Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 268 HIS Chi-restraints excluded: chain W residue 329 SER Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 287 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 115 optimal weight: 1.9990 chunk 380 optimal weight: 0.8980 chunk 311 optimal weight: 0.0570 chunk 270 optimal weight: 0.9990 chunk 199 optimal weight: 0.6980 chunk 233 optimal weight: 5.9990 chunk 300 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 104 optimal weight: 0.0670 chunk 320 optimal weight: 0.0980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN L 277 HIS L 305 GLN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 397 ASN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 374 ASN ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.119332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.095998 restraints weight = 66021.859| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.13 r_work: 0.3152 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.268 35352 Z= 0.127 Angle : 0.653 11.962 47878 Z= 0.321 Chirality : 0.042 0.343 5162 Planarity : 0.004 0.044 6010 Dihedral : 11.699 150.338 5379 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.19 % Favored : 95.55 % Rotamer: Outliers : 2.59 % Allowed : 15.11 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.13), residues: 4178 helix: 1.54 (0.11), residues: 2105 sheet: -1.41 (0.26), residues: 402 loop : -0.35 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 100 TYR 0.018 0.001 TYR V 224 PHE 0.025 0.001 PHE K 237 TRP 0.023 0.001 TRP V 379 HIS 0.013 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (35333) covalent geometry : angle 0.65041 / 0.32 (47868) SS BOND : bond 0.00146 / 0.08 ( 2) SS BOND : angle 0.47987 / 0.23 ( 4) hydrogen bonds : bond 0.03937 / 2.62 ( 1718) hydrogen bonds : angle 4.41919 / 3.11 ( 4881) metal coordination : bond 0.00421 / 0.28 ( 8) metal coordination : angle 5.20494 / 3.80 ( 6) Misc. bond : bond 0.10893 / 6.03 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 492 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.7305 (tpt170) REVERT: A 43 ARG cc_start: 0.8208 (ttp-110) cc_final: 0.7475 (mtt180) REVERT: A 48 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7675 (mpt180) REVERT: A 65 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8380 (mm-30) REVERT: C 101 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7086 (tttp) REVERT: C 231 PHE cc_start: 0.7398 (m-80) cc_final: 0.6959 (m-80) REVERT: C 239 HIS cc_start: 0.8159 (m90) cc_final: 0.7629 (m90) REVERT: D 51 LYS cc_start: 0.8771 (mttt) cc_final: 0.8421 (mtpp) REVERT: E 35 GLU cc_start: 0.8178 (pp20) cc_final: 0.7681 (pp20) REVERT: E 38 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7493 (mp0) REVERT: E 55 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8722 (mm-30) REVERT: E 79 ASP cc_start: 0.9099 (m-30) cc_final: 0.8704 (m-30) REVERT: G 15 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8646 (tmtt) REVERT: G 39 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8669 (tpp80) REVERT: G 43 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8299 (m-30) REVERT: H 244 MET cc_start: 0.8900 (ttp) cc_final: 0.8008 (ttp) REVERT: J 44 GLN cc_start: 0.9053 (mm110) cc_final: 0.8765 (mm-40) REVERT: J 375 LYS cc_start: 0.8424 (mttp) cc_final: 0.8169 (mttp) REVERT: K 414 GLN cc_start: 0.8592 (mp10) cc_final: 0.8333 (mp10) REVERT: L 279 ASP cc_start: 0.8289 (t70) cc_final: 0.7894 (t70) REVERT: L 305 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8548 (mp10) REVERT: N 11 MET cc_start: 0.9068 (ttp) cc_final: 0.8812 (ttp) REVERT: N 25 ARG cc_start: 0.7701 (ptt180) cc_final: 0.5733 (tpt-90) REVERT: N 32 THR cc_start: 0.8683 (p) cc_final: 0.8417 (t) REVERT: N 66 GLU cc_start: 0.7836 (tp30) cc_final: 0.7542 (mm-30) REVERT: P 220 LEU cc_start: 0.8584 (mt) cc_final: 0.8252 (mt) REVERT: P 270 MET cc_start: 0.6744 (mmp) cc_final: 0.6505 (mmt) REVERT: Q 34 ARG cc_start: 0.8268 (mmm160) cc_final: 0.7633 (tpp80) REVERT: Q 47 ILE cc_start: 0.9382 (tt) cc_final: 0.9130 (tt) REVERT: R 36 GLN cc_start: 0.8555 (mp10) cc_final: 0.8139 (mp10) REVERT: R 66 ASP cc_start: 0.7549 (t0) cc_final: 0.7062 (t70) REVERT: R 69 GLU cc_start: 0.8049 (tt0) cc_final: 0.7796 (tt0) REVERT: R 81 CYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7762 (p) REVERT: S 15 ASP cc_start: 0.8485 (t0) cc_final: 0.8081 (m-30) REVERT: U 190 ASN cc_start: 0.8185 (t0) cc_final: 0.7763 (t0) REVERT: U 199 TYR cc_start: 0.8444 (m-80) cc_final: 0.8181 (m-80) REVERT: U 244 MET cc_start: 0.8854 (ttp) cc_final: 0.8474 (ttp) REVERT: V 252 ASP cc_start: 0.8749 (t0) cc_final: 0.8355 (t0) REVERT: V 287 LYS cc_start: 0.8474 (tttp) cc_final: 0.7947 (mmtm) REVERT: W 135 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8249 (tp30) REVERT: W 214 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8009 (p) REVERT: W 235 GLU cc_start: 0.7252 (tp30) cc_final: 0.6958 (mm-30) REVERT: W 268 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7713 (p-80) REVERT: Y 42 LEU cc_start: 0.8366 (tt) cc_final: 0.7822 (mt) REVERT: Y 296 TRP cc_start: 0.8184 (OUTLIER) cc_final: 0.7349 (t-100) REVERT: Y 463 GLU cc_start: 0.7509 (tt0) cc_final: 0.7043 (pt0) outliers start: 92 outliers final: 56 residues processed: 555 average time/residue: 0.2289 time to fit residues: 205.8434 Evaluate side-chains 521 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 456 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 81 CYS Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 281 LEU Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 379 TRP Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain L residue 305 GLN Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 360 CYS Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 141 THR Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 119 LEU Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 343 VAL Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 214 THR Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 268 HIS Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 5 optimal weight: 0.8980 chunk 58 optimal weight: 0.0030 chunk 324 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 323 optimal weight: 0.7980 chunk 202 optimal weight: 3.9990 chunk 282 optimal weight: 0.0040 chunk 18 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 362 optimal weight: 0.8980 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 305 GLN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 119 GLN ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 397 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.119555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.095941 restraints weight = 66220.810| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.21 r_work: 0.3147 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.229 35352 Z= 0.138 Angle : 0.662 13.398 47878 Z= 0.324 Chirality : 0.042 0.339 5162 Planarity : 0.004 0.044 6010 Dihedral : 11.430 147.845 5377 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.38 % Favored : 95.38 % Rotamer: Outliers : 2.34 % Allowed : 15.62 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.13), residues: 4178 helix: 1.58 (0.11), residues: 2101 sheet: -1.38 (0.26), residues: 400 loop : -0.37 (0.16), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 100 TYR 0.017 0.001 TYR Y 420 PHE 0.023 0.001 PHE Y 358 TRP 0.021 0.001 TRP F 13 HIS 0.012 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (35333) covalent geometry : angle 0.65970 / 0.32 (47868) SS BOND : bond 0.00154 / 0.09 ( 2) SS BOND : angle 0.46863 / 0.23 ( 4) hydrogen bonds : bond 0.03947 / 2.63 ( 1718) hydrogen bonds : angle 4.41321 / 3.11 ( 4881) metal coordination : bond 0.00399 / 0.26 ( 8) metal coordination : angle 5.12920 / 3.71 ( 6) Misc. bond : bond 0.09809 / 5.54 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 470 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7273 (tpt170) REVERT: A 43 ARG cc_start: 0.8226 (ttp-110) cc_final: 0.7461 (mtt180) REVERT: A 48 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7864 (mpt180) REVERT: A 59 ILE cc_start: 0.9275 (mt) cc_final: 0.8992 (tt) REVERT: A 65 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8382 (mm-30) REVERT: C 101 LYS cc_start: 0.7951 (mmtt) cc_final: 0.7066 (tttp) REVERT: C 231 PHE cc_start: 0.7378 (m-80) cc_final: 0.6930 (m-80) REVERT: C 239 HIS cc_start: 0.8183 (m90) cc_final: 0.7653 (m90) REVERT: D 51 LYS cc_start: 0.8800 (mttt) cc_final: 0.8446 (mtpp) REVERT: E 35 GLU cc_start: 0.8075 (pp20) cc_final: 0.7622 (pp20) REVERT: E 38 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7496 (mp0) REVERT: E 55 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8783 (mm-30) REVERT: E 79 ASP cc_start: 0.9104 (m-30) cc_final: 0.8688 (m-30) REVERT: G 15 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8682 (tmtt) REVERT: G 39 ARG cc_start: 0.8901 (tpp80) cc_final: 0.8679 (tpp80) REVERT: G 43 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8335 (m-30) REVERT: H 244 MET cc_start: 0.8933 (ttp) cc_final: 0.7987 (ttp) REVERT: H 292 MET cc_start: 0.9420 (tmm) cc_final: 0.9102 (ppp) REVERT: J 44 GLN cc_start: 0.9120 (mm110) cc_final: 0.8858 (mm-40) REVERT: J 375 LYS cc_start: 0.8440 (mttp) cc_final: 0.8124 (mttp) REVERT: K 414 GLN cc_start: 0.8598 (mp10) cc_final: 0.8324 (mp10) REVERT: L 279 ASP cc_start: 0.8293 (t70) cc_final: 0.7889 (t70) REVERT: L 305 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8630 (mm-40) REVERT: N 11 MET cc_start: 0.9007 (ttp) cc_final: 0.8791 (ttp) REVERT: N 25 ARG cc_start: 0.7705 (ptt180) cc_final: 0.5717 (tpt-90) REVERT: N 32 THR cc_start: 0.8654 (p) cc_final: 0.8371 (t) REVERT: N 66 GLU cc_start: 0.7898 (tp30) cc_final: 0.7629 (mm-30) REVERT: P 220 LEU cc_start: 0.8625 (mt) cc_final: 0.8268 (mt) REVERT: Q 34 ARG cc_start: 0.8255 (mmm160) cc_final: 0.7610 (tpp80) REVERT: Q 47 ILE cc_start: 0.9420 (tt) cc_final: 0.9154 (tt) REVERT: R 36 GLN cc_start: 0.8552 (mp10) cc_final: 0.8125 (mp10) REVERT: R 66 ASP cc_start: 0.7555 (t0) cc_final: 0.7071 (t70) REVERT: R 69 GLU cc_start: 0.8070 (tt0) cc_final: 0.7824 (tt0) REVERT: R 81 CYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7769 (p) REVERT: S 15 ASP cc_start: 0.8487 (t0) cc_final: 0.8075 (m-30) REVERT: T 36 THR cc_start: 0.9089 (m) cc_final: 0.8858 (t) REVERT: U 190 ASN cc_start: 0.8230 (t0) cc_final: 0.7799 (t0) REVERT: U 244 MET cc_start: 0.8847 (ttp) cc_final: 0.8421 (ttp) REVERT: V 287 LYS cc_start: 0.8442 (tttp) cc_final: 0.7970 (mmtp) REVERT: W 135 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8261 (tp30) REVERT: W 214 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8070 (p) REVERT: W 235 GLU cc_start: 0.7207 (tp30) cc_final: 0.6912 (mm-30) REVERT: W 268 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7729 (p-80) REVERT: Y 42 LEU cc_start: 0.8372 (tt) cc_final: 0.7809 (mt) REVERT: Y 296 TRP cc_start: 0.8211 (OUTLIER) cc_final: 0.7300 (t-100) outliers start: 83 outliers final: 65 residues processed: 529 average time/residue: 0.2243 time to fit residues: 194.1050 Evaluate side-chains 528 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 454 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 81 CYS Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 281 LEU Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 379 TRP Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain L residue 305 GLN Chi-restraints excluded: chain L residue 340 SER Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 360 CYS Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 141 THR Chi-restraints excluded: chain U residue 155 GLN Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 119 LEU Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 254 ASP Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 343 VAL Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 214 THR Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 268 HIS Chi-restraints excluded: chain W residue 317 THR Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 64 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 234 optimal weight: 0.0470 chunk 349 optimal weight: 1.9990 chunk 396 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 330 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 305 GLN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN U 115 GLN ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 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 = 0.3704 r_free = 0.3704 target = 0.119457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.095373 restraints weight = 66807.025| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.18 r_work: 0.3145 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.237 35352 Z= 0.157 Angle : 0.678 13.885 47878 Z= 0.332 Chirality : 0.043 0.350 5162 Planarity : 0.004 0.063 6010 Dihedral : 11.304 146.394 5377 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.45 % Favored : 95.33 % Rotamer: Outliers : 2.28 % Allowed : 15.90 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.13), residues: 4178 helix: 1.57 (0.11), residues: 2104 sheet: -1.41 (0.25), residues: 400 loop : -0.39 (0.16), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 100 TYR 0.020 0.001 TYR C 263 PHE 0.026 0.001 PHE K 237 TRP 0.020 0.001 TRP V 163 HIS 0.011 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (35333) covalent geometry : angle 0.67543 / 0.33 (47868) SS BOND : bond 0.00152 / 0.08 ( 2) SS BOND : angle 0.46989 / 0.24 ( 4) hydrogen bonds : bond 0.04045 / 2.69 ( 1718) hydrogen bonds : angle 4.42567 / 3.12 ( 4881) metal coordination : bond 0.00418 / 0.26 ( 8) metal coordination : angle 5.34800 / 3.88 ( 6) Misc. bond : bond 0.10083 / 5.68 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 465 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7297 (tpt170) REVERT: A 43 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7431 (mtt180) REVERT: A 48 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7848 (mpt180) REVERT: A 59 ILE cc_start: 0.9280 (mt) cc_final: 0.9001 (tt) REVERT: A 65 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8372 (mm-30) REVERT: C 101 LYS cc_start: 0.7882 (mmtt) cc_final: 0.6967 (tttp) REVERT: C 231 PHE cc_start: 0.7354 (m-80) cc_final: 0.6908 (m-80) REVERT: C 239 HIS cc_start: 0.8196 (m90) cc_final: 0.7713 (m90) REVERT: D 51 LYS cc_start: 0.8802 (mttt) cc_final: 0.8445 (mtpp) REVERT: E 35 GLU cc_start: 0.8167 (pp20) cc_final: 0.7707 (pp20) REVERT: E 38 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7611 (mp0) REVERT: E 55 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8840 (mm-30) REVERT: E 79 ASP cc_start: 0.9110 (m-30) cc_final: 0.8695 (m-30) REVERT: G 15 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8696 (tmtt) REVERT: G 39 ARG cc_start: 0.8904 (tpp80) cc_final: 0.8683 (tpp80) REVERT: G 43 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8296 (m-30) REVERT: H 244 MET cc_start: 0.8957 (ttp) cc_final: 0.8029 (ttp) REVERT: H 292 MET cc_start: 0.9425 (tmm) cc_final: 0.9102 (ppp) REVERT: J 44 GLN cc_start: 0.9140 (mm110) cc_final: 0.8889 (mm-40) REVERT: J 375 LYS cc_start: 0.8429 (mttp) cc_final: 0.8116 (mttp) REVERT: L 279 ASP cc_start: 0.8269 (t70) cc_final: 0.7901 (t70) REVERT: L 305 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8571 (mm-40) REVERT: N 25 ARG cc_start: 0.7726 (ptt180) cc_final: 0.5728 (tpt-90) REVERT: N 32 THR cc_start: 0.8667 (p) cc_final: 0.8387 (t) REVERT: N 66 GLU cc_start: 0.7947 (tp30) cc_final: 0.7656 (tp30) REVERT: P 220 LEU cc_start: 0.8660 (mt) cc_final: 0.8294 (mt) REVERT: Q 34 ARG cc_start: 0.8244 (mmm160) cc_final: 0.7606 (tpp80) REVERT: Q 47 ILE cc_start: 0.9421 (tt) cc_final: 0.9158 (tt) REVERT: R 36 GLN cc_start: 0.8566 (mp10) cc_final: 0.8108 (mp10) REVERT: R 66 ASP cc_start: 0.7526 (t0) cc_final: 0.7048 (t70) REVERT: R 69 GLU cc_start: 0.8006 (tt0) cc_final: 0.7801 (tt0) REVERT: R 81 CYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7778 (p) REVERT: S 15 ASP cc_start: 0.8563 (t0) cc_final: 0.8127 (m-30) REVERT: U 244 MET cc_start: 0.8923 (ttp) cc_final: 0.8494 (ttp) REVERT: V 287 LYS cc_start: 0.8409 (tttp) cc_final: 0.7971 (mmtp) REVERT: W 135 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8270 (tp30) REVERT: W 214 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8073 (p) REVERT: W 235 GLU cc_start: 0.7223 (tp30) cc_final: 0.6879 (mm-30) REVERT: W 268 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7703 (p-80) REVERT: Y 296 TRP cc_start: 0.8211 (OUTLIER) cc_final: 0.7276 (t-100) outliers start: 81 outliers final: 64 residues processed: 520 average time/residue: 0.2223 time to fit residues: 189.2461 Evaluate side-chains 520 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 447 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 81 CYS Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain L residue 305 GLN Chi-restraints excluded: chain L residue 340 SER Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 360 CYS Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 141 THR Chi-restraints excluded: chain U residue 155 GLN Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 343 VAL Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 214 THR Chi-restraints excluded: chain W residue 257 GLU Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 268 HIS Chi-restraints excluded: chain W residue 317 THR Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 112 optimal weight: 0.8980 chunk 295 optimal weight: 0.8980 chunk 350 optimal weight: 3.9990 chunk 179 optimal weight: 0.0060 chunk 62 optimal weight: 0.7980 chunk 263 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 chunk 314 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 302 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 291 HIS L 305 GLN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 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 = 0.3709 r_free = 0.3709 target = 0.119787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.095766 restraints weight = 66358.509| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.17 r_work: 0.3155 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.235 35352 Z= 0.142 Angle : 0.672 14.737 47878 Z= 0.329 Chirality : 0.042 0.341 5162 Planarity : 0.004 0.067 6010 Dihedral : 11.134 145.462 5377 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.31 % Favored : 95.48 % Rotamer: Outliers : 2.26 % Allowed : 15.76 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.13), residues: 4178 helix: 1.59 (0.11), residues: 2104 sheet: -1.35 (0.26), residues: 400 loop : -0.39 (0.16), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 100 TYR 0.018 0.001 TYR Y 420 PHE 0.022 0.001 PHE Y 358 TRP 0.019 0.001 TRP V 163 HIS 0.010 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (35333) covalent geometry : angle 0.66987 / 0.33 (47868) SS BOND : bond 0.00145 / 0.08 ( 2) SS BOND : angle 0.46176 / 0.23 ( 4) hydrogen bonds : bond 0.03967 / 2.64 ( 1718) hydrogen bonds : angle 4.39700 / 3.10 ( 4881) metal coordination : bond 0.00386 / 0.25 ( 8) metal coordination : angle 5.20399 / 3.72 ( 6) Misc. bond : bond 0.09980 / 5.61 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7917.03 seconds wall clock time: 136 minutes 54.87 seconds (8214.87 seconds total)