Starting phenix.real_space_refine on Sat Mar 7 10:03:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n7p_0360/03_2026/6n7p_0360.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7p_0360/03_2026/6n7p_0360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6n7p_0360/03_2026/6n7p_0360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7p_0360/03_2026/6n7p_0360.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n7p_0360/03_2026/6n7p_0360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7p_0360/03_2026/6n7p_0360.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 Zn 3 6.06 5 P 580 5.49 5 S 93 5.16 5 C 23851 2.51 5 N 7348 2.21 5 O 9613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41488 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1207 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 14, 'TRANS': 171} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASN:plan1': 2, 'TYR:plan': 5, 'ARG:plan': 7, 'ASP:plan': 9, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 6, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 185 Chain: "B" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1570 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 186} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1058 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4561 Classifications: {'peptide': 544} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 531} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 3981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 3981 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 236} Link IDs: {'PTRANS': 19, 'TRANS': 556} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 942 Unresolved non-hydrogen angles: 1218 Unresolved non-hydrogen dihedrals: 808 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'ARG:plan': 11, 'ASP:plan': 14, 'GLN:plan1': 15, 'PHE:plan': 18, 'ASN:plan1': 19, 'TYR:plan': 10, 'TRP:plan': 9, 'GLU:plan': 16, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 552 Chain: "F" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1818 Classifications: {'peptide': 267} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 253} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASN:plan1': 6, 'PHE:plan': 6, 'ASP:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 137 Chain: "G" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1954 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 420 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "H" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 265 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'UNK:plan-1': 53} Unresolved non-hydrogen planarities: 53 Chain: "I" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1409 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 4, 'GLU:plan': 8, 'ARG:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 87 Chain: "J" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 984 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 185} Link IDs: {'PTRANS': 6, 'TRANS': 191} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 719 Unresolved non-hydrogen angles: 909 Unresolved non-hydrogen dihedrals: 604 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'ASP:plan': 20, 'ARG:plan': 15, 'ASN:plan1': 10, 'PHE:plan': 10, 'GLU:plan': 16, 'TRP:plan': 4, 'TYR:plan': 5, 'HIS:plan': 3, 'GLN:plan1': 13} Unresolved non-hydrogen planarities: 427 Chain: "K" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1008 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 858 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 710 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 85} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "P" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 584 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Q" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 543 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 11822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 11822 Classifications: {'RNA': 558} Modifications used: {'rna2p_pur': 24, 'rna2p_pyr': 35, 'rna3p_pur': 241, 'rna3p_pyr': 258} Link IDs: {'rna2p': 59, 'rna3p': 498} Chain breaks: 1 Chain: "r" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 471 Classifications: {'RNA': 22} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 19} Chain: "X" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 826, 4101 Classifications: {'peptide': 826} Incomplete info: {'truncation_to_alanine': 754} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 27, 'TRANS': 793} Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 2812 Unresolved non-hydrogen angles: 3630 Unresolved non-hydrogen dihedrals: 2338 Unresolved non-hydrogen chiralities: 252 Planarities with less than four sites: {'GLU:plan': 73, 'ASP:plan': 49, 'ARG:plan': 30, 'PHE:plan': 58, 'ASN:plan1': 68, 'TYR:plan': 35, 'HIS:plan': 8, 'GLN:plan1': 24, 'TRP:plan': 11} Unresolved non-hydrogen planarities: 1621 Chain: "Y" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 677 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 5, 'TRANS': 132} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 447 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 376 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ASP:plan': 11, 'ARG:plan': 11, 'TYR:plan': 6, 'ASN:plan1': 4, 'GLN:plan1': 4, 'GLU:plan': 9, 'PHE:plan': 11} Unresolved non-hydrogen planarities: 260 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1248 SG CYS B 6 120.136 144.976 97.700 1.00 27.17 S ATOM 1275 SG CYS B 9 118.651 142.217 100.534 1.00 25.43 S ATOM 17019 SG CYS I 45 152.320 157.333 120.894 1.00 84.64 S ATOM 17076 SG CYS I 53 149.669 154.790 119.783 1.00 77.17 S ATOM 17182 SG CYS I 68 148.399 157.764 120.616 1.00 89.42 S ATOM 17882 SG CYS I 201 142.303 134.067 118.473 1.00 73.68 S ATOM 17904 SG CYS I 204 141.052 136.818 119.134 1.00 72.15 S Time building chain proxies: 9.10, per 1000 atoms: 0.22 Number of scatterers: 41488 At special positions: 0 Unit cell: (201.28, 272, 213.52, 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) Zn 3 29.99 S 93 16.00 P 580 15.00 O 9613 8.00 N 7348 7.00 C 23851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 30 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 24 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 6 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 9 " pdb=" ZN I 501 " pdb="ZN ZN I 501 " - pdb=" NE2 HIS I 72 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 53 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 68 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 45 " pdb=" ZN I 502 " pdb="ZN ZN I 502 " - pdb=" ND1 HIS I 226 " pdb="ZN ZN I 502 " - pdb=" NE2 HIS I 220 " pdb="ZN ZN I 502 " - pdb=" SG CYS I 204 " pdb="ZN ZN I 502 " - pdb=" SG CYS I 201 " Number of angles added : 7 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8180 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 26 sheets defined 55.4% alpha, 8.7% beta 179 base pairs and 331 stacking pairs defined. Time for finding SS restraints: 6.41 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 removed outlier: 3.506A pdb=" N ARG A 14 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 57 Processing helix chain 'A' and resid 65 through 91 removed outlier: 3.615A pdb=" N ASN A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.569A pdb=" N ALA A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 26 removed outlier: 3.784A pdb=" N SER B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 48 Processing helix chain 'B' and resid 60 through 69 Processing helix chain 'B' and resid 79 through 100 Processing helix chain 'B' and resid 103 through 109 removed outlier: 3.889A pdb=" N LEU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.607A pdb=" N VAL B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.860A pdb=" N SER B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 28 removed outlier: 3.529A pdb=" N TYR C 19 " --> pdb=" O ASN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 removed outlier: 3.737A pdb=" N ASN C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 removed outlier: 3.578A pdb=" N ALA C 87 " --> pdb=" O THR C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 Processing helix chain 'C' and resid 134 through 148 Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 23 removed outlier: 4.469A pdb=" N SER D 14 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR D 15 " --> pdb=" O GLU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 40 removed outlier: 4.047A pdb=" N TRP D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 67 removed outlier: 3.838A pdb=" N LEU D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 removed outlier: 3.745A pdb=" N TYR D 74 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 101 removed outlier: 3.814A pdb=" N SER D 90 " --> pdb=" O ASN D 86 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS D 92 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 3.557A pdb=" N TRP D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL D 119 " --> pdb=" O PHE D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 138 Processing helix chain 'D' and resid 143 through 158 Processing helix chain 'D' and resid 162 through 173 removed outlier: 3.914A pdb=" N GLU D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 192 removed outlier: 3.912A pdb=" N TRP D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 202 removed outlier: 3.674A pdb=" N SER D 200 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 202 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 Processing helix chain 'D' and resid 222 through 255 removed outlier: 3.524A pdb=" N LEU D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 290 removed outlier: 3.576A pdb=" N ILE D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR D 288 " --> pdb=" O ASP D 284 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 289 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 303 Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.613A pdb=" N ILE D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 341 removed outlier: 3.688A pdb=" N LEU D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 358 removed outlier: 3.647A pdb=" N SER D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 375 removed outlier: 3.577A pdb=" N LEU D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 369 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 370 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 382 Processing helix chain 'D' and resid 384 through 403 removed outlier: 3.951A pdb=" N PHE D 388 " --> pdb=" O ASP D 384 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP D 390 " --> pdb=" O GLU D 386 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE D 394 " --> pdb=" O ASP D 390 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR D 403 " --> pdb=" O GLN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 429 removed outlier: 4.063A pdb=" N LYS D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 427 " --> pdb=" O LYS D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 443 Processing helix chain 'D' and resid 450 through 460 Processing helix chain 'D' and resid 460 through 468 Processing helix chain 'D' and resid 469 through 475 Processing helix chain 'D' and resid 475 through 488 removed outlier: 3.933A pdb=" N TRP D 479 " --> pdb=" O ASN D 475 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE D 486 " --> pdb=" O TYR D 482 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 488 " --> pdb=" O ARG D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 505 Processing helix chain 'D' and resid 506 through 509 removed outlier: 3.698A pdb=" N ILE D 509 " --> pdb=" O TRP D 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 506 through 509' Processing helix chain 'D' and resid 510 through 512 No H-bonds generated for 'chain 'D' and resid 510 through 512' Processing helix chain 'D' and resid 513 through 529 Proline residue: D 519 - end of helix removed outlier: 3.940A pdb=" N GLU D 523 " --> pdb=" O PRO D 519 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE D 524 " --> pdb=" O SER D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 3.673A pdb=" N LEU D 536 " --> pdb=" O GLU D 532 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 63 removed outlier: 3.595A pdb=" N LEU E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 84 Processing helix chain 'E' and resid 87 through 101 removed outlier: 4.100A pdb=" N SER E 93 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE E 94 " --> pdb=" O PRO E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 118 removed outlier: 3.509A pdb=" N TYR E 109 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Proline residue: E 110 - end of helix removed outlier: 3.500A pdb=" N PHE E 113 " --> pdb=" O TYR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 138 through 152 Proline residue: E 144 - end of helix Processing helix chain 'E' and resid 160 through 174 removed outlier: 3.692A pdb=" N GLU E 164 " --> pdb=" O ASN E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 190 Proline residue: E 187 - end of helix removed outlier: 3.579A pdb=" N ASP E 190 " --> pdb=" O HIS E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 206 removed outlier: 3.732A pdb=" N GLN E 206 " --> pdb=" O TRP E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 240 removed outlier: 3.905A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 252 removed outlier: 3.753A pdb=" N THR E 251 " --> pdb=" O ARG E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 265 Processing helix chain 'E' and resid 270 through 285 removed outlier: 3.766A pdb=" N LEU E 285 " --> pdb=" O TRP E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 304 removed outlier: 3.576A pdb=" N TRP E 293 " --> pdb=" O HIS E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 321 removed outlier: 3.974A pdb=" N VAL E 310 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 339 Processing helix chain 'E' and resid 340 through 342 No H-bonds generated for 'chain 'E' and resid 340 through 342' Processing helix chain 'E' and resid 344 through 362 removed outlier: 3.541A pdb=" N ASN E 348 " --> pdb=" O ASN E 344 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN E 349 " --> pdb=" O THR E 345 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE E 361 " --> pdb=" O ARG E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 380 Processing helix chain 'E' and resid 388 through 412 removed outlier: 3.578A pdb=" N ILE E 392 " --> pdb=" O SER E 388 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN E 412 " --> pdb=" O THR E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 425 removed outlier: 3.777A pdb=" N THR E 423 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 444 removed outlier: 3.939A pdb=" N VAL E 433 " --> pdb=" O ASN E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 459 Processing helix chain 'E' and resid 467 through 481 removed outlier: 3.553A pdb=" N TRP E 471 " --> pdb=" O SER E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 492 Processing helix chain 'E' and resid 501 through 520 removed outlier: 3.598A pdb=" N THR E 518 " --> pdb=" O THR E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 529 removed outlier: 3.790A pdb=" N SER E 527 " --> pdb=" O VAL E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 544 Processing helix chain 'E' and resid 561 through 565 removed outlier: 3.795A pdb=" N LYS E 564 " --> pdb=" O ASP E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 625 removed outlier: 3.544A pdb=" N GLU E 622 " --> pdb=" O ASP E 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 184 Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.528A pdb=" N GLU F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 334 removed outlier: 3.578A pdb=" N TYR F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE F 333 " --> pdb=" O LEU F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 368 Processing helix chain 'F' and resid 386 through 398 Processing helix chain 'F' and resid 500 through 519 removed outlier: 3.880A pdb=" N ASN F 504 " --> pdb=" O GLU F 500 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN F 518 " --> pdb=" O GLU F 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 57 removed outlier: 3.507A pdb=" N ASN G 50 " --> pdb=" O ASP G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 93 removed outlier: 3.906A pdb=" N PHE G 82 " --> pdb=" O ASP G 78 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS G 85 " --> pdb=" O GLN G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 142 removed outlier: 4.122A pdb=" N LYS G 137 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU G 139 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N TRP G 140 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 222 removed outlier: 4.026A pdb=" N GLN G 221 " --> pdb=" O ASN G 217 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL G 222 " --> pdb=" O PHE G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 251 Processing helix chain 'G' and resid 262 through 270 removed outlier: 4.059A pdb=" N SER G 268 " --> pdb=" O LYS G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 293 Processing helix chain 'H' and resid 8 through 14 removed outlier: 3.649A pdb=" N TYR H 12 " --> pdb=" O SER H 8 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER H 14 " --> pdb=" O GLN H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 41 Processing helix chain 'H' and resid 43 through 52 Processing helix chain 'H' and resid 1268 through 1272 removed outlier: 3.969A pdb=" N UNK H1271 " --> pdb=" O UNK H1268 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N UNK H1272 " --> pdb=" O UNK H1269 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1268 through 1272' Processing helix chain 'H' and resid 1277 through 1314 removed outlier: 3.715A pdb=" N UNK H1281 " --> pdb=" O UNK H1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 19 removed outlier: 3.555A pdb=" N GLU I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 51 Processing helix chain 'I' and resid 73 through 86 Processing helix chain 'I' and resid 90 through 124 removed outlier: 3.792A pdb=" N GLU I 94 " --> pdb=" O PHE I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 138 Processing helix chain 'I' and resid 173 through 196 removed outlier: 3.512A pdb=" N GLN I 196 " --> pdb=" O GLN I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 222 removed outlier: 3.657A pdb=" N LEU I 217 " --> pdb=" O THR I 213 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU I 222 " --> pdb=" O ALA I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 244 Processing helix chain 'J' and resid 356 through 369 Processing helix chain 'J' and resid 378 through 387 Proline residue: J 384 - end of helix Processing helix chain 'J' and resid 389 through 397 removed outlier: 3.672A pdb=" N LEU J 393 " --> pdb=" O ASP J 389 " (cutoff:3.500A) Processing helix chain 'J' and resid 399 through 431 Processing helix chain 'J' and resid 441 through 443 No H-bonds generated for 'chain 'J' and resid 441 through 443' Processing helix chain 'J' and resid 444 through 454 Processing helix chain 'J' and resid 463 through 508 removed outlier: 4.118A pdb=" N ILE J 467 " --> pdb=" O ASP J 463 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER J 468 " --> pdb=" O LYS J 464 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU J 469 " --> pdb=" O GLU J 465 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE J 492 " --> pdb=" O ASN J 488 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU J 493 " --> pdb=" O GLU J 489 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN J 495 " --> pdb=" O ARG J 491 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS J 496 " --> pdb=" O ILE J 492 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS J 498 " --> pdb=" O GLU J 494 " (cutoff:3.500A) Processing helix chain 'J' and resid 518 through 527 removed outlier: 3.759A pdb=" N GLU J 525 " --> pdb=" O LEU J 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 548 Processing helix chain 'K' and resid 56 through 62 removed outlier: 3.812A pdb=" N ASP K 59 " --> pdb=" O THR K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 131 Processing helix chain 'L' and resid 3 through 8 removed outlier: 3.622A pdb=" N LEU L 7 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 68 Processing helix chain 'L' and resid 102 through 107 Processing helix chain 'L' and resid 109 through 118 Processing helix chain 'M' and resid 3 through 8 removed outlier: 3.909A pdb=" N ARG M 8 " --> pdb=" O GLN M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 13 removed outlier: 3.658A pdb=" N LEU M 13 " --> pdb=" O LYS M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 28 Processing helix chain 'M' and resid 31 through 40 Processing helix chain 'N' and resid 4 through 14 removed outlier: 4.627A pdb=" N VAL N 8 " --> pdb=" O ASN N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 67 No H-bonds generated for 'chain 'N' and resid 65 through 67' Processing helix chain 'N' and resid 76 through 85 Proline residue: N 82 - end of helix Processing helix chain 'O' and resid 12 through 23 Processing helix chain 'P' and resid 14 through 22 Processing helix chain 'X' and resid 38 through 44 Processing helix chain 'X' and resid 52 through 68 Processing helix chain 'X' and resid 74 through 86 removed outlier: 3.614A pdb=" N SER X 80 " --> pdb=" O ASN X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 89 through 91 No H-bonds generated for 'chain 'X' and resid 89 through 91' Processing helix chain 'X' and resid 92 through 107 removed outlier: 3.549A pdb=" N LEU X 99 " --> pdb=" O ALA X 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 107 through 128 Processing helix chain 'X' and resid 129 through 131 No H-bonds generated for 'chain 'X' and resid 129 through 131' Processing helix chain 'X' and resid 132 through 137 Processing helix chain 'X' and resid 144 through 157 Processing helix chain 'X' and resid 162 through 175 Processing helix chain 'X' and resid 188 through 203 removed outlier: 3.541A pdb=" N THR X 199 " --> pdb=" O ILE X 195 " (cutoff:3.500A) Processing helix chain 'X' and resid 212 through 234 removed outlier: 4.007A pdb=" N LEU X 232 " --> pdb=" O GLU X 228 " (cutoff:3.500A) Processing helix chain 'X' and resid 235 through 242 removed outlier: 3.949A pdb=" N ASN X 239 " --> pdb=" O THR X 235 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU X 240 " --> pdb=" O THR X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 269 removed outlier: 3.631A pdb=" N LEU X 260 " --> pdb=" O VAL X 256 " (cutoff:3.500A) Proline residue: X 261 - end of helix Processing helix chain 'X' and resid 294 through 299 removed outlier: 3.525A pdb=" N THR X 299 " --> pdb=" O ASN X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 349 through 367 removed outlier: 3.511A pdb=" N SER X 365 " --> pdb=" O ASP X 361 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU X 366 " --> pdb=" O LEU X 362 " (cutoff:3.500A) Processing helix chain 'X' and resid 369 through 378 removed outlier: 3.723A pdb=" N ARG X 375 " --> pdb=" O LYS X 371 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN X 376 " --> pdb=" O GLU X 372 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE X 378 " --> pdb=" O ALA X 374 " (cutoff:3.500A) Processing helix chain 'X' and resid 413 through 427 removed outlier: 3.874A pdb=" N LEU X 417 " --> pdb=" O LYS X 413 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE X 419 " --> pdb=" O GLU X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 435 through 449 removed outlier: 3.773A pdb=" N PHE X 439 " --> pdb=" O PRO X 435 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR X 440 " --> pdb=" O PHE X 436 " (cutoff:3.500A) Processing helix chain 'X' and resid 453 through 468 Processing helix chain 'X' and resid 469 through 472 Processing helix chain 'X' and resid 473 through 489 Processing helix chain 'X' and resid 496 through 499 Processing helix chain 'X' and resid 500 through 505 removed outlier: 3.507A pdb=" N SER X 504 " --> pdb=" O TRP X 500 " (cutoff:3.500A) Processing helix chain 'X' and resid 513 through 531 removed outlier: 3.504A pdb=" N LEU X 529 " --> pdb=" O LYS X 525 " (cutoff:3.500A) Processing helix chain 'X' and resid 532 through 540 removed outlier: 3.534A pdb=" N VAL X 536 " --> pdb=" O ASN X 532 " (cutoff:3.500A) Processing helix chain 'X' and resid 543 through 548 removed outlier: 3.541A pdb=" N LYS X 546 " --> pdb=" O GLU X 543 " (cutoff:3.500A) Processing helix chain 'X' and resid 563 through 568 Processing helix chain 'X' and resid 590 through 600 Processing helix chain 'X' and resid 606 through 623 removed outlier: 3.606A pdb=" N ILE X 616 " --> pdb=" O GLU X 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU X 617 " --> pdb=" O LEU X 613 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU X 623 " --> pdb=" O GLU X 619 " (cutoff:3.500A) Processing helix chain 'X' and resid 632 through 647 Processing helix chain 'X' and resid 650 through 661 Processing helix chain 'X' and resid 661 through 668 Processing helix chain 'X' and resid 675 through 691 removed outlier: 3.870A pdb=" N LYS X 679 " --> pdb=" O ASP X 675 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE X 682 " --> pdb=" O THR X 678 " (cutoff:3.500A) Processing helix chain 'X' and resid 694 through 708 removed outlier: 3.538A pdb=" N LEU X 700 " --> pdb=" O GLN X 696 " (cutoff:3.500A) Processing helix chain 'X' and resid 712 through 720 Processing helix chain 'X' and resid 724 through 728 removed outlier: 3.953A pdb=" N LYS X 727 " --> pdb=" O THR X 724 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN X 728 " --> pdb=" O GLY X 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 724 through 728' Processing helix chain 'X' and resid 733 through 764 Processing helix chain 'X' and resid 771 through 781 Processing helix chain 'X' and resid 811 through 821 Processing helix chain 'X' and resid 823 through 830 Processing helix chain 'X' and resid 830 through 836 Processing helix chain 'X' and resid 848 through 860 removed outlier: 3.952A pdb=" N TRP X 854 " --> pdb=" O THR X 850 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE X 855 " --> pdb=" O ILE X 851 " (cutoff:3.500A) Processing helix chain 'Y' and resid 34 through 40 Processing helix chain 'Y' and resid 58 through 67 Processing helix chain 'Y' and resid 68 through 70 No H-bonds generated for 'chain 'Y' and resid 68 through 70' Processing helix chain 'Y' and resid 96 through 107 Processing helix chain 'Y' and resid 150 through 153 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 140 removed outlier: 6.644A pdb=" N VAL A 154 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE A 136 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE A 152 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE A 138 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N TYR A 150 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS A 140 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LYS A 148 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 176 Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.891A pdb=" N TYR B 4 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER B 11 " --> pdb=" O CYS B 6 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AA5, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'E' and resid 576 through 577 Processing sheet with id=AA8, first strand: chain 'E' and resid 582 through 583 Processing sheet with id=AA9, first strand: chain 'F' and resid 163 through 167 removed outlier: 4.920A pdb=" N TYR F 207 " --> pdb=" O VAL F 196 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AB2, first strand: chain 'F' and resid 339 through 341 removed outlier: 3.627A pdb=" N TYR F 341 " --> pdb=" O GLN F 354 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 444 through 446 Processing sheet with id=AB4, first strand: chain 'G' and resid 69 through 76 removed outlier: 3.527A pdb=" N THR G 76 " --> pdb=" O MET G 111 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET G 111 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 157 through 164 removed outlier: 5.841A pdb=" N LEU G 157 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY G 159 " --> pdb=" O VAL G 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 167 through 168 Processing sheet with id=AB7, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AB8, first strand: chain 'I' and resid 199 through 200 Processing sheet with id=AB9, first strand: chain 'K' and resid 80 through 81 removed outlier: 3.507A pdb=" N ILE K 31 " --> pdb=" O ILE K 49 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG K 21 " --> pdb=" O VAL K 97 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL K 97 " --> pdb=" O ARG K 21 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU K 23 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N THR K 95 " --> pdb=" O LEU K 23 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL K 97 " --> pdb=" O TYR L 84 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N TYR L 84 " --> pdb=" O VAL K 97 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR L 41 " --> pdb=" O TYR L 84 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN L 86 " --> pdb=" O ILE L 39 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE L 39 " --> pdb=" O ASN L 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 80 through 81 removed outlier: 3.507A pdb=" N ILE K 31 " --> pdb=" O ILE K 49 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL K 44 " --> pdb=" O MET K 35 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU N 22 " --> pdb=" O LYS N 70 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE N 72 " --> pdb=" O SER N 20 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N SER N 20 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 24 through 28 removed outlier: 6.290A pdb=" N THR L 16 " --> pdb=" O ILE L 95 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE L 95 " --> pdb=" O THR L 16 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU L 18 " --> pdb=" O ARG L 93 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN M 83 " --> pdb=" O LYS M 80 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS M 93 " --> pdb=" O GLU M 70 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU M 70 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE M 95 " --> pdb=" O VAL M 68 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL M 68 " --> pdb=" O PHE M 95 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU M 69 " --> pdb=" O LYS M 59 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS M 59 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASN M 71 " --> pdb=" O ARG M 57 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG M 57 " --> pdb=" O ASN M 71 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL M 103 " --> pdb=" O SER M 47 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU P 70 " --> pdb=" O LYS M 106 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN P 52 " --> pdb=" O SER P 44 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER P 44 " --> pdb=" O GLN P 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AC4, first strand: chain 'N' and resid 43 through 50 removed outlier: 7.326A pdb=" N ASP N 60 " --> pdb=" O ASP N 46 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE N 48 " --> pdb=" O HIS N 58 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N HIS N 58 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR N 50 " --> pdb=" O VAL N 56 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL N 56 " --> pdb=" O THR N 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 76 through 78 removed outlier: 6.059A pdb=" N ALA O 57 " --> pdb=" O LEU O 77 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS P 30 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE P 81 " --> pdb=" O GLY P 28 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY P 28 " --> pdb=" O ILE P 81 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLU P 83 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ARG P 26 " --> pdb=" O GLU P 83 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 76 through 78 removed outlier: 6.059A pdb=" N ALA O 57 " --> pdb=" O LEU O 77 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL O 53 " --> pdb=" O VAL O 44 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS O 42 " --> pdb=" O ASP O 55 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA O 57 " --> pdb=" O LYS O 40 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS O 40 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU O 59 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG O 38 " --> pdb=" O GLU O 59 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU O 89 " --> pdb=" O TRP O 30 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS Q 55 " --> pdb=" O GLU Q 45 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ALA Q 43 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU Q 59 " --> pdb=" O ASP Q 41 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP Q 41 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR Q 61 " --> pdb=" O VAL Q 39 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL Q 39 " --> pdb=" O THR Q 61 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL Q 39 " --> pdb=" O ARG Q 30 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA Q 43 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA Q 26 " --> pdb=" O ALA Q 43 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER Q 70 " --> pdb=" O ASN Q 18 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Y' and resid 47 through 51 removed outlier: 4.466A pdb=" N PHE Y 89 " --> pdb=" O GLY Y 78 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 148 through 149 1653 hydrogen bonds defined for protein. 4788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 428 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 179 basepair parallelities 331 stacking parallelities Total time for adding SS restraints: 11.21 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5954 1.31 - 1.44: 14259 1.44 - 1.56: 21797 1.56 - 1.69: 1158 1.69 - 1.81: 152 Bond restraints: 43320 Sorted by residual: bond pdb=" CA HIS A 99 " pdb=" C HIS A 99 " ideal model delta sigma weight residual 1.523 1.587 -0.064 1.34e-02 5.57e+03 2.28e+01 bond pdb=" CG1 ILE D 171 " pdb=" CD1 ILE D 171 " ideal model delta sigma weight residual 1.513 1.363 0.150 3.90e-02 6.57e+02 1.49e+01 bond pdb=" N SER D 266 " pdb=" CA SER D 266 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.46e+01 bond pdb=" N VAL D 445 " pdb=" CA VAL D 445 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.09e-02 8.42e+03 1.12e+01 bond pdb=" N ASN X 282 " pdb=" CA ASN X 282 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.04e+01 ... (remaining 43315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.16: 61301 5.16 - 10.33: 360 10.33 - 15.49: 13 15.49 - 20.66: 2 20.66 - 25.82: 2 Bond angle restraints: 61678 Sorted by residual: angle pdb=" N TRP X 281 " pdb=" CA TRP X 281 " pdb=" C TRP X 281 " ideal model delta sigma weight residual 110.61 121.80 -11.19 1.25e+00 6.40e-01 8.01e+01 angle pdb=" C GLU X 673 " pdb=" N LEU X 674 " pdb=" CA LEU X 674 " ideal model delta sigma weight residual 121.54 138.02 -16.48 1.91e+00 2.74e-01 7.45e+01 angle pdb=" O3' U R 442 " pdb=" P U R 443 " pdb=" OP2 U R 443 " ideal model delta sigma weight residual 108.00 82.18 25.82 3.00e+00 1.11e-01 7.41e+01 angle pdb=" O3' U R 442 " pdb=" P U R 443 " pdb=" OP1 U R 443 " ideal model delta sigma weight residual 108.00 82.20 25.80 3.00e+00 1.11e-01 7.40e+01 angle pdb=" N GLU J 528 " pdb=" CA GLU J 528 " pdb=" C GLU J 528 " ideal model delta sigma weight residual 114.75 104.43 10.32 1.26e+00 6.30e-01 6.71e+01 ... (remaining 61673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 25275 35.91 - 71.83: 1431 71.83 - 107.74: 154 107.74 - 143.66: 8 143.66 - 179.57: 14 Dihedral angle restraints: 26882 sinusoidal: 14362 harmonic: 12520 Sorted by residual: dihedral pdb=" CA ARG C 12 " pdb=" C ARG C 12 " pdb=" N PRO C 13 " pdb=" CA PRO C 13 " ideal model delta harmonic sigma weight residual 180.00 56.69 123.31 0 5.00e+00 4.00e-02 6.08e+02 dihedral pdb=" CA THR X 379 " pdb=" C THR X 379 " pdb=" N LEU X 380 " pdb=" CA LEU X 380 " ideal model delta harmonic sigma weight residual 180.00 121.71 58.29 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA LEU X 674 " pdb=" C LEU X 674 " pdb=" N ASP X 675 " pdb=" CA ASP X 675 " ideal model delta harmonic sigma weight residual 180.00 130.86 49.14 0 5.00e+00 4.00e-02 9.66e+01 ... (remaining 26879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.383: 7742 0.383 - 0.765: 6 0.765 - 1.148: 0 1.148 - 1.531: 0 1.531 - 1.914: 1 Chirality restraints: 7749 Sorted by residual: chirality pdb=" P U R 443 " pdb=" OP1 U R 443 " pdb=" OP2 U R 443 " pdb=" O5' U R 443 " both_signs ideal model delta sigma weight residual True 2.41 0.50 1.91 2.00e-01 2.50e+01 9.16e+01 chirality pdb=" CA ASP E 324 " pdb=" N ASP E 324 " pdb=" C ASP E 324 " pdb=" CB ASP E 324 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" CB VAL D 137 " pdb=" CA VAL D 137 " pdb=" CG1 VAL D 137 " pdb=" CG2 VAL D 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 7746 not shown) Planarity restraints: 5874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 12 " 1.059 9.50e-02 1.11e+02 4.74e-01 1.36e+02 pdb=" NE ARG C 12 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG C 12 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 12 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 12 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 316 " 0.039 2.00e-02 2.50e+03 3.17e-02 2.01e+01 pdb=" CG TYR D 316 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TYR D 316 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR D 316 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 316 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 316 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 316 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR D 316 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 150 " 0.033 2.00e-02 2.50e+03 2.60e-02 1.35e+01 pdb=" CG TYR D 150 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR D 150 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 150 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 150 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR D 150 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 150 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR D 150 " 0.006 2.00e-02 2.50e+03 ... (remaining 5871 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 4050 2.73 - 3.27: 38806 3.27 - 3.81: 71747 3.81 - 4.36: 82970 4.36 - 4.90: 128577 Nonbonded interactions: 326150 Sorted by model distance: nonbonded pdb=" OD1 ASN C 15 " pdb=" N LYS C 16 " model vdw 2.186 3.120 nonbonded pdb=" O2 U R 217 " pdb=" O6 G R 220 " model vdw 2.198 2.432 nonbonded pdb=" O2' U R 16 " pdb=" OP2 C R 168 " model vdw 2.234 3.040 nonbonded pdb=" OE1 GLU D 372 " pdb=" OH TYR D 391 " model vdw 2.234 3.040 nonbonded pdb=" O2' A r -2 " pdb=" OP1 G r -1 " model vdw 2.238 3.040 ... (remaining 326145 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.780 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: 0.550 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 49.490 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.011 0.348 43332 Z= 0.478 Angle : 1.179 28.878 61685 Z= 0.648 Chirality : 0.065 1.914 7749 Planarity : 0.009 0.474 5874 Dihedral : 19.809 179.569 18702 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.93 % Favored : 92.44 % Rotamer: Outliers : 3.35 % Allowed : 7.51 % Favored : 89.14 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 1.29 % Twisted General : 0.57 % 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: -3.75 (0.11), residues: 4140 helix: -2.31 (0.08), residues: 2081 sheet: -2.63 (0.27), residues: 299 loop : -2.54 (0.13), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG D 104 TYR 0.077 0.004 TYR D 316 PHE 0.053 0.004 PHE D 77 TRP 0.035 0.004 TRP E 362 HIS 0.022 0.003 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.01055 (43320) covalent geometry : angle 1.16653 (61678) hydrogen bonds : bond 0.19304 ( 2075) hydrogen bonds : angle 7.34305 ( 5532) metal coordination : bond 0.11534 ( 12) metal coordination : angle 15.96040 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 423 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6074 (tt) REVERT: B 87 MET cc_start: 0.7291 (mmt) cc_final: 0.7052 (mmm) REVERT: B 103 ASP cc_start: 0.7958 (t70) cc_final: 0.7486 (t70) REVERT: B 124 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7055 (mtt90) REVERT: B 135 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.6264 (ttpt) REVERT: C 12 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7407 (mtp180) REVERT: C 62 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8147 (tt) REVERT: C 71 SER cc_start: 0.8475 (m) cc_final: 0.8197 (t) REVERT: C 88 ASP cc_start: 0.6873 (m-30) cc_final: 0.6508 (p0) REVERT: D 367 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8941 (tt) REVERT: D 411 GLN cc_start: 0.7612 (mt0) cc_final: 0.7311 (mt0) REVERT: D 446 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7478 (mt0) REVERT: D 477 MET cc_start: 0.8092 (tpt) cc_final: 0.7698 (tpp) REVERT: E 315 GLN cc_start: 0.7527 (mm110) cc_final: 0.7262 (tm-30) REVERT: E 454 TYR cc_start: 0.8630 (m-80) cc_final: 0.8381 (m-80) REVERT: E 507 ASP cc_start: 0.7240 (m-30) cc_final: 0.6987 (m-30) REVERT: F 317 ILE cc_start: 0.8917 (tt) cc_final: 0.8571 (mt) REVERT: F 332 TYR cc_start: 0.9008 (m-80) cc_final: 0.8724 (m-80) REVERT: F 368 MET cc_start: 0.8535 (tpp) cc_final: 0.7803 (tpp) REVERT: F 410 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8805 (tt) REVERT: G 89 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8025 (tm) REVERT: I 10 GLU cc_start: 0.7945 (tp30) cc_final: 0.7554 (tp30) REVERT: I 78 ILE cc_start: 0.7914 (pt) cc_final: 0.7646 (tp) REVERT: I 210 ARG cc_start: 0.8141 (ttp-110) cc_final: 0.7229 (tpm170) REVERT: I 238 ARG cc_start: 0.7657 (tpp80) cc_final: 0.7392 (ttp80) REVERT: I 240 MET cc_start: 0.6449 (mmp) cc_final: 0.6072 (mmp) REVERT: K 127 LYS cc_start: 0.7756 (ttpt) cc_final: 0.6977 (tmtt) REVERT: K 128 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6493 (tt0) REVERT: L 109 ASP cc_start: 0.7942 (t0) cc_final: 0.7699 (t0) REVERT: M 18 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8500 (mm) REVERT: M 39 VAL cc_start: 0.9182 (t) cc_final: 0.8949 (m) REVERT: Q 6 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7919 (mt-10) REVERT: Q 45 GLU cc_start: 0.8253 (tt0) cc_final: 0.8019 (tt0) outliers start: 78 outliers final: 43 residues processed: 492 average time/residue: 0.2530 time to fit residues: 203.4699 Evaluate side-chains 331 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 278 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 263 TYR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 446 GLN Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 HIS Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 63 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 40.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 470 optimal weight: 5.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN B 40 ASN B 47 ASN B 80 ASN D 9 HIS D 72 ASN D 102 ASN D 153 GLN D 298 ASN D 393 GLN D 411 GLN D 417 ASN D 443 ASN E 348 ASN E 349 ASN E 352 ASN E 409 ASN E 488 ASN E 582 GLN E 617 ASN F 301 GLN F 311 ASN F 312 ASN F 334 GLN F 375 ASN F 411 GLN F 497 GLN F 515 GLN ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 HIS I 118 ASN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN L 114 ASN M 51 ASN M 86 ASN N 17 HIS N 41 ASN O 15 ASN O 24 GLN P 24 ASN P 47 ASN P 50 ASN P 65 HIS Q 66 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.179069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129590 restraints weight = 79951.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123414 restraints weight = 106708.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116571 restraints weight = 67759.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116347 restraints weight = 80927.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116378 restraints weight = 69986.972| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 43332 Z= 0.204 Angle : 0.699 26.158 61685 Z= 0.365 Chirality : 0.046 1.872 7749 Planarity : 0.005 0.082 5874 Dihedral : 20.843 176.570 13555 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.89 % Favored : 93.82 % Rotamer: Outliers : 5.20 % Allowed : 10.86 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 1.29 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.12), residues: 4140 helix: -0.33 (0.11), residues: 2141 sheet: -2.19 (0.27), residues: 323 loop : -2.03 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 14 TYR 0.035 0.002 TYR D 316 PHE 0.027 0.002 PHE O 32 TRP 0.019 0.002 TRP G 48 HIS 0.009 0.002 HIS H 45 Details of bonding type rmsd covalent geometry : bond 0.00457 (43320) covalent geometry : angle 0.69857 (61678) hydrogen bonds : bond 0.05072 ( 2075) hydrogen bonds : angle 4.58779 ( 5532) metal coordination : bond 0.01406 ( 12) metal coordination : angle 3.35025 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 325 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: B 87 MET cc_start: 0.7428 (mmt) cc_final: 0.7118 (mmm) REVERT: B 103 ASP cc_start: 0.8022 (t70) cc_final: 0.7416 (t70) REVERT: C 71 SER cc_start: 0.8861 (m) cc_final: 0.8380 (t) REVERT: C 78 PHE cc_start: 0.7374 (m-80) cc_final: 0.6727 (m-80) REVERT: C 84 GLN cc_start: 0.7672 (mm110) cc_final: 0.7257 (tp-100) REVERT: C 88 ASP cc_start: 0.6733 (m-30) cc_final: 0.6337 (p0) REVERT: D 7 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7982 (tp) REVERT: D 89 MET cc_start: 0.8479 (tpp) cc_final: 0.8278 (tpp) REVERT: D 194 MET cc_start: 0.7357 (mmt) cc_final: 0.6906 (mmt) REVERT: D 446 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7783 (mt0) REVERT: D 477 MET cc_start: 0.8117 (tpt) cc_final: 0.7689 (tpp) REVERT: E 507 ASP cc_start: 0.7502 (m-30) cc_final: 0.7090 (m-30) REVERT: E 517 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8772 (mm) REVERT: F 332 TYR cc_start: 0.9052 (m-80) cc_final: 0.8742 (m-80) REVERT: F 341 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8713 (p90) REVERT: F 368 MET cc_start: 0.8677 (tpp) cc_final: 0.7941 (tpp) REVERT: F 446 TYR cc_start: 0.9105 (m-80) cc_final: 0.8861 (m-80) REVERT: G 246 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8742 (mm) REVERT: G 248 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8467 (tt) REVERT: I 10 GLU cc_start: 0.8200 (tp30) cc_final: 0.7659 (tp30) REVERT: I 78 ILE cc_start: 0.7877 (pt) cc_final: 0.7589 (tp) REVERT: I 104 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7713 (t80) REVERT: I 210 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7225 (tpm170) REVERT: I 238 ARG cc_start: 0.7751 (tpp80) cc_final: 0.7380 (ttp80) REVERT: K 19 LYS cc_start: 0.8669 (tttp) cc_final: 0.8392 (ttmt) REVERT: K 107 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7477 (mt-10) REVERT: K 127 LYS cc_start: 0.7603 (ttpt) cc_final: 0.6896 (tmtt) REVERT: M 39 VAL cc_start: 0.9163 (t) cc_final: 0.8831 (m) REVERT: N 46 ASP cc_start: 0.8212 (t70) cc_final: 0.7874 (t70) REVERT: Q 45 GLU cc_start: 0.8010 (tt0) cc_final: 0.7803 (tt0) outliers start: 121 outliers final: 63 residues processed: 420 average time/residue: 0.2290 time to fit residues: 162.3774 Evaluate side-chains 342 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 272 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 446 GLN Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 63 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 468 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 396 optimal weight: 8.9990 chunk 450 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 409 optimal weight: 8.9990 chunk 385 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 ASN D 400 ASN E 563 HIS F 306 HIS F 334 GLN G 90 HIS G 200 GLN G 292 ASN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN L 21 ASN M 52 HIS O 22 GLN O 86 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.174979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.133243 restraints weight = 79677.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126608 restraints weight = 147766.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122080 restraints weight = 143721.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122221 restraints weight = 127149.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121749 restraints weight = 95114.738| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.123 43332 Z= 0.410 Angle : 0.847 26.275 61685 Z= 0.436 Chirality : 0.052 1.880 7749 Planarity : 0.006 0.084 5874 Dihedral : 20.846 175.079 13499 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.29 % Favored : 92.44 % Rotamer: Outliers : 6.14 % Allowed : 13.44 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 1.29 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.13), residues: 4140 helix: 0.16 (0.11), residues: 2164 sheet: -2.17 (0.27), residues: 320 loop : -2.12 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 104 TYR 0.045 0.003 TYR D 150 PHE 0.033 0.003 PHE D 397 TRP 0.024 0.003 TRP D 186 HIS 0.012 0.002 HIS Q 55 Details of bonding type rmsd covalent geometry : bond 0.00958 (43320) covalent geometry : angle 0.84615 (61678) hydrogen bonds : bond 0.05952 ( 2075) hydrogen bonds : angle 4.67428 ( 5532) metal coordination : bond 0.01518 ( 12) metal coordination : angle 3.68641 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 259 time to evaluate : 1.225 Fit side-chains REVERT: B 82 GLU cc_start: 0.8006 (mp0) cc_final: 0.7785 (mp0) REVERT: B 87 MET cc_start: 0.7544 (mmt) cc_final: 0.7283 (mmm) REVERT: B 103 ASP cc_start: 0.8176 (t70) cc_final: 0.7526 (t70) REVERT: B 138 GLN cc_start: 0.8130 (pm20) cc_final: 0.7604 (pm20) REVERT: C 71 SER cc_start: 0.8955 (m) cc_final: 0.8529 (t) REVERT: C 85 GLU cc_start: 0.6362 (tp30) cc_final: 0.6080 (tp30) REVERT: D 446 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7519 (mt0) REVERT: D 495 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9131 (mm) REVERT: F 332 TYR cc_start: 0.9057 (m-80) cc_final: 0.8753 (m-80) REVERT: F 341 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8719 (p90) REVERT: F 368 MET cc_start: 0.9033 (tpp) cc_final: 0.7893 (tpt) REVERT: G 260 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8413 (pp) REVERT: I 10 GLU cc_start: 0.8216 (tp30) cc_final: 0.7579 (tp30) REVERT: I 104 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7706 (t80) REVERT: I 210 ARG cc_start: 0.7961 (ttp-110) cc_final: 0.7144 (tpm170) REVERT: I 238 ARG cc_start: 0.7862 (tpp80) cc_final: 0.7560 (ttp80) REVERT: K 78 GLU cc_start: 0.8360 (mp0) cc_final: 0.8147 (mp0) REVERT: K 82 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8400 (mt) REVERT: K 104 SER cc_start: 0.8545 (m) cc_final: 0.7794 (p) REVERT: K 107 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7125 (mt-10) REVERT: K 109 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8523 (mm) REVERT: P 82 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8504 (ptm-80) REVERT: Q 40 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9055 (pp) REVERT: Q 45 GLU cc_start: 0.8356 (tt0) cc_final: 0.8001 (tt0) outliers start: 143 outliers final: 99 residues processed: 373 average time/residue: 0.2244 time to fit residues: 143.5799 Evaluate side-chains 355 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 247 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 446 GLN Chi-restraints excluded: chain D residue 448 TYR Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain H residue 3 ASP Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 63 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 312 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 437 optimal weight: 50.0000 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 186 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN E 563 HIS F 334 GLN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.179266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.131614 restraints weight = 79547.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.122260 restraints weight = 108809.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118344 restraints weight = 89115.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.117974 restraints weight = 80674.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118125 restraints weight = 68217.863| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 43332 Z= 0.141 Angle : 0.611 26.328 61685 Z= 0.316 Chirality : 0.044 1.868 7749 Planarity : 0.004 0.069 5874 Dihedral : 20.593 176.329 13491 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.48 % Favored : 94.37 % Rotamer: Outliers : 4.85 % Allowed : 15.33 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 1.29 % Twisted General : 0.12 % 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: -0.59 (0.13), residues: 4140 helix: 0.90 (0.11), residues: 2157 sheet: -1.81 (0.28), residues: 332 loop : -1.83 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 51 TYR 0.021 0.001 TYR B 8 PHE 0.020 0.001 PHE O 32 TRP 0.015 0.002 TRP G 48 HIS 0.005 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00310 (43320) covalent geometry : angle 0.61072 (61678) hydrogen bonds : bond 0.04169 ( 2075) hydrogen bonds : angle 4.06716 ( 5532) metal coordination : bond 0.01188 ( 12) metal coordination : angle 2.34398 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 301 time to evaluate : 1.298 Fit side-chains REVERT: A 74 ILE cc_start: 0.7859 (tt) cc_final: 0.7528 (mm) REVERT: B 87 MET cc_start: 0.7396 (mmt) cc_final: 0.7145 (mmm) REVERT: B 103 ASP cc_start: 0.7822 (t70) cc_final: 0.7233 (t70) REVERT: B 138 GLN cc_start: 0.8129 (pm20) cc_final: 0.7705 (pm20) REVERT: C 71 SER cc_start: 0.8912 (m) cc_final: 0.8446 (t) REVERT: D 303 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8789 (mp) REVERT: E 517 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8871 (mm) REVERT: F 341 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8810 (p90) REVERT: F 368 MET cc_start: 0.8774 (tpp) cc_final: 0.7609 (tpp) REVERT: F 389 THR cc_start: 0.8939 (m) cc_final: 0.8697 (m) REVERT: G 246 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8744 (mm) REVERT: G 248 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8439 (tt) REVERT: I 10 GLU cc_start: 0.8041 (tp30) cc_final: 0.7566 (tp30) REVERT: I 104 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7501 (t80) REVERT: I 210 ARG cc_start: 0.8105 (ttp-110) cc_final: 0.7006 (tpp-160) REVERT: I 227 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8182 (mm) REVERT: I 238 ARG cc_start: 0.7755 (tpp80) cc_final: 0.7332 (ttp80) REVERT: K 19 LYS cc_start: 0.8583 (tttp) cc_final: 0.8279 (ttmt) REVERT: K 64 ARG cc_start: 0.6346 (mmp80) cc_final: 0.5788 (ttt90) REVERT: K 107 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7504 (mt-10) REVERT: K 112 ASP cc_start: 0.8094 (m-30) cc_final: 0.7727 (m-30) REVERT: L 74 THR cc_start: 0.7485 (OUTLIER) cc_final: 0.7230 (p) REVERT: M 39 VAL cc_start: 0.9080 (t) cc_final: 0.8765 (m) outliers start: 113 outliers final: 67 residues processed: 392 average time/residue: 0.2266 time to fit residues: 151.7233 Evaluate side-chains 339 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 264 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 448 TYR Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 32 optimal weight: 30.0000 chunk 178 optimal weight: 4.9990 chunk 432 optimal weight: 40.0000 chunk 461 optimal weight: 10.0000 chunk 88 optimal weight: 0.0970 chunk 155 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 445 optimal weight: 1.9990 chunk 393 optimal weight: 5.9990 chunk 459 optimal weight: 50.0000 chunk 82 optimal weight: 0.4980 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN E 563 HIS F 334 GLN G 207 HIS ** I 226 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 = 0.4324 r_free = 0.4324 target = 0.176534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.129042 restraints weight = 79377.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118661 restraints weight = 120249.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114536 restraints weight = 100982.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.114047 restraints weight = 86011.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.114461 restraints weight = 70408.524| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 43332 Z= 0.271 Angle : 0.698 26.325 61685 Z= 0.359 Chirality : 0.047 1.873 7749 Planarity : 0.004 0.079 5874 Dihedral : 20.553 174.742 13477 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.64 % Favored : 93.21 % Rotamer: Outliers : 6.10 % Allowed : 15.46 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 1.29 % Twisted General : 0.10 % 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: -0.55 (0.13), residues: 4140 helix: 0.97 (0.11), residues: 2156 sheet: -1.80 (0.28), residues: 333 loop : -1.88 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 51 TYR 0.032 0.002 TYR B 8 PHE 0.025 0.002 PHE D 397 TRP 0.018 0.002 TRP D 186 HIS 0.009 0.002 HIS Q 55 Details of bonding type rmsd covalent geometry : bond 0.00632 (43320) covalent geometry : angle 0.69738 (61678) hydrogen bonds : bond 0.04834 ( 2075) hydrogen bonds : angle 4.19000 ( 5532) metal coordination : bond 0.01005 ( 12) metal coordination : angle 2.39975 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 256 time to evaluate : 1.498 Fit side-chains REVERT: B 87 MET cc_start: 0.7562 (mmt) cc_final: 0.7283 (mmm) REVERT: B 103 ASP cc_start: 0.8018 (t70) cc_final: 0.7396 (t70) REVERT: B 105 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9344 (mt) REVERT: C 71 SER cc_start: 0.8968 (m) cc_final: 0.8527 (t) REVERT: C 84 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7765 (tm-30) REVERT: C 107 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7513 (mtm180) REVERT: D 44 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8103 (tt) REVERT: D 303 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8817 (mp) REVERT: D 495 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8973 (mm) REVERT: F 341 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8938 (p90) REVERT: F 368 MET cc_start: 0.8606 (tpp) cc_final: 0.7529 (tpp) REVERT: G 122 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9001 (tt) REVERT: G 204 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7259 (ptpp) REVERT: G 260 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8538 (pp) REVERT: I 10 GLU cc_start: 0.8225 (tp30) cc_final: 0.7798 (tp30) REVERT: I 104 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7463 (t80) REVERT: I 210 ARG cc_start: 0.7959 (ttp-110) cc_final: 0.6981 (tpm170) REVERT: I 238 ARG cc_start: 0.7897 (tpp80) cc_final: 0.7528 (ttp80) REVERT: K 64 ARG cc_start: 0.6552 (mmp80) cc_final: 0.6149 (ttt90) REVERT: K 82 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8544 (mt) REVERT: K 107 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7598 (mt-10) REVERT: K 112 ASP cc_start: 0.8065 (m-30) cc_final: 0.7848 (m-30) REVERT: L 74 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.7108 (p) REVERT: N 33 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8968 (tp) REVERT: P 82 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8364 (ptm-80) REVERT: Q 11 MET cc_start: 0.8689 (mmm) cc_final: 0.8191 (mmm) REVERT: Q 40 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8979 (pp) outliers start: 142 outliers final: 94 residues processed: 374 average time/residue: 0.2278 time to fit residues: 145.4055 Evaluate side-chains 358 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 249 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 448 TYR Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 372 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 250 optimal weight: 7.9990 chunk 414 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 360 optimal weight: 40.0000 chunk 80 optimal weight: 0.5980 chunk 328 optimal weight: 4.9990 chunk 362 optimal weight: 20.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 ASN E 563 HIS H 10 GLN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.175028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.133577 restraints weight = 79825.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.126837 restraints weight = 145352.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122634 restraints weight = 134585.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.122567 restraints weight = 124809.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122430 restraints weight = 90845.976| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 43332 Z= 0.337 Angle : 0.767 26.162 61685 Z= 0.393 Chirality : 0.050 1.882 7749 Planarity : 0.005 0.079 5874 Dihedral : 20.636 176.445 13475 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.25 % Favored : 92.63 % Rotamer: Outliers : 7.08 % Allowed : 16.62 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 0.65 % Twisted General : 0.10 % 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: -0.75 (0.13), residues: 4140 helix: 0.80 (0.11), residues: 2163 sheet: -1.86 (0.29), residues: 295 loop : -1.99 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 51 TYR 0.035 0.003 TYR B 8 PHE 0.026 0.002 PHE D 397 TRP 0.020 0.002 TRP D 186 HIS 0.014 0.002 HIS G 207 Details of bonding type rmsd covalent geometry : bond 0.00785 (43320) covalent geometry : angle 0.76642 (61678) hydrogen bonds : bond 0.05377 ( 2075) hydrogen bonds : angle 4.40442 ( 5532) metal coordination : bond 0.01133 ( 12) metal coordination : angle 2.44746 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 249 time to evaluate : 1.264 Fit side-chains REVERT: B 87 MET cc_start: 0.7677 (mmt) cc_final: 0.7303 (mmm) REVERT: B 103 ASP cc_start: 0.7959 (t70) cc_final: 0.7295 (t70) REVERT: C 71 SER cc_start: 0.8716 (m) cc_final: 0.8361 (t) REVERT: C 84 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7655 (tm-30) REVERT: D 44 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8058 (tt) REVERT: D 258 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8973 (mmtp) REVERT: D 303 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8849 (mp) REVERT: D 495 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9082 (mm) REVERT: E 472 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8870 (tt) REVERT: E 517 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8914 (mm) REVERT: E 613 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: F 332 TYR cc_start: 0.9041 (m-80) cc_final: 0.8592 (m-80) REVERT: F 368 MET cc_start: 0.8759 (tpp) cc_final: 0.7586 (tpp) REVERT: G 63 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: G 122 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9024 (tt) REVERT: G 204 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7306 (ptpp) REVERT: I 10 GLU cc_start: 0.8187 (tp30) cc_final: 0.7537 (tp30) REVERT: I 104 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7506 (t80) REVERT: I 238 ARG cc_start: 0.7902 (tpp80) cc_final: 0.7676 (ttp80) REVERT: K 82 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8449 (mt) REVERT: K 107 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7578 (mt-10) REVERT: L 74 THR cc_start: 0.7397 (OUTLIER) cc_final: 0.7109 (p) REVERT: M 39 VAL cc_start: 0.9264 (t) cc_final: 0.8888 (m) REVERT: N 35 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7727 (mm-30) REVERT: P 82 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8458 (ptm-80) REVERT: Q 40 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9018 (pp) outliers start: 165 outliers final: 119 residues processed: 384 average time/residue: 0.2244 time to fit residues: 147.8472 Evaluate side-chains 371 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 237 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 448 TYR Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 613 GLN Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 63 GLN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain H residue 3 ASP Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 232 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 114 optimal weight: 30.0000 chunk 323 optimal weight: 10.0000 chunk 424 optimal weight: 20.0000 chunk 375 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 333 optimal weight: 4.9990 chunk 368 optimal weight: 40.0000 chunk 301 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 HIS E 563 HIS ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS K 120 GLN Q 20 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.176126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134732 restraints weight = 79739.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.128990 restraints weight = 150297.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.124489 restraints weight = 133636.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124092 restraints weight = 127055.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124109 restraints weight = 93998.375| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 43332 Z= 0.255 Angle : 0.681 26.185 61685 Z= 0.350 Chirality : 0.047 1.877 7749 Planarity : 0.004 0.078 5874 Dihedral : 20.536 174.836 13473 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.59 % Favored : 93.29 % Rotamer: Outliers : 6.48 % Allowed : 17.17 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 0.65 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 4140 helix: 1.04 (0.12), residues: 2150 sheet: -1.88 (0.28), residues: 321 loop : -1.90 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 51 TYR 0.026 0.002 TYR B 8 PHE 0.019 0.002 PHE O 32 TRP 0.020 0.002 TRP D 186 HIS 0.008 0.001 HIS Q 55 Details of bonding type rmsd covalent geometry : bond 0.00593 (43320) covalent geometry : angle 0.68090 (61678) hydrogen bonds : bond 0.04737 ( 2075) hydrogen bonds : angle 4.20612 ( 5532) metal coordination : bond 0.00940 ( 12) metal coordination : angle 1.87550 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 254 time to evaluate : 1.230 Fit side-chains REVERT: B 82 GLU cc_start: 0.8028 (mp0) cc_final: 0.7813 (mp0) REVERT: B 87 MET cc_start: 0.7588 (mmt) cc_final: 0.7243 (mmm) REVERT: B 103 ASP cc_start: 0.8067 (t70) cc_final: 0.7383 (t70) REVERT: B 105 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9383 (mt) REVERT: C 71 SER cc_start: 0.8654 (m) cc_final: 0.8311 (t) REVERT: D 44 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8035 (tt) REVERT: D 303 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8860 (mp) REVERT: D 326 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7912 (t0) REVERT: D 495 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9026 (mm) REVERT: F 332 TYR cc_start: 0.9045 (m-80) cc_final: 0.8679 (m-80) REVERT: F 368 MET cc_start: 0.9014 (tpp) cc_final: 0.7869 (tpp) REVERT: F 410 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8977 (tt) REVERT: G 54 ILE cc_start: 0.8725 (tp) cc_final: 0.8390 (tp) REVERT: G 122 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9033 (tt) REVERT: G 204 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7263 (ptpp) REVERT: G 260 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8477 (pp) REVERT: I 10 GLU cc_start: 0.8110 (tp30) cc_final: 0.7718 (tp30) REVERT: I 80 TYR cc_start: 0.8309 (t80) cc_final: 0.7661 (t80) REVERT: I 104 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7345 (t80) REVERT: I 120 LYS cc_start: 0.5724 (mtpp) cc_final: 0.5502 (pttp) REVERT: I 227 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8487 (mm) REVERT: I 238 ARG cc_start: 0.7916 (tpp80) cc_final: 0.7673 (ttp80) REVERT: K 82 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8506 (mt) REVERT: K 107 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7585 (mt-10) REVERT: L 74 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.7071 (p) REVERT: N 35 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7665 (mm-30) REVERT: P 82 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8457 (ptm-80) REVERT: Q 11 MET cc_start: 0.8718 (mmm) cc_final: 0.8247 (mmm) REVERT: Q 40 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9038 (pp) REVERT: Q 55 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7155 (p90) outliers start: 151 outliers final: 115 residues processed: 381 average time/residue: 0.2258 time to fit residues: 147.3991 Evaluate side-chains 371 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 240 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 448 TYR Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 88 ARG Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 55 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 105 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 300 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 10 optimal weight: 50.0000 chunk 158 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 chunk 210 optimal weight: 0.5980 chunk 213 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 389 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 563 HIS ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.178513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136686 restraints weight = 79915.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.131091 restraints weight = 145525.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125123 restraints weight = 120904.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.124770 restraints weight = 112648.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.124627 restraints weight = 87721.803| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 43332 Z= 0.144 Angle : 0.593 26.245 61685 Z= 0.304 Chirality : 0.044 1.873 7749 Planarity : 0.004 0.072 5874 Dihedral : 20.366 177.178 13472 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.39 % Favored : 94.52 % Rotamer: Outliers : 4.89 % Allowed : 18.68 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 0.65 % Twisted General : 0.10 % 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: -0.03 (0.14), residues: 4140 helix: 1.44 (0.12), residues: 2160 sheet: -1.69 (0.28), residues: 309 loop : -1.69 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 51 TYR 0.020 0.001 TYR B 8 PHE 0.025 0.001 PHE C 78 TRP 0.017 0.002 TRP D 186 HIS 0.005 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00321 (43320) covalent geometry : angle 0.59300 (61678) hydrogen bonds : bond 0.03965 ( 2075) hydrogen bonds : angle 3.88482 ( 5532) metal coordination : bond 0.01190 ( 12) metal coordination : angle 1.87743 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 267 time to evaluate : 1.058 Fit side-chains REVERT: B 82 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: B 87 MET cc_start: 0.7301 (mmt) cc_final: 0.7011 (mmm) REVERT: B 103 ASP cc_start: 0.7868 (t70) cc_final: 0.7173 (t70) REVERT: C 71 SER cc_start: 0.8657 (m) cc_final: 0.8264 (t) REVERT: D 103 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8387 (mt0) REVERT: D 289 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8622 (mt) REVERT: D 303 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8675 (mp) REVERT: D 326 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7717 (t0) REVERT: E 613 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: F 332 TYR cc_start: 0.9079 (m-80) cc_final: 0.8820 (m-80) REVERT: F 368 MET cc_start: 0.8710 (tpp) cc_final: 0.7612 (tpp) REVERT: F 389 THR cc_start: 0.8841 (m) cc_final: 0.8577 (m) REVERT: F 410 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8835 (tt) REVERT: G 63 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7536 (pm20) REVERT: G 122 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9036 (tt) REVERT: G 204 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6718 (ptpp) REVERT: G 246 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8461 (mm) REVERT: G 248 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8171 (tt) REVERT: G 260 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8453 (pp) REVERT: I 10 GLU cc_start: 0.8049 (tp30) cc_final: 0.7646 (tp30) REVERT: I 80 TYR cc_start: 0.8148 (t80) cc_final: 0.7918 (t80) REVERT: I 104 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7491 (t80) REVERT: I 120 LYS cc_start: 0.5746 (mtpp) cc_final: 0.5387 (pttp) REVERT: I 210 ARG cc_start: 0.8103 (ttp-110) cc_final: 0.7154 (tpp-160) REVERT: I 227 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8375 (mm) REVERT: I 238 ARG cc_start: 0.7765 (tpp80) cc_final: 0.7473 (ttp80) REVERT: K 107 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7549 (mp0) REVERT: K 112 ASP cc_start: 0.8042 (m-30) cc_final: 0.7775 (m-30) REVERT: N 35 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7536 (mm-30) REVERT: P 44 SER cc_start: 0.9280 (p) cc_final: 0.8921 (t) REVERT: P 82 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8372 (ptm-80) REVERT: Q 11 MET cc_start: 0.8711 (mmm) cc_final: 0.8332 (mmm) REVERT: Q 40 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9036 (pp) outliers start: 114 outliers final: 76 residues processed: 362 average time/residue: 0.2183 time to fit residues: 134.7813 Evaluate side-chains 345 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 252 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 448 TYR Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 613 GLN Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 63 GLN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 21 optimal weight: 1.9990 chunk 374 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 chunk 357 optimal weight: 40.0000 chunk 445 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 379 optimal weight: 50.0000 chunk 463 optimal weight: 40.0000 chunk 432 optimal weight: 30.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 563 HIS ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.177431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135464 restraints weight = 79889.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129043 restraints weight = 147254.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.124921 restraints weight = 127349.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.125109 restraints weight = 113493.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124912 restraints weight = 91465.801| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 43332 Z= 0.193 Angle : 0.624 26.201 61685 Z= 0.319 Chirality : 0.045 1.877 7749 Planarity : 0.004 0.077 5874 Dihedral : 20.324 176.067 13467 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.35 % Favored : 93.55 % Rotamer: Outliers : 4.89 % Allowed : 19.28 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 0.65 % Twisted General : 0.10 % 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: 0.01 (0.14), residues: 4140 helix: 1.50 (0.12), residues: 2151 sheet: -1.67 (0.28), residues: 320 loop : -1.69 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 139 TYR 0.029 0.002 TYR C 5 PHE 0.033 0.002 PHE C 78 TRP 0.022 0.002 TRP D 147 HIS 0.006 0.001 HIS Q 55 Details of bonding type rmsd covalent geometry : bond 0.00447 (43320) covalent geometry : angle 0.62358 (61678) hydrogen bonds : bond 0.04211 ( 2075) hydrogen bonds : angle 3.91339 ( 5532) metal coordination : bond 0.00814 ( 12) metal coordination : angle 1.85604 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 259 time to evaluate : 1.246 Fit side-chains REVERT: B 82 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: B 87 MET cc_start: 0.7311 (mmt) cc_final: 0.7036 (mmm) REVERT: B 103 ASP cc_start: 0.7929 (t70) cc_final: 0.7258 (t70) REVERT: C 71 SER cc_start: 0.8666 (m) cc_final: 0.8286 (t) REVERT: C 73 MET cc_start: 0.6494 (ppp) cc_final: 0.5530 (ptm) REVERT: D 103 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8350 (mt0) REVERT: D 145 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7885 (mt-10) REVERT: D 258 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9071 (mmtp) REVERT: D 289 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8651 (mt) REVERT: D 303 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8706 (mp) REVERT: D 326 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7854 (t0) REVERT: E 613 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: F 332 TYR cc_start: 0.9071 (m-80) cc_final: 0.8831 (m-80) REVERT: F 368 MET cc_start: 0.8748 (tpp) cc_final: 0.7643 (tpp) REVERT: F 389 THR cc_start: 0.8920 (m) cc_final: 0.8700 (m) REVERT: F 410 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8849 (tt) REVERT: G 63 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: G 204 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6712 (ptpp) REVERT: G 246 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8701 (mp) REVERT: G 248 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8535 (tt) REVERT: G 260 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8367 (pp) REVERT: I 10 GLU cc_start: 0.8109 (tp30) cc_final: 0.7706 (tp30) REVERT: I 104 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7435 (t80) REVERT: I 210 ARG cc_start: 0.8084 (ttp-110) cc_final: 0.7250 (tpm170) REVERT: I 227 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8491 (mm) REVERT: I 238 ARG cc_start: 0.7759 (tpp80) cc_final: 0.7500 (ttp80) REVERT: K 82 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8455 (mt) REVERT: K 107 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7581 (mt-10) REVERT: N 35 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7574 (mm-30) REVERT: P 44 SER cc_start: 0.9278 (p) cc_final: 0.8932 (t) REVERT: P 82 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8418 (ptm-80) REVERT: Q 40 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8784 (pp) outliers start: 114 outliers final: 87 residues processed: 349 average time/residue: 0.2246 time to fit residues: 133.7868 Evaluate side-chains 354 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 249 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 448 TYR Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 613 GLN Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 63 GLN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 207 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 331 optimal weight: 8.9990 chunk 365 optimal weight: 40.0000 chunk 264 optimal weight: 0.8980 chunk 356 optimal weight: 40.0000 chunk 185 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 563 HIS F 407 GLN ** I 226 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 = 0.4355 r_free = 0.4355 target = 0.178988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.136888 restraints weight = 79718.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.130032 restraints weight = 142925.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.125626 restraints weight = 124955.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125613 restraints weight = 115327.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125543 restraints weight = 88647.556| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 43332 Z= 0.133 Angle : 0.578 26.218 61685 Z= 0.295 Chirality : 0.043 1.873 7749 Planarity : 0.004 0.072 5874 Dihedral : 20.202 177.245 13467 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.65 % Favored : 94.25 % Rotamer: Outliers : 4.55 % Allowed : 19.88 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 0.65 % Twisted General : 0.10 % 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: 0.23 (0.14), residues: 4140 helix: 1.70 (0.12), residues: 2149 sheet: -1.56 (0.28), residues: 318 loop : -1.62 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 51 TYR 0.020 0.001 TYR C 5 PHE 0.027 0.001 PHE C 78 TRP 0.015 0.001 TRP D 186 HIS 0.005 0.001 HIS E 563 Details of bonding type rmsd covalent geometry : bond 0.00297 (43320) covalent geometry : angle 0.57725 (61678) hydrogen bonds : bond 0.03777 ( 2075) hydrogen bonds : angle 3.74398 ( 5532) metal coordination : bond 0.01123 ( 12) metal coordination : angle 1.91401 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8280 Ramachandran restraints generated. 4140 Oldfield, 0 Emsley, 4140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 276 time to evaluate : 1.324 Fit side-chains REVERT: A 74 ILE cc_start: 0.7943 (tt) cc_final: 0.7683 (mm) REVERT: B 82 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: B 87 MET cc_start: 0.7284 (mmt) cc_final: 0.7030 (mmm) REVERT: B 103 ASP cc_start: 0.7826 (t70) cc_final: 0.7151 (t70) REVERT: C 71 SER cc_start: 0.8661 (m) cc_final: 0.8249 (t) REVERT: D 103 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8345 (mt0) REVERT: D 258 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9107 (mmtp) REVERT: D 289 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8628 (mt) REVERT: D 303 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8554 (mp) REVERT: D 326 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7788 (t0) REVERT: E 613 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: F 332 TYR cc_start: 0.9027 (m-80) cc_final: 0.8810 (m-80) REVERT: F 368 MET cc_start: 0.8737 (tpp) cc_final: 0.7581 (tpp) REVERT: F 389 THR cc_start: 0.8869 (m) cc_final: 0.8600 (m) REVERT: G 63 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: G 204 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6701 (ptpp) REVERT: G 248 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8314 (tt) REVERT: G 260 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8391 (pp) REVERT: I 10 GLU cc_start: 0.8099 (tp30) cc_final: 0.7694 (tp30) REVERT: I 104 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7468 (t80) REVERT: I 210 ARG cc_start: 0.7997 (ttp-110) cc_final: 0.7227 (tpm170) REVERT: I 227 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8350 (mm) REVERT: I 238 ARG cc_start: 0.7728 (tpp80) cc_final: 0.7474 (ttp80) REVERT: N 35 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7576 (mm-30) REVERT: P 44 SER cc_start: 0.9270 (p) cc_final: 0.8917 (t) REVERT: P 82 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8336 (ptm-80) REVERT: Q 11 MET cc_start: 0.8723 (mmm) cc_final: 0.8214 (mmm) outliers start: 106 outliers final: 82 residues processed: 361 average time/residue: 0.2187 time to fit residues: 134.5641 Evaluate side-chains 358 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 262 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 613 GLN Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 63 GLN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 7 optimal weight: 0.0980 chunk 84 optimal weight: 0.6980 chunk 302 optimal weight: 0.6980 chunk 279 optimal weight: 2.9990 chunk 312 optimal weight: 0.0000 chunk 469 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 280 optimal weight: 0.0270 chunk 343 optimal weight: 20.0000 overall best weight: 0.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 HIS D 411 GLN E 304 ASN E 379 HIS F 375 ASN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.181987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.141396 restraints weight = 80973.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134980 restraints weight = 138528.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.131386 restraints weight = 125053.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131717 restraints weight = 106267.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.131481 restraints weight = 80148.440| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 43332 Z= 0.100 Angle : 0.549 26.209 61685 Z= 0.278 Chirality : 0.041 1.872 7749 Planarity : 0.003 0.067 5874 Dihedral : 20.032 179.773 13465 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.07 % Favored : 94.83 % Rotamer: Outliers : 3.13 % Allowed : 21.47 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 0.65 % Twisted General : 0.07 % 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 (0.14), residues: 4140 helix: 2.00 (0.12), residues: 2145 sheet: -1.44 (0.28), residues: 307 loop : -1.42 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 108 TYR 0.017 0.001 TYR C 5 PHE 0.026 0.001 PHE C 78 TRP 0.016 0.001 TRP D 186 HIS 0.007 0.001 HIS I 226 Details of bonding type rmsd covalent geometry : bond 0.00206 (43320) covalent geometry : angle 0.54834 (61678) hydrogen bonds : bond 0.03371 ( 2075) hydrogen bonds : angle 3.53361 ( 5532) metal coordination : bond 0.01630 ( 12) metal coordination : angle 2.33422 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8008.08 seconds wall clock time: 138 minutes 38.29 seconds (8318.29 seconds total)