Starting phenix.real_space_refine on Tue Sep 15 15:43:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6n7p_0360/09_2026/6n7p_0360.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7p_0360/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6n7p_0360/09_2026/6n7p_0360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7p_0360/09_2026/6n7p_0360.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6n7p_0360/09_2026/6n7p_0360.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6n7p_0360/09_2026/6n7p_0360.cif" model { file = "/net/cci-nas-00/data/ceres_data/6n7p_0360/09_2026/6n7p_0360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7p_0360/09_2026/6n7p_0360.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 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: {'RNAv2': 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: 7.68, per 1000 atoms: 0.19 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: 2.99 Conformation dependent library (CDL) restraints added in 1.1 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: 5.10 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: 9.44 Time building geometry restraints manager: 4.14 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: 61265 5.16 - 10.33: 396 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 - 35.88: 23578 35.88 - 71.77: 1199 71.77 - 107.65: 64 107.65 - 143.53: 6 143.53 - 179.41: 5 Dihedral angle restraints: 24852 sinusoidal: 12332 harmonic: 12520 Sorted by residual: dihedral pdb=" C4' A R 64 " pdb=" C3' A R 64 " pdb=" C2' A R 64 " pdb=" C1' A R 64 " ideal model delta sinusoidal sigma weight residual 36.34 -40.06 76.41 1 3.10e+00 1.04e-01 7.64e+02 dihedral pdb=" C4' C R 140 " pdb=" C3' C R 140 " pdb=" C2' C R 140 " pdb=" C1' C R 140 " ideal model delta sinusoidal sigma weight residual 36.34 -39.59 75.93 1 3.10e+00 1.04e-01 7.56e+02 dihedral pdb=" C4' G R 134 " pdb=" C3' G R 134 " pdb=" C2' G R 134 " pdb=" C1' G R 134 " ideal model delta sinusoidal sigma weight residual 36.34 -39.33 75.68 1 3.10e+00 1.04e-01 7.52e+02 ... (remaining 24849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.335: 7729 0.335 - 0.671: 19 0.671 - 1.006: 0 1.006 - 1.341: 0 1.341 - 1.677: 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 2.17 0.50 1.68 2.00e-01 2.50e+01 7.03e+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=" P A R 506 " pdb=" OP1 A R 506 " pdb=" OP2 A R 506 " pdb=" O5' A R 506 " both_signs ideal model delta sigma weight residual True 2.17 -2.60 -0.43 2.00e-01 2.50e+01 4.58e+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: 3.430 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: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 42.340 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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= 0.477 Angle : 1.276 28.878 61685 Z= 0.653 Chirality : 0.096 1.677 7749 Planarity : 0.009 0.474 5874 Dihedral : 17.677 179.414 16672 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/Z covalent geometry : bond 0.01064 / 0.47 (43320) covalent geometry : angle 1.26420 / 0.65 (61678) hydrogen bonds : bond 0.19304 / 13.31 ( 2075) hydrogen bonds : angle 7.34305 / 5.10 ( 5532) metal coordination : bond 0.11534 / 6.33 ( 12) metal coordination : angle 15.96040 / 9.35 ( 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 : 1.303 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: 0.2468 time to fit residues: 198.9326 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 : 1.236 ------------------------------------------------------------------------------- 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... B 29 ASN B 40 ASN B 47 ASN B 80 ASN C 18 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 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN F 312 ASN F 334 GLN F 375 ASN F 411 GLN F 497 GLN F 515 GLN G 90 HIS I 76 HIS I 118 ASN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.179364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.133465 restraints weight = 80089.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122909 restraints weight = 116061.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119938 restraints weight = 109244.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.119516 restraints weight = 80623.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119170 restraints weight = 79843.384| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 43332 Z= 0.232 Angle : 1.084 23.802 61685 Z= 0.466 Chirality : 0.092 1.806 7749 Planarity : 0.005 0.090 5874 Dihedral : 16.807 170.231 11525 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.89 % Favored : 93.77 % Rotamer: Outliers : 4.98 % Allowed : 10.73 % Favored : 84.29 % 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: -0.31 (0.11), residues: 2146 sheet: -2.17 (0.27), residues: 312 loop : -2.08 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 14 TYR 0.034 0.002 TYR D 316 PHE 0.028 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/Z covalent geometry : bond 0.00500 / 0.23 (43320) covalent geometry : angle 1.08314 / 0.47 (61678) hydrogen bonds : bond 0.05353 / 3.73 ( 2075) hydrogen bonds : angle 4.68818 / 3.28 ( 5532) metal coordination : bond 0.01577 / 1.04 ( 12) metal coordination : angle 3.47875 / 1.89 ( 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 439 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 323 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: B 87 MET cc_start: 0.7428 (mmt) cc_final: 0.7150 (mmm) REVERT: B 103 ASP cc_start: 0.8002 (t70) cc_final: 0.7423 (t70) REVERT: C 71 SER cc_start: 0.8750 (m) cc_final: 0.8287 (t) REVERT: C 78 PHE cc_start: 0.7649 (m-80) cc_final: 0.6862 (m-10) REVERT: C 84 GLN cc_start: 0.7658 (mm110) cc_final: 0.7271 (tp-100) REVERT: C 88 ASP cc_start: 0.6655 (m-30) cc_final: 0.6287 (p0) REVERT: D 7 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7870 (tp) REVERT: D 89 MET cc_start: 0.8452 (tpp) cc_final: 0.8240 (tpp) REVERT: D 250 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8345 (tm-30) REVERT: D 367 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8949 (tt) REVERT: D 446 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7704 (mt0) REVERT: D 477 MET cc_start: 0.8119 (tpt) cc_final: 0.7709 (tpp) REVERT: E 507 ASP cc_start: 0.7614 (m-30) cc_final: 0.7124 (m-30) REVERT: E 517 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9004 (mm) REVERT: F 332 TYR cc_start: 0.9020 (m-80) cc_final: 0.8690 (m-80) REVERT: F 368 MET cc_start: 0.8728 (tpp) cc_final: 0.7954 (tpp) REVERT: F 446 TYR cc_start: 0.9085 (m-80) cc_final: 0.8838 (m-80) REVERT: G 69 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8614 (tp) REVERT: G 122 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8797 (tt) REVERT: G 246 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8726 (mp) REVERT: G 248 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8556 (tt) REVERT: I 10 GLU cc_start: 0.8030 (tp30) cc_final: 0.7555 (tp30) REVERT: I 78 ILE cc_start: 0.7886 (pt) cc_final: 0.7599 (tp) REVERT: I 104 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7707 (t80) REVERT: I 210 ARG cc_start: 0.8177 (ttp-110) cc_final: 0.7228 (tpm170) REVERT: I 238 ARG cc_start: 0.7743 (tpp80) cc_final: 0.7431 (ttp80) REVERT: K 19 LYS cc_start: 0.8694 (tttp) cc_final: 0.8324 (ttmm) REVERT: K 107 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7558 (mt-10) REVERT: K 127 LYS cc_start: 0.7666 (ttpt) cc_final: 0.6904 (tmtt) REVERT: M 39 VAL cc_start: 0.9170 (t) cc_final: 0.8858 (m) REVERT: N 45 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8121 (ttt-90) REVERT: N 46 ASP cc_start: 0.8152 (t70) cc_final: 0.7823 (t70) REVERT: Q 45 GLU cc_start: 0.8071 (tt0) cc_final: 0.7852 (tt0) outliers start: 116 outliers final: 61 residues processed: 415 average time/residue: 0.2232 time to fit residues: 157.1068 Evaluate side-chains 339 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 268 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 367 LEU 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 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 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 69 LEU 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 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 104 PHE Chi-restraints excluded: chain I residue 211 LEU 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 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 36 SER Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE 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: 5.9990 chunk 108 optimal weight: 9.9990 chunk 56 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 396 optimal weight: 6.9990 chunk 450 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 409 optimal weight: 8.9990 chunk 385 optimal weight: 8.9990 chunk 13 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 HIS C 75 ASN D 400 ASN F 407 GLN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN M 52 HIS O 22 GLN P 25 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.182452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.136617 restraints weight = 80249.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.125380 restraints weight = 102851.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122681 restraints weight = 97326.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.122349 restraints weight = 80983.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122592 restraints weight = 66220.882| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43332 Z= 0.141 Angle : 0.853 23.834 61685 Z= 0.368 Chirality : 0.068 1.798 7749 Planarity : 0.004 0.060 5874 Dihedral : 16.299 179.514 11473 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Rotamer: Outliers : 4.16 % Allowed : 13.01 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.05 % Twisted Proline : 1.29 % Twisted General : 0.15 % 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: -0.64 (0.13), residues: 4140 helix: 0.82 (0.11), residues: 2136 sheet: -1.85 (0.27), residues: 319 loop : -1.77 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 51 TYR 0.021 0.001 TYR D 316 PHE 0.027 0.001 PHE O 49 TRP 0.015 0.001 TRP E 362 HIS 0.005 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (43320) covalent geometry : angle 0.85258 / 0.37 (61678) hydrogen bonds : bond 0.04139 / 2.85 ( 2075) hydrogen bonds : angle 3.97509 / 2.80 ( 5532) metal coordination : bond 0.01193 / 0.77 ( 12) metal coordination : angle 3.01601 / 1.71 ( 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 445 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 348 time to evaluate : 1.301 Fit side-chains REVERT: A 10 ASP cc_start: 0.7974 (m-30) cc_final: 0.7520 (t0) REVERT: A 74 ILE cc_start: 0.7968 (tt) cc_final: 0.7590 (mm) REVERT: B 87 MET cc_start: 0.7102 (mmt) cc_final: 0.6893 (mmm) REVERT: B 103 ASP cc_start: 0.7964 (t70) cc_final: 0.7324 (t70) REVERT: B 138 GLN cc_start: 0.7938 (pm20) cc_final: 0.7726 (pm20) REVERT: C 71 SER cc_start: 0.8891 (m) cc_final: 0.8395 (t) REVERT: C 73 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6151 (ptp) REVERT: C 78 PHE cc_start: 0.7380 (m-80) cc_final: 0.6792 (m-10) REVERT: C 85 GLU cc_start: 0.6733 (tp30) cc_final: 0.6472 (tp30) REVERT: C 108 MET cc_start: 0.9051 (pmt) cc_final: 0.8757 (pmm) REVERT: D 89 MET cc_start: 0.8384 (tpp) cc_final: 0.8111 (tpp) REVERT: D 194 MET cc_start: 0.7006 (mmt) cc_final: 0.6746 (mmp) REVERT: E 507 ASP cc_start: 0.7441 (m-30) cc_final: 0.7109 (m-30) REVERT: F 368 MET cc_start: 0.8740 (tpp) cc_final: 0.7914 (tpp) REVERT: F 389 THR cc_start: 0.8839 (m) cc_final: 0.8563 (m) REVERT: I 10 GLU cc_start: 0.8078 (tp30) cc_final: 0.7546 (tp30) REVERT: I 78 ILE cc_start: 0.7725 (pt) cc_final: 0.7498 (tp) REVERT: I 104 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7451 (t80) REVERT: I 210 ARG cc_start: 0.8199 (ttp-110) cc_final: 0.7173 (tpm170) REVERT: I 238 ARG cc_start: 0.7650 (tpp80) cc_final: 0.7343 (ttp80) REVERT: K 127 LYS cc_start: 0.7717 (ttpt) cc_final: 0.6910 (tmtt) REVERT: M 39 VAL cc_start: 0.9020 (t) cc_final: 0.8667 (m) REVERT: N 45 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8116 (ttt-90) REVERT: N 46 ASP cc_start: 0.8134 (t70) cc_final: 0.7698 (t70) REVERT: Q 45 GLU cc_start: 0.8097 (tt0) cc_final: 0.7817 (tt0) outliers start: 97 outliers final: 56 residues processed: 415 average time/residue: 0.2231 time to fit residues: 157.7256 Evaluate side-chains 339 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 280 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 129 ASP Chi-restraints excluded: chain B residue 131 VAL 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 73 MET 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 1 MET 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 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 528 SER 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 342 VAL Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 203 VAL 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 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 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 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain M residue 6 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 45 ARG Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 77 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 312 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 152 optimal weight: 0.6980 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: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN D 102 ASN D 125 GLN E 563 HIS F 306 HIS F 507 ASN G 200 GLN G 292 ASN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN O 22 GLN Q 60 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.179490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.133972 restraints weight = 79837.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120500 restraints weight = 101637.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117778 restraints weight = 98532.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.117376 restraints weight = 81596.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117674 restraints weight = 66562.064| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 43332 Z= 0.209 Angle : 0.885 23.762 61685 Z= 0.384 Chirality : 0.070 1.801 7749 Planarity : 0.004 0.072 5874 Dihedral : 16.015 175.411 11435 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.04 % Favored : 93.82 % Rotamer: Outliers : 4.89 % Allowed : 14.17 % Favored : 80.94 % 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: -0.34 (0.13), residues: 4140 helix: 1.11 (0.11), residues: 2148 sheet: -1.69 (0.28), residues: 318 loop : -1.72 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 107 TYR 0.027 0.002 TYR D 316 PHE 0.022 0.002 PHE D 397 TRP 0.014 0.002 TRP D 186 HIS 0.006 0.001 HIS E 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (43320) covalent geometry : angle 0.88422 / 0.38 (61678) hydrogen bonds : bond 0.04403 / 3.05 ( 2075) hydrogen bonds : angle 3.98428 / 2.80 ( 5532) metal coordination : bond 0.00693 / 0.50 ( 12) metal coordination : angle 2.75150 / 1.49 ( 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 389 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 275 time to evaluate : 1.123 Fit side-chains REVERT: A 74 ILE cc_start: 0.7775 (tt) cc_final: 0.7384 (mm) REVERT: B 87 MET cc_start: 0.7328 (mmt) cc_final: 0.7042 (mmm) REVERT: B 103 ASP cc_start: 0.8013 (t70) cc_final: 0.7367 (t70) REVERT: B 105 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8972 (mt) REVERT: B 138 GLN cc_start: 0.8144 (pm20) cc_final: 0.7748 (pm20) REVERT: C 71 SER cc_start: 0.8944 (m) cc_final: 0.8464 (t) REVERT: C 73 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6449 (ptp) REVERT: C 78 PHE cc_start: 0.7728 (m-80) cc_final: 0.6836 (m-10) REVERT: C 88 ASP cc_start: 0.6878 (p0) cc_final: 0.6617 (p0) REVERT: C 108 MET cc_start: 0.8801 (pmt) cc_final: 0.8577 (pmm) REVERT: D 89 MET cc_start: 0.8343 (tpp) cc_final: 0.8135 (tpp) REVERT: E 507 ASP cc_start: 0.7491 (m-30) cc_final: 0.7223 (m-30) REVERT: E 517 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8943 (mm) REVERT: F 332 TYR cc_start: 0.8986 (m-80) cc_final: 0.8696 (m-80) REVERT: F 368 MET cc_start: 0.8790 (tpp) cc_final: 0.7585 (tpp) REVERT: G 122 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8725 (tt) REVERT: G 248 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8418 (tt) REVERT: I 10 GLU cc_start: 0.8165 (tp30) cc_final: 0.7689 (tp30) REVERT: I 104 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7481 (t80) REVERT: I 210 ARG cc_start: 0.7987 (ttp-110) cc_final: 0.7106 (tpm170) REVERT: I 238 ARG cc_start: 0.7663 (tpp80) cc_final: 0.7376 (ttp80) REVERT: K 64 ARG cc_start: 0.6471 (mmp80) cc_final: 0.5727 (ttt90) REVERT: K 82 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8477 (mt) REVERT: L 74 THR cc_start: 0.7122 (OUTLIER) cc_final: 0.6917 (p) REVERT: M 39 VAL cc_start: 0.9006 (t) cc_final: 0.8672 (m) REVERT: N 45 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8241 (ttt-90) REVERT: Q 11 MET cc_start: 0.8624 (mmm) cc_final: 0.8418 (mmm) REVERT: Q 45 GLU cc_start: 0.8218 (tt0) cc_final: 0.7922 (tt0) outliers start: 114 outliers final: 81 residues processed: 361 average time/residue: 0.2138 time to fit residues: 133.4776 Evaluate side-chains 350 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 260 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 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 67 ILE Chi-restraints excluded: chain C residue 73 MET 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 286 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 338 LEU 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 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 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 339 ILE Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 365 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 F residue 517 SER Chi-restraints excluded: chain G residue 50 ASN 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 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 71 MET 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 120 GLN 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 M residue 6 ILE 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 39 SER Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE 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 58 GLU 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 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 32 optimal weight: 50.0000 chunk 178 optimal weight: 3.9990 chunk 432 optimal weight: 0.4980 chunk 461 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 445 optimal weight: 20.0000 chunk 393 optimal weight: 7.9990 chunk 459 optimal weight: 9.9990 chunk 82 optimal weight: 0.5980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.179019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132956 restraints weight = 79682.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.121615 restraints weight = 109927.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118082 restraints weight = 106497.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.117667 restraints weight = 85596.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117896 restraints weight = 69934.020| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 43332 Z= 0.218 Angle : 0.877 23.689 61685 Z= 0.380 Chirality : 0.069 1.804 7749 Planarity : 0.004 0.068 5874 Dihedral : 16.011 178.262 11433 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.09 % Favored : 93.77 % Rotamer: Outliers : 4.94 % Allowed : 15.07 % Favored : 79.99 % 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: -0.18 (0.13), residues: 4140 helix: 1.27 (0.12), residues: 2148 sheet: -1.64 (0.28), residues: 323 loop : -1.68 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 51 TYR 0.024 0.002 TYR D 316 PHE 0.021 0.002 PHE D 397 TRP 0.016 0.002 TRP D 186 HIS 0.007 0.001 HIS Q 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (43320) covalent geometry : angle 0.87679 / 0.38 (61678) hydrogen bonds : bond 0.04359 / 3.03 ( 2075) hydrogen bonds : angle 3.95907 / 2.78 ( 5532) metal coordination : bond 0.00679 / 0.45 ( 12) metal coordination : angle 2.45382 / 1.30 ( 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 383 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 268 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: A 74 ILE cc_start: 0.7794 (tt) cc_final: 0.7533 (mm) REVERT: B 87 MET cc_start: 0.7300 (mmt) cc_final: 0.6984 (mmm) REVERT: B 103 ASP cc_start: 0.7828 (t70) cc_final: 0.7244 (t70) REVERT: B 138 GLN cc_start: 0.8127 (pm20) cc_final: 0.7747 (pm20) REVERT: C 71 SER cc_start: 0.8929 (m) cc_final: 0.8476 (t) REVERT: C 73 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6236 (ptp) REVERT: C 78 PHE cc_start: 0.7720 (m-80) cc_final: 0.6877 (m-10) REVERT: D 495 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8949 (mm) REVERT: E 507 ASP cc_start: 0.7603 (m-30) cc_final: 0.7322 (m-30) REVERT: F 332 TYR cc_start: 0.9023 (m-80) cc_final: 0.8766 (m-80) REVERT: F 368 MET cc_start: 0.8822 (tpp) cc_final: 0.7580 (tpp) REVERT: F 389 THR cc_start: 0.9000 (m) cc_final: 0.8734 (m) REVERT: G 122 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9028 (tt) REVERT: G 248 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8454 (tt) REVERT: G 260 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8458 (pp) REVERT: I 10 GLU cc_start: 0.8058 (tp30) cc_final: 0.7613 (tp30) REVERT: I 104 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7446 (t80) REVERT: I 210 ARG cc_start: 0.7979 (ttp-110) cc_final: 0.7104 (tpm170) REVERT: I 238 ARG cc_start: 0.7588 (tpp80) cc_final: 0.7277 (ttp80) REVERT: I 241 LYS cc_start: 0.7136 (tptp) cc_final: 0.6155 (pttt) REVERT: K 19 LYS cc_start: 0.8585 (tttp) cc_final: 0.8275 (ttmm) REVERT: K 64 ARG cc_start: 0.6570 (mmp80) cc_final: 0.5771 (ttt90) REVERT: K 82 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8492 (mt) REVERT: L 74 THR cc_start: 0.7155 (OUTLIER) cc_final: 0.6935 (p) REVERT: M 39 VAL cc_start: 0.9051 (t) cc_final: 0.8691 (m) REVERT: N 45 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8218 (ttt-90) REVERT: P 82 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8324 (ptm-80) REVERT: Q 45 GLU cc_start: 0.8220 (tt0) cc_final: 0.7939 (tt0) outliers start: 115 outliers final: 89 residues processed: 356 average time/residue: 0.2098 time to fit residues: 129.3721 Evaluate side-chains 352 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 253 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 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 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 73 MET 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 203 THR 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 338 LEU Chi-restraints excluded: chain D residue 341 SER 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 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 496 VAL 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 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 365 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 F residue 502 VAL Chi-restraints excluded: chain F residue 517 SER Chi-restraints excluded: chain G residue 50 ASN 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 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 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 71 MET Chi-restraints excluded: chain I residue 104 PHE 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 198 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 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 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 45 ARG Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE 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 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 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: 0.2980 chunk 250 optimal weight: 8.9990 chunk 414 optimal weight: 30.0000 chunk 216 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 360 optimal weight: 30.0000 chunk 80 optimal weight: 0.6980 chunk 328 optimal weight: 3.9990 chunk 362 optimal weight: 10.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN D 411 GLN E 563 HIS F 354 GLN G 207 HIS ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.177463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.136506 restraints weight = 79982.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.129709 restraints weight = 142203.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.125945 restraints weight = 137314.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.126121 restraints weight = 119438.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125771 restraints weight = 88023.406| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 43332 Z= 0.268 Angle : 0.934 23.626 61685 Z= 0.407 Chirality : 0.072 1.805 7749 Planarity : 0.004 0.074 5874 Dihedral : 16.101 179.101 11432 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.57 % Favored : 93.31 % Rotamer: Outliers : 6.18 % Allowed : 15.11 % Favored : 78.70 % 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: -0.28 (0.13), residues: 4140 helix: 1.21 (0.12), residues: 2164 sheet: -1.64 (0.28), residues: 323 loop : -1.81 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 51 TYR 0.036 0.002 TYR B 8 PHE 0.025 0.002 PHE D 397 TRP 0.017 0.002 TRP E 299 HIS 0.009 0.002 HIS Q 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.27 (43320) covalent geometry : angle 0.93340 / 0.41 (61678) hydrogen bonds : bond 0.04794 / 3.33 ( 2075) hydrogen bonds : angle 4.10483 / 2.88 ( 5532) metal coordination : bond 0.01000 / 0.74 ( 12) metal coordination : angle 2.59833 / 1.40 ( 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 403 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 259 time to evaluate : 1.252 Fit side-chains REVERT: A 74 ILE cc_start: 0.7659 (tt) cc_final: 0.7374 (mm) REVERT: A 80 LYS cc_start: 0.7858 (tmmt) cc_final: 0.7647 (ttpt) REVERT: B 82 GLU cc_start: 0.7969 (mp0) cc_final: 0.7760 (mp0) REVERT: B 87 MET cc_start: 0.7512 (mmt) cc_final: 0.7223 (mmm) REVERT: B 103 ASP cc_start: 0.8026 (t70) cc_final: 0.7345 (t70) REVERT: B 138 GLN cc_start: 0.8174 (pm20) cc_final: 0.7826 (pm20) REVERT: C 71 SER cc_start: 0.8945 (m) cc_final: 0.8517 (t) REVERT: C 73 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6035 (ptm) REVERT: D 495 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8948 (mm) REVERT: E 507 ASP cc_start: 0.7723 (m-30) cc_final: 0.7486 (m-30) REVERT: F 332 TYR cc_start: 0.9092 (m-80) cc_final: 0.8776 (m-80) REVERT: F 341 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.8888 (p90) REVERT: F 368 MET cc_start: 0.8847 (tpp) cc_final: 0.7606 (tpp) REVERT: F 410 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9035 (tt) REVERT: G 54 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8574 (tp) REVERT: G 122 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.8962 (tt) REVERT: G 204 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7163 (ptpp) REVERT: G 248 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8625 (tt) REVERT: G 260 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8349 (pp) REVERT: I 10 GLU cc_start: 0.8145 (tp30) cc_final: 0.7736 (tp30) REVERT: I 210 ARG cc_start: 0.8059 (ttp-110) cc_final: 0.7255 (tpm170) REVERT: K 64 ARG cc_start: 0.6494 (mmp80) cc_final: 0.6003 (ttt90) REVERT: K 82 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8456 (mt) REVERT: K 109 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8411 (mm) REVERT: L 74 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.7195 (p) REVERT: N 45 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8237 (ttt-90) REVERT: P 82 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8386 (ptm-80) REVERT: Q 11 MET cc_start: 0.8633 (mmm) cc_final: 0.8178 (mmm) REVERT: Q 40 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8992 (pp) REVERT: Q 45 GLU cc_start: 0.8342 (tt0) cc_final: 0.7999 (tt0) outliers start: 144 outliers final: 99 residues processed: 376 average time/residue: 0.2079 time to fit residues: 135.0217 Evaluate side-chains 362 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 248 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 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 73 MET 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 69 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 203 THR 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 338 LEU Chi-restraints excluded: chain D residue 341 SER 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 495 LEU 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 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 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 341 TYR Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 365 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 517 SER Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 54 ILE 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 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 G residue 294 ILE 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 39 LEU Chi-restraints excluded: chain I residue 71 MET 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 109 LEU 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 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 39 SER Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 45 ARG 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 58 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 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: 20.0000 chunk 166 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 323 optimal weight: 9.9990 chunk 424 optimal weight: 50.0000 chunk 375 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 333 optimal weight: 3.9990 chunk 368 optimal weight: 30.0000 chunk 301 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 HIS F 334 GLN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.176944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.130041 restraints weight = 80003.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.120818 restraints weight = 122403.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.116014 restraints weight = 104623.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115314 restraints weight = 96699.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115575 restraints weight = 74793.418| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 43332 Z= 0.283 Angle : 0.934 23.607 61685 Z= 0.406 Chirality : 0.072 1.807 7749 Planarity : 0.004 0.071 5874 Dihedral : 16.191 179.846 11432 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.57 % Favored : 93.31 % Rotamer: Outliers : 5.88 % Allowed : 16.27 % Favored : 77.84 % 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: -0.24 (0.13), residues: 4140 helix: 1.25 (0.12), residues: 2147 sheet: -1.81 (0.28), residues: 325 loop : -1.73 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 238 TYR 0.029 0.002 TYR B 8 PHE 0.022 0.002 PHE D 397 TRP 0.017 0.002 TRP D 186 HIS 0.009 0.002 HIS Q 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.28 (43320) covalent geometry : angle 0.93333 / 0.41 (61678) hydrogen bonds : bond 0.04741 / 3.30 ( 2075) hydrogen bonds : angle 4.11914 / 2.89 ( 5532) metal coordination : bond 0.00772 / 0.52 ( 12) metal coordination : angle 2.21269 / 1.19 ( 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 393 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 256 time to evaluate : 1.210 Fit side-chains REVERT: B 82 GLU cc_start: 0.8073 (mp0) cc_final: 0.7755 (mp0) REVERT: B 87 MET cc_start: 0.7578 (mmt) cc_final: 0.7259 (mmm) REVERT: B 103 ASP cc_start: 0.7973 (t70) cc_final: 0.7299 (t70) REVERT: C 71 SER cc_start: 0.8705 (m) cc_final: 0.8370 (t) REVERT: C 73 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6240 (ptm) REVERT: D 44 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8045 (tt) REVERT: D 495 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9011 (mm) REVERT: E 507 ASP cc_start: 0.7517 (m-30) cc_final: 0.7307 (m-30) REVERT: F 332 TYR cc_start: 0.9086 (m-80) cc_final: 0.8875 (m-80) REVERT: F 368 MET cc_start: 0.8816 (tpp) cc_final: 0.7672 (tpp) REVERT: G 122 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8922 (tt) REVERT: G 204 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7329 (ptpp) REVERT: G 248 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8552 (tt) REVERT: G 260 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8588 (pp) REVERT: H 10 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8151 (mp-120) REVERT: I 10 GLU cc_start: 0.8151 (tp30) cc_final: 0.7721 (tp30) REVERT: I 210 ARG cc_start: 0.7999 (ttp-110) cc_final: 0.7027 (tpm170) REVERT: I 227 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8350 (mm) REVERT: I 241 LYS cc_start: 0.6971 (tptp) cc_final: 0.6084 (pttt) REVERT: K 64 ARG cc_start: 0.6461 (mmp80) cc_final: 0.6010 (ttt90) REVERT: K 82 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8561 (mt) REVERT: K 112 ASP cc_start: 0.8032 (m-30) cc_final: 0.7774 (m-30) REVERT: K 120 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: L 74 THR cc_start: 0.7332 (OUTLIER) cc_final: 0.7093 (p) REVERT: N 45 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8226 (ttt-90) REVERT: N 86 LYS cc_start: 0.7696 (ttpt) cc_final: 0.7396 (ttpt) REVERT: P 82 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8415 (ptm-80) REVERT: Q 45 GLU cc_start: 0.8286 (tt0) cc_final: 0.7922 (tt0) outliers start: 137 outliers final: 101 residues processed: 367 average time/residue: 0.2141 time to fit residues: 135.5663 Evaluate side-chains 363 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 248 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 26 VAL 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 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 73 MET 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 18 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 203 THR 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 338 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 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 449 MET 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 304 LEU Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE 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 F residue 517 SER Chi-restraints excluded: chain G residue 50 ASN 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 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 10 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 71 MET 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 198 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 212 ASP 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 82 LEU Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 120 GLN 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 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 42 VAL Chi-restraints excluded: chain N residue 45 ARG 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 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 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: 0.7980 chunk 134 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 288 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 213 optimal weight: 0.0050 chunk 68 optimal weight: 0.5980 chunk 389 optimal weight: 10.0000 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN C 18 ASN D 366 ASN E 563 HIS F 334 GLN F 354 GLN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Q 20 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.180978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134748 restraints weight = 80315.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124926 restraints weight = 113376.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119836 restraints weight = 97798.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.119342 restraints weight = 93020.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120139 restraints weight = 71979.939| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 43332 Z= 0.130 Angle : 0.809 23.760 61685 Z= 0.346 Chirality : 0.064 1.799 7749 Planarity : 0.004 0.066 5874 Dihedral : 16.009 178.796 11432 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.71 % Rotamer: Outliers : 3.99 % Allowed : 18.55 % Favored : 77.46 % 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: 0.26 (0.14), residues: 4140 helix: 1.69 (0.12), residues: 2157 sheet: -1.59 (0.28), residues: 306 loop : -1.55 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 238 TYR 0.017 0.001 TYR D 448 PHE 0.012 0.001 PHE O 32 TRP 0.015 0.002 TRP D 186 HIS 0.006 0.001 HIS E 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (43320) covalent geometry : angle 0.80914 / 0.35 (61678) hydrogen bonds : bond 0.03758 / 2.62 ( 2075) hydrogen bonds : angle 3.74700 / 2.63 ( 5532) metal coordination : bond 0.01208 / 0.83 ( 12) metal coordination : angle 2.25876 / 1.25 ( 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 370 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 277 time to evaluate : 1.048 Fit side-chains REVERT: A 74 ILE cc_start: 0.7877 (tt) cc_final: 0.7622 (mm) REVERT: B 87 MET cc_start: 0.7350 (mmt) cc_final: 0.7074 (mmm) REVERT: B 103 ASP cc_start: 0.7587 (t70) cc_final: 0.6961 (t70) REVERT: C 71 SER cc_start: 0.8767 (m) cc_final: 0.8374 (t) REVERT: C 73 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.5641 (ptm) REVERT: D 326 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7738 (t0) REVERT: F 368 MET cc_start: 0.8725 (tpp) cc_final: 0.7833 (tpp) REVERT: F 389 THR cc_start: 0.8861 (m) cc_final: 0.8571 (m) REVERT: G 248 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8695 (mt) REVERT: I 10 GLU cc_start: 0.7971 (tp30) cc_final: 0.7545 (tp30) REVERT: I 80 TYR cc_start: 0.8058 (t80) cc_final: 0.7802 (t80) REVERT: I 120 LYS cc_start: 0.5737 (mtpp) cc_final: 0.5317 (pttp) REVERT: I 210 ARG cc_start: 0.7995 (ttp-110) cc_final: 0.7084 (tpm170) REVERT: I 241 LYS cc_start: 0.6757 (tptp) cc_final: 0.5894 (pttp) REVERT: K 19 LYS cc_start: 0.8455 (tttp) cc_final: 0.8101 (ttmt) REVERT: K 64 ARG cc_start: 0.6537 (mmp80) cc_final: 0.5735 (ttt90) REVERT: K 120 GLN cc_start: 0.7791 (mp10) cc_final: 0.7546 (mp10) REVERT: L 74 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7203 (p) REVERT: N 45 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8122 (ttt-90) REVERT: N 86 LYS cc_start: 0.7844 (ttpt) cc_final: 0.7556 (ttpt) REVERT: P 82 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8339 (ptm-80) REVERT: Q 11 MET cc_start: 0.8690 (mmm) cc_final: 0.8143 (mmm) outliers start: 93 outliers final: 65 residues processed: 353 average time/residue: 0.2125 time to fit residues: 128.3865 Evaluate side-chains 320 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 249 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 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 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 73 MET 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 D residue 69 TYR 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 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 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 304 LEU 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 443 ILE Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 203 VAL 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 I residue 71 MET 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 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 102 LEU 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 L residue 85 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 45 ARG Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain P residue 29 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 21 optimal weight: 3.9990 chunk 374 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 298 optimal weight: 0.9980 chunk 357 optimal weight: 30.0000 chunk 445 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 379 optimal weight: 50.0000 chunk 463 optimal weight: 50.0000 chunk 432 optimal weight: 0.9980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4357 r_free = 0.4357 target = 0.179236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131148 restraints weight = 80301.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122015 restraints weight = 112105.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118139 restraints weight = 91486.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.117062 restraints weight = 89670.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.117572 restraints weight = 74300.812| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 43332 Z= 0.183 Angle : 0.836 23.622 61685 Z= 0.359 Chirality : 0.066 1.803 7749 Planarity : 0.004 0.067 5874 Dihedral : 15.947 179.969 11432 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.18 % Favored : 93.72 % Rotamer: Outliers : 3.65 % Allowed : 19.24 % Favored : 77.11 % 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: 0.29 (0.14), residues: 4140 helix: 1.72 (0.12), residues: 2158 sheet: -1.53 (0.28), residues: 315 loop : -1.56 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 238 TYR 0.022 0.002 TYR B 8 PHE 0.016 0.001 PHE D 397 TRP 0.020 0.002 TRP D 147 HIS 0.006 0.001 HIS Q 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (43320) covalent geometry : angle 0.83540 / 0.36 (61678) hydrogen bonds : bond 0.04063 / 2.84 ( 2075) hydrogen bonds : angle 3.78931 / 2.66 ( 5532) metal coordination : bond 0.00635 / 0.38 ( 12) metal coordination : angle 2.24705 / 1.21 ( 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 338 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 253 time to evaluate : 1.111 Fit side-chains REVERT: A 74 ILE cc_start: 0.7530 (tt) cc_final: 0.7292 (mm) REVERT: B 22 LYS cc_start: 0.8256 (tptp) cc_final: 0.8053 (tptp) REVERT: B 87 MET cc_start: 0.7375 (mmt) cc_final: 0.7065 (mmm) REVERT: B 103 ASP cc_start: 0.7949 (t70) cc_final: 0.7325 (t70) REVERT: C 71 SER cc_start: 0.8718 (m) cc_final: 0.8338 (t) REVERT: C 73 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6113 (ptm) REVERT: F 368 MET cc_start: 0.8792 (tpp) cc_final: 0.7860 (tpp) REVERT: F 389 THR cc_start: 0.8909 (m) cc_final: 0.8609 (m) REVERT: G 248 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8840 (mt) REVERT: G 260 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8427 (pp) REVERT: I 10 GLU cc_start: 0.8145 (tp30) cc_final: 0.7686 (tp30) REVERT: I 80 TYR cc_start: 0.7992 (t80) cc_final: 0.7732 (t80) REVERT: I 120 LYS cc_start: 0.5669 (mtpp) cc_final: 0.5406 (pttp) REVERT: I 210 ARG cc_start: 0.8024 (ttp-110) cc_final: 0.7071 (tpm170) REVERT: I 241 LYS cc_start: 0.6839 (tptp) cc_final: 0.6019 (pttt) REVERT: K 64 ARG cc_start: 0.6660 (mmp80) cc_final: 0.5845 (ttt90) REVERT: K 112 ASP cc_start: 0.8081 (m-30) cc_final: 0.7801 (m-30) REVERT: L 74 THR cc_start: 0.7569 (OUTLIER) cc_final: 0.7269 (p) REVERT: M 31 MET cc_start: 0.8201 (mtp) cc_final: 0.7955 (mmt) REVERT: N 45 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8180 (ttt-90) REVERT: N 86 LYS cc_start: 0.7762 (ttpt) cc_final: 0.7481 (ttpt) REVERT: P 82 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8376 (ptm-80) REVERT: Q 11 MET cc_start: 0.8777 (mmm) cc_final: 0.8271 (mmm) outliers start: 85 outliers final: 70 residues processed: 321 average time/residue: 0.2073 time to fit residues: 115.0418 Evaluate side-chains 321 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 245 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 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 129 ASP Chi-restraints excluded: chain B residue 131 VAL 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 73 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 306 LEU 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 415 ILE 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 304 LEU Chi-restraints excluded: chain F residue 317 ILE 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 203 VAL 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 294 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 71 MET 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 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 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 L residue 85 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 45 ARG Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain P residue 29 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 207 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 87 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 331 optimal weight: 7.9990 chunk 365 optimal weight: 30.0000 chunk 264 optimal weight: 0.8980 chunk 356 optimal weight: 30.0000 chunk 185 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4383 r_free = 0.4383 target = 0.181354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140192 restraints weight = 80442.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.135032 restraints weight = 149050.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.131286 restraints weight = 117409.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.130475 restraints weight = 122817.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130816 restraints weight = 94366.799| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43332 Z= 0.131 Angle : 0.791 23.696 61685 Z= 0.338 Chirality : 0.063 1.798 7749 Planarity : 0.003 0.063 5874 Dihedral : 15.840 179.945 11432 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.14 % Favored : 94.76 % Rotamer: Outliers : 3.22 % Allowed : 19.79 % Favored : 76.99 % 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: 0.54 (0.14), residues: 4140 helix: 1.98 (0.12), residues: 2138 sheet: -1.39 (0.29), residues: 305 loop : -1.50 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 238 TYR 0.016 0.001 TYR B 8 PHE 0.011 0.001 PHE O 32 TRP 0.015 0.001 TRP D 186 HIS 0.006 0.001 HIS E 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (43320) covalent geometry : angle 0.79062 / 0.34 (61678) hydrogen bonds : bond 0.03653 / 2.55 ( 2075) hydrogen bonds : angle 3.63681 / 2.56 ( 5532) metal coordination : bond 0.01061 / 0.73 ( 12) metal coordination : angle 2.36269 / 1.31 ( 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 343 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 268 time to evaluate : 1.306 Fit side-chains REVERT: A 74 ILE cc_start: 0.7743 (tt) cc_final: 0.7511 (mm) REVERT: B 87 MET cc_start: 0.7357 (mmt) cc_final: 0.7081 (mmm) REVERT: B 103 ASP cc_start: 0.7738 (t70) cc_final: 0.7052 (t70) REVERT: C 60 MET cc_start: 0.7673 (mmt) cc_final: 0.7256 (mmm) REVERT: C 71 SER cc_start: 0.8670 (m) cc_final: 0.8291 (t) REVERT: C 73 MET cc_start: 0.6291 (OUTLIER) cc_final: 0.5582 (ptm) REVERT: C 88 ASP cc_start: 0.7232 (t0) cc_final: 0.6434 (p0) REVERT: C 108 MET cc_start: 0.8573 (pmt) cc_final: 0.8337 (pmm) REVERT: D 326 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7823 (t0) REVERT: F 332 TYR cc_start: 0.8799 (m-80) cc_final: 0.8511 (m-80) REVERT: F 368 MET cc_start: 0.8738 (tpp) cc_final: 0.7856 (tpp) REVERT: F 389 THR cc_start: 0.8825 (m) cc_final: 0.8526 (m) REVERT: G 248 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8594 (mt) REVERT: I 10 GLU cc_start: 0.7982 (tp30) cc_final: 0.7537 (tp30) REVERT: I 210 ARG cc_start: 0.8182 (ttp-110) cc_final: 0.7129 (tpm170) REVERT: I 241 LYS cc_start: 0.6682 (tptp) cc_final: 0.5923 (pttp) REVERT: K 64 ARG cc_start: 0.6618 (mmp80) cc_final: 0.5772 (ttt90) REVERT: N 45 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8093 (ttt-90) REVERT: Q 11 MET cc_start: 0.8713 (mmm) cc_final: 0.8212 (mmm) outliers start: 75 outliers final: 67 residues processed: 325 average time/residue: 0.2139 time to fit residues: 119.6190 Evaluate side-chains 324 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 253 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 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 73 MET 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 D residue 69 TYR Chi-restraints excluded: chain D residue 265 THR 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 393 LEU Chi-restraints excluded: chain E residue 415 ILE 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 304 LEU Chi-restraints excluded: chain F residue 317 ILE 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 203 VAL 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 294 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 198 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 K residue 102 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 85 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 45 ARG Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain O residue 58 VAL 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 34 ILE 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: 0.9990 chunk 84 optimal weight: 0.9990 chunk 302 optimal weight: 0.5980 chunk 279 optimal weight: 3.9990 chunk 312 optimal weight: 0.6980 chunk 469 optimal weight: 50.0000 chunk 197 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 71 optimal weight: 0.0970 chunk 280 optimal weight: 4.9990 chunk 343 optimal weight: 20.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 125 GLN E 563 HIS ** 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 = 0.4396 r_free = 0.4396 target = 0.182484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.141531 restraints weight = 81226.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.135505 restraints weight = 138514.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.131347 restraints weight = 121194.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.131116 restraints weight = 115051.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.131075 restraints weight = 84029.410| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43332 Z= 0.121 Angle : 0.770 23.658 61685 Z= 0.328 Chirality : 0.062 1.798 7749 Planarity : 0.003 0.061 5874 Dihedral : 15.656 179.175 11431 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.29 % Favored : 94.61 % Rotamer: Outliers : 3.05 % Allowed : 19.71 % Favored : 77.24 % 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: 0.77 (0.14), residues: 4140 helix: 2.17 (0.12), residues: 2133 sheet: -1.17 (0.29), residues: 302 loop : -1.39 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 89 TYR 0.025 0.001 TYR I 80 PHE 0.011 0.001 PHE O 32 TRP 0.015 0.001 TRP D 313 HIS 0.005 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (43320) covalent geometry : angle 0.76949 / 0.33 (61678) hydrogen bonds : bond 0.03523 / 2.47 ( 2075) hydrogen bonds : angle 3.51094 / 2.47 ( 5532) metal coordination : bond 0.01125 / 0.79 ( 12) metal coordination : angle 2.33681 / 1.29 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7887.78 seconds wall clock time: 136 minutes 10.23 seconds (8170.23 seconds total)