Starting phenix.real_space_refine on Mon Aug 10 09:35:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qkv_18472/08_2026/8qkv_18472.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qkv_18472/08_2026/8qkv_18472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qkv_18472/08_2026/8qkv_18472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qkv_18472/08_2026/8qkv_18472.map" model { file = "/net/cci-nas-00/data/ceres_data/8qkv_18472/08_2026/8qkv_18472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qkv_18472/08_2026/8qkv_18472.cif" } resolution = 4.7 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= 0.002 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 404 5.49 5 Mg 8 5.21 5 S 121 5.16 5 Be 2 3.05 5 C 27635 2.51 5 N 8117 2.21 5 O 9551 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 45846 Number of models: 1 Model: "" Number of chains: 29 Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 651 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "F" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 767 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "H" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 712 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3960 Classifications: {'DNA': 194} Link IDs: {'rna3p': 193} Chain: "J" Number of atoms: 3994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3994 Classifications: {'DNA': 194} Link IDs: {'rna3p': 193} Chain: "Z" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1367 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 6, 'TRP:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 123 Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 5398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5398 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 19, 'TRANS': 668} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 5, 'TRP:plan': 1, 'PHE:plan': 5, 'GLN:plan1': 7, 'ASP:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 167 Chain: "R" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3335 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 25, 'TRANS': 385} Chain breaks: 1 Chain: "S" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1499 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 2 Chain: "T" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3391 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 424} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3299 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 419} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3336 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3325 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3410 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 436} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" 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} Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25184 SG CYS S 244 79.787 63.002 94.214 1.00751.63 S ATOM 25204 SG CYS S 247 79.015 60.595 91.282 1.00700.40 S ATOM 25320 SG CYS S 264 80.050 64.153 90.565 1.00760.94 S ATOM 25345 SG CYS S 268 76.671 63.420 92.135 1.00772.89 S ATOM 25264 SG CYS S 256 77.139 72.265 101.215 1.00771.26 S ATOM 25285 SG CYS S 259 77.516 69.427 103.713 1.00774.32 S ATOM 25424 SG CYS S 277 74.116 71.089 103.244 1.00803.47 S Time building chain proxies: 8.24, per 1000 atoms: 0.18 Number of scatterers: 45846 At special positions: 0 Unit cell: (209, 195.8, 181.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 121 16.00 P 404 15.00 Mg 8 11.99 F 6 9.00 O 9551 8.00 N 8117 7.00 C 27635 6.00 Be 2 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S 501 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 268 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 264 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 247 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 244 " pdb=" ZN S 502 " pdb="ZN ZN S 502 " - pdb=" NE2 HIS S 272 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 259 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 256 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 277 " Number of angles added : 9 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9076 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 35 sheets defined 51.1% alpha, 9.2% beta 174 base pairs and 292 stacking pairs defined. Time for finding SS restraints: 6.24 Creating SS restraints... Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.918A pdb=" N LYS B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 79 removed outlier: 3.546A pdb=" N PHE B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 114 Processing helix chain 'B' and resid 120 through 131 Processing helix chain 'C' and resid 25 through 29 removed outlier: 3.710A pdb=" N ILE C 29 " --> pdb=" O ILE C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 40 removed outlier: 3.501A pdb=" N ARG C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 76 removed outlier: 3.654A pdb=" N ASP C 68 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.555A pdb=" N VAL C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG C 92 " --> pdb=" O TYR C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.536A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 47 through 76 removed outlier: 3.864A pdb=" N TYR D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU D 52 " --> pdb=" O GLY D 48 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 removed outlier: 3.821A pdb=" N ARG D 92 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.512A pdb=" N ALA F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 18 through 22' Processing helix chain 'F' and resid 27 through 38 Processing helix chain 'F' and resid 46 through 74 removed outlier: 4.217A pdb=" N VAL F 50 " --> pdb=" O SER F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 91 Processing helix chain 'F' and resid 91 through 98 Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'G' and resid 40 through 52 Processing helix chain 'G' and resid 58 through 87 Processing helix chain 'G' and resid 93 through 105 removed outlier: 3.608A pdb=" N ILE G 97 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 128 Processing helix chain 'H' and resid 40 through 52 Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.618A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 125 Processing helix chain 'Z' and resid 196 through 228 removed outlier: 3.862A pdb=" N ASN Z 202 " --> pdb=" O SER Z 198 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR Z 203 " --> pdb=" O VAL Z 199 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET Z 204 " --> pdb=" O MET Z 200 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS Z 205 " --> pdb=" O GLU Z 201 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN Z 221 " --> pdb=" O ARG Z 217 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS Z 228 " --> pdb=" O ILE Z 224 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 275 removed outlier: 4.320A pdb=" N LYS Z 246 " --> pdb=" O LEU Z 242 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE Z 259 " --> pdb=" O SER Z 255 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS Z 260 " --> pdb=" O LEU Z 256 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS Z 266 " --> pdb=" O GLN Z 262 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU Z 268 " --> pdb=" O VAL Z 264 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS Z 275 " --> pdb=" O LEU Z 271 " (cutoff:3.500A) Processing helix chain 'Z' and resid 300 through 321 Processing helix chain 'Z' and resid 611 through 616 Processing helix chain 'Z' and resid 617 through 624 Processing helix chain 'E' and resid 27 through 37 removed outlier: 3.936A pdb=" N VAL E 31 " --> pdb=" O PRO E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 73 removed outlier: 4.172A pdb=" N VAL E 50 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 90 removed outlier: 3.745A pdb=" N LEU E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 98 Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.508A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 114 Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'M' and resid 697 through 712 removed outlier: 4.010A pdb=" N SER M 709 " --> pdb=" O ASN M 705 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU M 710 " --> pdb=" O TRP M 706 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR M 711 " --> pdb=" O LEU M 707 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN M 712 " --> pdb=" O ALA M 708 " (cutoff:3.500A) Processing helix chain 'M' and resid 726 through 742 removed outlier: 3.638A pdb=" N LYS M 742 " --> pdb=" O LEU M 738 " (cutoff:3.500A) Processing helix chain 'M' and resid 756 through 767 Processing helix chain 'M' and resid 781 through 789 removed outlier: 4.132A pdb=" N GLU M 785 " --> pdb=" O GLN M 781 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY M 789 " --> pdb=" O GLU M 785 " (cutoff:3.500A) Processing helix chain 'M' and resid 790 through 792 No H-bonds generated for 'chain 'M' and resid 790 through 792' Processing helix chain 'M' and resid 803 through 809 Processing helix chain 'M' and resid 809 through 814 Processing helix chain 'M' and resid 834 through 840 removed outlier: 4.022A pdb=" N GLN M 838 " --> pdb=" O SER M 834 " (cutoff:3.500A) Processing helix chain 'M' and resid 859 through 871 removed outlier: 4.036A pdb=" N LEU M 863 " --> pdb=" O ASN M 859 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET M 871 " --> pdb=" O LEU M 867 " (cutoff:3.500A) Processing helix chain 'M' and resid 914 through 923 Processing helix chain 'M' and resid 933 through 938 removed outlier: 3.762A pdb=" N ASP M 936 " --> pdb=" O LEU M 933 " (cutoff:3.500A) Processing helix chain 'M' and resid 954 through 972 Processing helix chain 'M' and resid 978 through 994 removed outlier: 3.675A pdb=" N ILE M 982 " --> pdb=" O ASN M 978 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN M 994 " --> pdb=" O ARG M 990 " (cutoff:3.500A) Processing helix chain 'M' and resid 1013 through 1030 removed outlier: 3.763A pdb=" N ASP M1017 " --> pdb=" O CYS M1013 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR M1018 " --> pdb=" O VAL M1014 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP M1020 " --> pdb=" O SER M1016 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL M1021 " --> pdb=" O ASP M1017 " (cutoff:3.500A) Processing helix chain 'M' and resid 1033 through 1037 removed outlier: 3.898A pdb=" N ARG M1037 " --> pdb=" O GLN M1034 " (cutoff:3.500A) Processing helix chain 'M' and resid 1046 through 1054 removed outlier: 4.438A pdb=" N ASP M1051 " --> pdb=" O THR M1048 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS M1052 " --> pdb=" O LEU M1049 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU M1054 " --> pdb=" O ASP M1051 " (cutoff:3.500A) Processing helix chain 'M' and resid 1055 through 1065 Processing helix chain 'M' and resid 1069 through 1090 removed outlier: 3.698A pdb=" N GLU M1074 " --> pdb=" O ASN M1070 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU M1080 " --> pdb=" O ASN M1076 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR M1081 " --> pdb=" O LYS M1077 " (cutoff:3.500A) Processing helix chain 'M' and resid 1095 through 1101 removed outlier: 3.854A pdb=" N ASN M1101 " --> pdb=" O PHE M1097 " (cutoff:3.500A) Processing helix chain 'M' and resid 1104 through 1133 Processing helix chain 'M' and resid 1141 through 1149 Processing helix chain 'M' and resid 1158 through 1164 removed outlier: 3.935A pdb=" N LYS M1164 " --> pdb=" O ASN M1160 " (cutoff:3.500A) Processing helix chain 'M' and resid 1165 through 1173 Processing helix chain 'M' and resid 1173 through 1180 Processing helix chain 'M' and resid 1191 through 1198 removed outlier: 3.570A pdb=" N LEU M1195 " --> pdb=" O ASP M1191 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU M1197 " --> pdb=" O ARG M1193 " (cutoff:3.500A) Processing helix chain 'M' and resid 1208 through 1220 Processing helix chain 'M' and resid 1224 through 1233 removed outlier: 3.560A pdb=" N ILE M1233 " --> pdb=" O THR M1229 " (cutoff:3.500A) Processing helix chain 'M' and resid 1239 through 1244 removed outlier: 3.846A pdb=" N TYR M1243 " --> pdb=" O SER M1239 " (cutoff:3.500A) Processing helix chain 'M' and resid 1245 through 1262 removed outlier: 3.609A pdb=" N LYS M1250 " --> pdb=" O GLY M1246 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE M1253 " --> pdb=" O GLN M1249 " (cutoff:3.500A) Processing helix chain 'M' and resid 1271 through 1286 removed outlier: 3.729A pdb=" N LEU M1275 " --> pdb=" O MET M1271 " (cutoff:3.500A) Processing helix chain 'M' and resid 1299 through 1310 removed outlier: 4.298A pdb=" N ILE M1303 " --> pdb=" O GLU M1299 " (cutoff:3.500A) Processing helix chain 'M' and resid 1346 through 1354 removed outlier: 3.610A pdb=" N GLN M1350 " --> pdb=" O ALA M1346 " (cutoff:3.500A) Processing helix chain 'M' and resid 1374 through 1386 Processing helix chain 'R' and resid 45 through 49 Processing helix chain 'R' and resid 68 through 81 Processing helix chain 'R' and resid 108 through 122 Processing helix chain 'R' and resid 132 through 137 removed outlier: 3.720A pdb=" N PHE R 136 " --> pdb=" O PRO R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 143 removed outlier: 4.288A pdb=" N LYS R 141 " --> pdb=" O PRO R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 213 Processing helix chain 'R' and resid 219 through 235 Processing helix chain 'R' and resid 242 through 252 Processing helix chain 'R' and resid 260 through 266 Processing helix chain 'R' and resid 308 through 313 removed outlier: 4.083A pdb=" N THR R 312 " --> pdb=" O ASP R 308 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE R 313 " --> pdb=" O GLU R 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 308 through 313' Processing helix chain 'R' and resid 314 through 319 removed outlier: 4.251A pdb=" N PHE R 318 " --> pdb=" O PRO R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 324 Processing helix chain 'R' and resid 329 through 341 Processing helix chain 'R' and resid 345 through 351 Processing helix chain 'R' and resid 357 through 362 removed outlier: 3.506A pdb=" N PHE R 360 " --> pdb=" O GLY R 357 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU R 362 " --> pdb=" O ASN R 359 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 377 Processing helix chain 'R' and resid 391 through 406 removed outlier: 3.584A pdb=" N ALA R 404 " --> pdb=" O MET R 400 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS R 405 " --> pdb=" O SER R 401 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR R 406 " --> pdb=" O GLN R 402 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 413 removed outlier: 4.203A pdb=" N ARG R 410 " --> pdb=" O THR R 406 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS R 411 " --> pdb=" O ASP R 407 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 removed outlier: 3.742A pdb=" N HIS R 422 " --> pdb=" O GLU R 418 " (cutoff:3.500A) Processing helix chain 'R' and resid 423 through 430 removed outlier: 3.901A pdb=" N CYS R 427 " --> pdb=" O GLY R 423 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR R 428 " --> pdb=" O PRO R 424 " (cutoff:3.500A) Processing helix chain 'R' and resid 433 through 437 Processing helix chain 'S' and resid 93 through 106 Processing helix chain 'S' and resid 115 through 125 removed outlier: 3.935A pdb=" N LEU S 119 " --> pdb=" O ASN S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 135 Processing helix chain 'S' and resid 168 through 179 removed outlier: 3.574A pdb=" N TYR S 179 " --> pdb=" O ILE S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 200 removed outlier: 3.931A pdb=" N ILE S 195 " --> pdb=" O ASN S 191 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS S 200 " --> pdb=" O VAL S 196 " (cutoff:3.500A) Processing helix chain 'S' and resid 218 through 227 Processing helix chain 'S' and resid 265 through 273 Processing helix chain 'T' and resid 51 through 67 Processing helix chain 'T' and resid 84 through 97 Processing helix chain 'T' and resid 107 through 111 removed outlier: 4.283A pdb=" N TYR T 111 " --> pdb=" O GLY T 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 107 through 111' Processing helix chain 'T' and resid 116 through 129 removed outlier: 3.658A pdb=" N THR T 120 " --> pdb=" O LYS T 116 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE T 129 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing helix chain 'T' and resid 182 through 193 Processing helix chain 'T' and resid 217 through 221 removed outlier: 4.077A pdb=" N THR T 220 " --> pdb=" O ALA T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 249 through 258 Processing helix chain 'T' and resid 264 through 274 removed outlier: 4.065A pdb=" N LYS T 274 " --> pdb=" O GLY T 270 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 299 removed outlier: 3.954A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 312 through 316 removed outlier: 3.923A pdb=" N MET T 315 " --> pdb=" O GLU T 312 " (cutoff:3.500A) Processing helix chain 'T' and resid 317 through 328 removed outlier: 3.747A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU T 328 " --> pdb=" O LEU T 324 " (cutoff:3.500A) Processing helix chain 'T' and resid 360 through 365 removed outlier: 3.536A pdb=" N ILE T 364 " --> pdb=" O PRO T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 410 Processing helix chain 'T' and resid 411 through 429 removed outlier: 3.718A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix Processing helix chain 'T' and resid 435 through 446 Processing helix chain 'T' and resid 448 through 458 removed outlier: 3.825A pdb=" N THR T 458 " --> pdb=" O LYS T 454 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 64 Processing helix chain 'U' and resid 80 through 93 Processing helix chain 'U' and resid 112 through 125 removed outlier: 3.674A pdb=" N SER U 124 " --> pdb=" O ALA U 120 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE U 125 " --> pdb=" O PHE U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 182 Processing helix chain 'U' and resid 241 through 250 removed outlier: 3.540A pdb=" N ARG U 250 " --> pdb=" O VAL U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 252 through 260 Processing helix chain 'U' and resid 266 through 284 Processing helix chain 'U' and resid 298 through 301 Processing helix chain 'U' and resid 302 through 313 Processing helix chain 'U' and resid 339 through 343 Processing helix chain 'U' and resid 344 through 350 removed outlier: 3.921A pdb=" N ARG U 350 " --> pdb=" O ASP U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 360 through 375 Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 412 removed outlier: 3.756A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 Processing helix chain 'U' and resid 432 through 442 Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.612A pdb=" N ALA V 67 " --> pdb=" O ASP V 63 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS V 68 " --> pdb=" O LEU V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 97 removed outlier: 3.626A pdb=" N GLY V 97 " --> pdb=" O SER V 93 " (cutoff:3.500A) Processing helix chain 'V' and resid 116 through 129 removed outlier: 3.582A pdb=" N ILE V 129 " --> pdb=" O PHE V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 182 through 192 Processing helix chain 'V' and resid 217 through 219 No H-bonds generated for 'chain 'V' and resid 217 through 219' Processing helix chain 'V' and resid 249 through 258 Processing helix chain 'V' and resid 264 through 274 removed outlier: 3.650A pdb=" N MET V 268 " --> pdb=" O ASP V 264 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS V 274 " --> pdb=" O GLY V 270 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 Processing helix chain 'V' and resid 312 through 316 Processing helix chain 'V' and resid 317 through 328 removed outlier: 4.081A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 356 through 359 Processing helix chain 'V' and resid 360 through 366 removed outlier: 3.835A pdb=" N ARG V 366 " --> pdb=" O ASP V 362 " (cutoff:3.500A) Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 removed outlier: 3.955A pdb=" N THR V 408 " --> pdb=" O ALA V 404 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU V 409 " --> pdb=" O THR V 405 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR V 410 " --> pdb=" O MET V 406 " (cutoff:3.500A) Processing helix chain 'V' and resid 411 through 429 removed outlier: 3.908A pdb=" N ALA V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA V 420 " --> pdb=" O LEU V 416 " (cutoff:3.500A) Proline residue: V 421 - end of helix Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 458 removed outlier: 3.647A pdb=" N THR V 458 " --> pdb=" O LYS V 454 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 64 Processing helix chain 'W' and resid 80 through 93 Processing helix chain 'W' and resid 104 through 107 removed outlier: 3.538A pdb=" N PHE W 107 " --> pdb=" O SER W 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 104 through 107' Processing helix chain 'W' and resid 112 through 124 removed outlier: 3.682A pdb=" N SER W 124 " --> pdb=" O ALA W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 172 through 182 removed outlier: 3.565A pdb=" N GLU W 182 " --> pdb=" O GLY W 178 " (cutoff:3.500A) Processing helix chain 'W' and resid 241 through 250 removed outlier: 4.042A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 260 Processing helix chain 'W' and resid 266 through 284 Processing helix chain 'W' and resid 302 through 314 removed outlier: 4.177A pdb=" N GLU W 314 " --> pdb=" O ASN W 310 " (cutoff:3.500A) Processing helix chain 'W' and resid 339 through 343 Processing helix chain 'W' and resid 344 through 351 removed outlier: 3.567A pdb=" N LEU W 348 " --> pdb=" O PRO W 344 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 376 Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 413 removed outlier: 3.582A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN W 407 " --> pdb=" O ILE W 403 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN W 408 " --> pdb=" O SER W 404 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG W 413 " --> pdb=" O ILE W 409 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 Processing helix chain 'W' and resid 432 through 443 Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.528A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 97 Processing helix chain 'X' and resid 116 through 129 removed outlier: 3.701A pdb=" N ALA X 128 " --> pdb=" O ASN X 124 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE X 129 " --> pdb=" O PHE X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 184 through 193 removed outlier: 4.140A pdb=" N SER X 188 " --> pdb=" O THR X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 222 removed outlier: 4.414A pdb=" N THR X 220 " --> pdb=" O ALA X 217 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE X 222 " --> pdb=" O ALA X 219 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 258 Processing helix chain 'X' and resid 264 through 271 removed outlier: 3.763A pdb=" N MET X 268 " --> pdb=" O ASP X 264 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN X 271 " --> pdb=" O SER X 267 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.501A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN X 298 " --> pdb=" O LYS X 294 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 316 Processing helix chain 'X' and resid 317 through 328 Processing helix chain 'X' and resid 356 through 359 Processing helix chain 'X' and resid 360 through 366 removed outlier: 3.520A pdb=" N ILE X 364 " --> pdb=" O PRO X 360 " (cutoff:3.500A) Processing helix chain 'X' and resid 376 through 392 Processing helix chain 'X' and resid 396 through 410 Processing helix chain 'X' and resid 411 through 417 removed outlier: 3.713A pdb=" N ALA X 415 " --> pdb=" O SER X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 418 through 429 Processing helix chain 'X' and resid 435 through 446 removed outlier: 3.667A pdb=" N PHE X 446 " --> pdb=" O ALA X 442 " (cutoff:3.500A) Processing helix chain 'X' and resid 448 through 459 Processing helix chain 'Y' and resid 47 through 64 Processing helix chain 'Y' and resid 80 through 93 Processing helix chain 'Y' and resid 112 through 125 removed outlier: 3.579A pdb=" N SER Y 124 " --> pdb=" O ALA Y 120 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE Y 125 " --> pdb=" O PHE Y 121 " (cutoff:3.500A) Processing helix chain 'Y' and resid 172 through 181 Processing helix chain 'Y' and resid 206 through 211 removed outlier: 4.197A pdb=" N ARG Y 210 " --> pdb=" O ALA Y 207 " (cutoff:3.500A) Processing helix chain 'Y' and resid 241 through 250 Processing helix chain 'Y' and resid 252 through 260 removed outlier: 4.163A pdb=" N ALA Y 256 " --> pdb=" O GLN Y 252 " (cutoff:3.500A) Processing helix chain 'Y' and resid 267 through 283 removed outlier: 3.685A pdb=" N ASP Y 271 " --> pdb=" O SER Y 267 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN Y 272 " --> pdb=" O GLU Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 302 through 313 Processing helix chain 'Y' and resid 340 through 343 Processing helix chain 'Y' and resid 344 through 350 removed outlier: 3.627A pdb=" N ARG Y 350 " --> pdb=" O ASP Y 346 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 375 Processing helix chain 'Y' and resid 380 through 394 Processing helix chain 'Y' and resid 395 through 414 removed outlier: 3.739A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER Y 400 " --> pdb=" O LEU Y 396 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN Y 401 " --> pdb=" O ARG Y 397 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 Processing helix chain 'Y' and resid 432 through 443 Processing sheet with id=AA1, first strand: chain 'D' and resid 45 through 46 removed outlier: 7.762A pdb=" N ARG D 45 " --> pdb=" O ILE A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.637A pdb=" N VAL D 81 " --> pdb=" O ARG A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 43 through 44 removed outlier: 6.651A pdb=" N ARG F 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'Z' and resid 289 through 295 removed outlier: 3.628A pdb=" N THR Z 591 " --> pdb=" O TRP Z 295 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 591 through 595 current: chain 'W' and resid 152 through 161 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 166 through 171 current: chain 'W' and resid 199 through 204 Processing sheet with id=AA5, first strand: chain 'M' and resid 718 through 719 removed outlier: 6.073A pdb=" N GLN M 819 " --> pdb=" O ARG M 847 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU M 849 " --> pdb=" O GLN M 819 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N MET M 821 " --> pdb=" O LEU M 849 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU M 851 " --> pdb=" O MET M 821 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU M 823 " --> pdb=" O LEU M 851 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU M 749 " --> pdb=" O TYR M 820 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL M 822 " --> pdb=" O LEU M 749 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL M 801 " --> pdb=" O ILE M 750 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 944 through 950 removed outlier: 6.484A pdb=" N TYR M 945 " --> pdb=" O ILE M1366 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ARG M1368 " --> pdb=" O TYR M 945 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N HIS M 947 " --> pdb=" O ARG M1368 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL M1370 " --> pdb=" O HIS M 947 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL M 949 " --> pdb=" O VAL M1370 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU M1266 " --> pdb=" O ILE M1337 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE M1317 " --> pdb=" O ALA M1265 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE M1267 " --> pdb=" O PHE M1317 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N MET M1290 " --> pdb=" O ILE M1318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 26 through 29 removed outlier: 3.703A pdb=" N ALA R 28 " --> pdb=" O ILE R 15 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE R 6 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER R 102 " --> pdb=" O ILE R 6 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE R 8 " --> pdb=" O SER R 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 40 through 41 removed outlier: 3.873A pdb=" N ALA R 33 " --> pdb=" O TYR R 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR R 56 " --> pdb=" O LYS R 34 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 148 through 151 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 148 through 151 current: chain 'R' and resid 198 through 204 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 207 through 208 current: chain 'R' and resid 384 through 387 Processing sheet with id=AB1, first strand: chain 'R' and resid 286 through 288 Processing sheet with id=AB2, first strand: chain 'S' and resid 19 through 20 removed outlier: 6.639A pdb=" N THR U 159 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE U 143 " --> pdb=" O LYS U 157 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS U 157 " --> pdb=" O ILE U 143 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE U 145 " --> pdb=" O GLN U 155 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLN U 155 " --> pdb=" O ILE U 145 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG U 147 " --> pdb=" O HIS U 153 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS U 153 " --> pdb=" O ARG U 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 171 current: chain 'U' and resid 199 through 201 Processing sheet with id=AB3, first strand: chain 'S' and resid 254 through 255 Processing sheet with id=AB4, first strand: chain 'T' and resid 44 through 45 Processing sheet with id=AB5, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.642A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU T 308 " --> pdb=" O VAL T 337 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ALA T 339 " --> pdb=" O LEU T 308 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE T 310 " --> pdb=" O ALA T 339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 246 through 248 Processing sheet with id=AB7, first strand: chain 'T' and resid 229 through 230 removed outlier: 5.492A pdb=" N VAL T 230 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ARG T 214 " --> pdb=" O VAL T 230 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL T 212 " --> pdb=" O VAL T 199 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL T 199 " --> pdb=" O VAL T 212 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'T' and resid 167 through 169 Processing sheet with id=AB9, first strand: chain 'T' and resid 344 through 346 Processing sheet with id=AC1, first strand: chain 'T' and resid 394 through 395 removed outlier: 8.063A pdb=" N GLN T 394 " --> pdb=" O ILE T 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'U' and resid 40 through 41 Processing sheet with id=AC3, first strand: chain 'U' and resid 98 through 102 removed outlier: 3.614A pdb=" N ILE U 295 " --> pdb=" O MET U 322 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 102 through 106 removed outlier: 6.552A pdb=" N CYS V 103 " --> pdb=" O PHE V 309 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASP V 311 " --> pdb=" O CYS V 103 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU V 105 " --> pdb=" O ASP V 311 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU V 308 " --> pdb=" O VAL V 337 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ALA V 339 " --> pdb=" O LEU V 308 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE V 310 " --> pdb=" O ALA V 339 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 130 through 132 Processing sheet with id=AC6, first strand: chain 'V' and resid 135 through 149 removed outlier: 5.884A pdb=" N VAL V 144 " --> pdb=" O LYS V 171 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS V 171 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLU V 146 " --> pdb=" O GLY V 169 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY V 169 " --> pdb=" O GLU V 146 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR V 148 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL V 166 " --> pdb=" O LEU V 181 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 176 through 181 current: chain 'V' and resid 209 through 215 removed outlier: 6.109A pdb=" N VAL V 230 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ARG V 214 " --> pdb=" O VAL V 230 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V' and resid 345 through 346 Processing sheet with id=AC8, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AC9, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.174A pdb=" N LEU W 293 " --> pdb=" O MET W 322 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA W 324 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE W 295 " --> pdb=" O ALA W 324 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'W' and resid 378 through 379 removed outlier: 7.013A pdb=" N GLU W 378 " --> pdb=" O VAL W 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'X' and resid 103 through 106 removed outlier: 5.976A pdb=" N LEU X 308 " --> pdb=" O VAL X 337 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ALA X 339 " --> pdb=" O LEU X 308 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE X 310 " --> pdb=" O ALA X 339 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE X 75 " --> pdb=" O LEU X 338 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 130 through 151 removed outlier: 6.188A pdb=" N GLY X 169 " --> pdb=" O THR X 145 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU X 147 " --> pdb=" O ILE X 167 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE X 167 " --> pdb=" O LEU X 147 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N HIS X 165 " --> pdb=" O PRO X 149 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP X 151 " --> pdb=" O ILE X 163 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE X 163 " --> pdb=" O ASP X 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 175 through 181 current: chain 'X' and resid 207 through 214 Processing sheet with id=AD4, first strand: chain 'X' and resid 345 through 346 Processing sheet with id=AD5, first strand: chain 'Y' and resid 40 through 41 removed outlier: 3.718A pdb=" N SER Y 41 " --> pdb=" O MET Y 44 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 98 through 102 removed outlier: 3.521A pdb=" N ASP Y 296 " --> pdb=" O ILE Y 101 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU Y 293 " --> pdb=" O MET Y 322 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ALA Y 324 " --> pdb=" O LEU Y 293 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE Y 295 " --> pdb=" O ALA Y 324 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR Y 325 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 126 through 144 removed outlier: 6.566A pdb=" N THR Y 159 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE Y 143 " --> pdb=" O LYS Y 157 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LYS Y 157 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 166 through 170 current: chain 'Y' and resid 199 through 204 Processing sheet with id=AD8, first strand: chain 'Y' and resid 330 through 331 1706 hydrogen bonds defined for protein. 4935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 447 hydrogen bonds 882 hydrogen bond angles 0 basepair planarities 174 basepair parallelities 292 stacking parallelities Total time for adding SS restraints: 14.42 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10673 1.33 - 1.45: 10497 1.45 - 1.57: 25190 1.57 - 1.69: 798 1.69 - 1.81: 200 Bond restraints: 47358 Sorted by residual: bond pdb=" CA PRO X 360 " pdb=" C PRO X 360 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.54e+01 bond pdb=" C3' DG J 63 " pdb=" C2' DG J 63 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.40e+01 bond pdb=" C3' DC J -84 " pdb=" C2' DC J -84 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.36e+01 bond pdb=" C3' DG I -80 " pdb=" C2' DG I -80 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.35e+01 bond pdb=" C3' DA I 23 " pdb=" C2' DA I 23 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 ... (remaining 47353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 64857 2.48 - 4.95: 737 4.95 - 7.43: 107 7.43 - 9.91: 10 9.91 - 12.38: 3 Bond angle restraints: 65714 Sorted by residual: angle pdb=" C PRO Z 587 " pdb=" N GLU Z 588 " pdb=" CA GLU Z 588 " ideal model delta sigma weight residual 121.70 134.08 -12.38 1.80e+00 3.09e-01 4.73e+01 angle pdb=" O4' DG J 74 " pdb=" C4' DG J 74 " pdb=" C3' DG J 74 " ideal model delta sigma weight residual 106.00 102.72 3.28 6.00e-01 2.78e+00 2.99e+01 angle pdb=" O4' DA I -66 " pdb=" C4' DA I -66 " pdb=" C3' DA I -66 " ideal model delta sigma weight residual 106.00 102.87 3.13 6.00e-01 2.78e+00 2.72e+01 angle pdb=" O4' DA I -15 " pdb=" C4' DA I -15 " pdb=" C3' DA I -15 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.14e+01 angle pdb=" C4' DG J 78 " pdb=" O4' DG J 78 " pdb=" C1' DG J 78 " ideal model delta sigma weight residual 110.10 105.49 4.61 1.00e+00 1.00e+00 2.13e+01 ... (remaining 65709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.36: 25163 32.36 - 64.72: 2527 64.72 - 97.08: 134 97.08 - 129.44: 2 129.44 - 161.80: 4 Dihedral angle restraints: 27830 sinusoidal: 13806 harmonic: 14024 Sorted by residual: dihedral pdb=" CA THR Z 298 " pdb=" C THR Z 298 " pdb=" N PRO Z 299 " pdb=" CA PRO Z 299 " ideal model delta harmonic sigma weight residual -180.00 -142.16 -37.84 0 5.00e+00 4.00e-02 5.73e+01 dihedral pdb=" CA PHE S 211 " pdb=" C PHE S 211 " pdb=" N LEU S 212 " pdb=" CA LEU S 212 " ideal model delta harmonic sigma weight residual 180.00 147.71 32.29 0 5.00e+00 4.00e-02 4.17e+01 dihedral pdb=" CA PHE E 26 " pdb=" C PHE E 26 " pdb=" N PRO E 27 " pdb=" CA PRO E 27 " ideal model delta harmonic sigma weight residual 180.00 148.36 31.64 0 5.00e+00 4.00e-02 4.01e+01 ... (remaining 27827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 6386 0.058 - 0.117: 1191 0.117 - 0.175: 77 0.175 - 0.234: 1 0.234 - 0.292: 2 Chirality restraints: 7657 Sorted by residual: chirality pdb=" CG LEU V 416 " pdb=" CB LEU V 416 " pdb=" CD1 LEU V 416 " pdb=" CD2 LEU V 416 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA PRO Z 299 " pdb=" N PRO Z 299 " pdb=" C PRO Z 299 " pdb=" CB PRO Z 299 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL M 756 " pdb=" CA VAL M 756 " pdb=" CG1 VAL M 756 " pdb=" CG2 VAL M 756 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.98e-01 ... (remaining 7654 not shown) Planarity restraints: 6997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR Z 298 " 0.083 5.00e-02 4.00e+02 1.29e-01 2.68e+01 pdb=" N PRO Z 299 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO Z 299 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO Z 299 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 76 " 0.017 2.00e-02 2.50e+03 1.86e-02 8.67e+00 pdb=" CG TRP R 76 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP R 76 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP R 76 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 76 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 76 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 76 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 76 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 76 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 76 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS G 52 " -0.036 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO G 53 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.030 5.00e-02 4.00e+02 ... (remaining 6994 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 719 2.59 - 3.16: 39638 3.16 - 3.74: 82934 3.74 - 4.32: 105206 4.32 - 4.90: 160492 Nonbonded interactions: 388989 Sorted by model distance: nonbonded pdb=" O2B ADP V 501 " pdb="MG MG V 502 " model vdw 2.007 2.170 nonbonded pdb=" O2A ADP W 501 " pdb="MG MG W 502 " model vdw 2.015 2.170 nonbonded pdb=" O2A ADP V 501 " pdb="MG MG V 502 " model vdw 2.032 2.170 nonbonded pdb=" O2 DC I -51 " pdb=" N2 DG J 51 " model vdw 2.033 2.496 nonbonded pdb=" O2B ADP Y 501 " pdb="MG MG Y 502 " model vdw 2.038 2.170 ... (remaining 388984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 23 through 102) selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 17 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 or (resid 77 through 78 and (name N or nam \ e CA or name C or name O or name CB )) or resid 79 through 117)) selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 35 through 125) selection = chain 'H' } ncs_group { reference = (chain 'T' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 502)) selection = (chain 'V' and (resid 22 through 161 or (resid 162 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 502)) selection = (chain 'X' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 161 through 163 and (name N or name CA or \ name C or name O or name CB )) or resid 164 through 502)) } ncs_group { reference = (chain 'U' and (resid 15 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 145 or (resid 146 through 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 222 or (resid 223 and (name N or name C \ A or name C or name O or name CB )) or resid 224 through 459 or resid 501 throug \ h 502)) selection = (chain 'W' and (resid 15 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 145 or (resid 146 through 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 200 or (resid 201 and (name N or name C \ A or name C or name O or name CB )) or resid 202 through 205 or resid 222 throug \ h 502)) selection = (chain 'Y' and (resid 15 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 205 or resid 222 or (resid 223 \ and (name N or name CA or name C or name O or name CB )) or resid 224 through 45 \ 9 or resid 501 through 502)) } 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: 3.610 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: 0.040 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 52.690 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 : 0.004 0.056 47367 Z= 0.324 Angle : 0.706 12.383 65723 Z= 0.496 Chirality : 0.043 0.292 7657 Planarity : 0.004 0.129 6997 Dihedral : 21.573 161.801 18754 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.78 % Favored : 95.11 % Rotamer: Outliers : 0.02 % Allowed : 0.54 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.21 % Twisted General : 0.04 % 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: -0.33 (0.12), residues: 4788 helix: 0.62 (0.11), residues: 2193 sheet: 0.11 (0.20), residues: 635 loop : -1.25 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 836 TYR 0.021 0.001 TYR C 88 PHE 0.023 0.001 PHE W 121 TRP 0.051 0.002 TRP R 76 HIS 0.009 0.001 HIS M1285 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.32 (47358) covalent geometry : angle 0.70611 / 0.50 (65714) hydrogen bonds : bond 0.14594 / 9.96 ( 2153) hydrogen bonds : angle 5.61851 / 4.11 ( 5817) metal coordination : bond 0.00925 / 0.66 ( 8) metal coordination : angle 1.56935 / 1.01 ( 9) Misc. bond : bond 0.00267 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 62 MET cc_start: 0.2611 (tpt) cc_final: 0.2342 (tpt) REVERT: R 422 HIS cc_start: 0.8729 (m90) cc_final: 0.8525 (m90) REVERT: T 193 LYS cc_start: 0.6451 (tppt) cc_final: 0.5988 (tmmt) REVERT: U 165 MET cc_start: 0.3812 (mpp) cc_final: 0.2897 (mmt) REVERT: V 315 MET cc_start: 0.8916 (tpt) cc_final: 0.8671 (tpp) REVERT: W 175 MET cc_start: 0.8051 (mpp) cc_final: 0.7835 (mpp) outliers start: 1 outliers final: 1 residues processed: 222 average time/residue: 0.2730 time to fit residues: 101.7068 Evaluate side-chains 167 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 0.9990 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 20.0000 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN ** M 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 811 HIS ** M 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1249 GLN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 246 ASN ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 286 GLN ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 453 ASN ** W 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 119 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.070371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.048648 restraints weight = 786221.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.049238 restraints weight = 659289.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.049732 restraints weight = 569441.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.050142 restraints weight = 504423.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.050481 restraints weight = 457051.082| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 47367 Z= 0.224 Angle : 0.708 9.338 65723 Z= 0.383 Chirality : 0.046 0.346 7657 Planarity : 0.005 0.090 6997 Dihedral : 25.281 165.586 9516 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.41 % Favored : 94.49 % Rotamer: Outliers : 0.12 % Allowed : 7.61 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.21 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.12), residues: 4788 helix: 0.42 (0.11), residues: 2228 sheet: -0.28 (0.20), residues: 616 loop : -1.24 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M1169 TYR 0.022 0.002 TYR F 51 PHE 0.023 0.002 PHE B 54 TRP 0.019 0.002 TRP R 426 HIS 0.011 0.002 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.22 (47358) covalent geometry : angle 0.70755 / 0.38 (65714) hydrogen bonds : bond 0.06275 / 4.16 ( 2153) hydrogen bonds : angle 4.94210 / 3.58 ( 5817) metal coordination : bond 0.00734 / 0.43 ( 8) metal coordination : angle 2.40530 / 1.44 ( 9) Misc. bond : bond 0.00098 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 205 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 62 MET cc_start: 0.2419 (tpt) cc_final: 0.2132 (tpt) REVERT: U 94 LYS cc_start: 0.8848 (tptp) cc_final: 0.8452 (mmtt) REVERT: U 95 ASP cc_start: 0.9011 (m-30) cc_final: 0.8755 (m-30) REVERT: U 165 MET cc_start: 0.4131 (mpp) cc_final: 0.2715 (mmt) REVERT: V 315 MET cc_start: 0.8909 (tpt) cc_final: 0.8621 (tpp) REVERT: W 86 MET cc_start: 0.9253 (tpt) cc_final: 0.9052 (tpt) REVERT: W 175 MET cc_start: 0.8155 (mpp) cc_final: 0.7845 (mpp) REVERT: X 70 MET cc_start: 0.6474 (mmt) cc_final: 0.6025 (mmt) outliers start: 5 outliers final: 2 residues processed: 210 average time/residue: 0.2619 time to fit residues: 92.5487 Evaluate side-chains 155 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 74 optimal weight: 50.0000 chunk 350 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 51 optimal weight: 40.0000 chunk 6 optimal weight: 30.0000 chunk 180 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 chunk 288 optimal weight: 0.9980 chunk 53 optimal weight: 40.0000 chunk 430 optimal weight: 0.9980 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 39 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 828 ASN ** M 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN T 271 GLN ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 401 ASN ** V 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.070676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.048715 restraints weight = 776429.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.049352 restraints weight = 645268.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.049887 restraints weight = 553302.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.050314 restraints weight = 488184.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.050676 restraints weight = 438895.127| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 47367 Z= 0.156 Angle : 0.656 9.922 65723 Z= 0.355 Chirality : 0.045 0.358 7657 Planarity : 0.005 0.092 6997 Dihedral : 25.285 167.489 9516 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.22 % Favored : 94.65 % Rotamer: Outliers : 0.12 % Allowed : 5.00 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.21 % Twisted General : 0.02 % 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: -0.61 (0.12), residues: 4788 helix: 0.38 (0.11), residues: 2231 sheet: -0.36 (0.20), residues: 636 loop : -1.28 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 55 TYR 0.029 0.001 TYR S 18 PHE 0.024 0.001 PHE W 121 TRP 0.018 0.001 TRP R 426 HIS 0.007 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (47358) covalent geometry : angle 0.65603 / 0.36 (65714) hydrogen bonds : bond 0.05030 / 3.34 ( 2153) hydrogen bonds : angle 4.81826 / 3.49 ( 5817) metal coordination : bond 0.00461 / 0.31 ( 8) metal coordination : angle 1.98795 / 1.19 ( 9) Misc. bond : bond 0.00155 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 208 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 62 MET cc_start: 0.2877 (tpt) cc_final: 0.2607 (tpt) REVERT: H 57 ILE cc_start: 0.4435 (tt) cc_final: 0.4094 (tt) REVERT: R 422 HIS cc_start: 0.8719 (m90) cc_final: 0.8508 (m90) REVERT: S 174 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.5584 (pm20) REVERT: U 94 LYS cc_start: 0.8855 (tptp) cc_final: 0.8454 (mmtt) REVERT: U 95 ASP cc_start: 0.9004 (m-30) cc_final: 0.8726 (m-30) REVERT: U 165 MET cc_start: 0.4168 (mpp) cc_final: 0.3394 (mmt) REVERT: V 315 MET cc_start: 0.8851 (tpt) cc_final: 0.8566 (tpp) REVERT: W 175 MET cc_start: 0.8224 (mpp) cc_final: 0.7908 (mpp) REVERT: X 70 MET cc_start: 0.6275 (mmt) cc_final: 0.6002 (mmt) REVERT: X 122 MET cc_start: 0.9202 (tpt) cc_final: 0.8993 (tpp) outliers start: 5 outliers final: 0 residues processed: 213 average time/residue: 0.2513 time to fit residues: 90.0507 Evaluate side-chains 161 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 395 optimal weight: 0.9990 chunk 127 optimal weight: 40.0000 chunk 273 optimal weight: 0.0070 chunk 28 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 456 optimal weight: 10.0000 chunk 238 optimal weight: 0.1980 chunk 459 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 overall best weight: 2.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 25 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 969 GLN ** M1050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS ** S 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.070668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.048677 restraints weight = 776825.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.049313 restraints weight = 645189.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.049828 restraints weight = 554819.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.050265 restraints weight = 489644.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.050611 restraints weight = 441502.112| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 47367 Z= 0.148 Angle : 0.649 9.620 65723 Z= 0.349 Chirality : 0.044 0.359 7657 Planarity : 0.004 0.127 6997 Dihedral : 25.261 168.165 9516 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.35 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.21 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.12), residues: 4788 helix: 0.40 (0.11), residues: 2220 sheet: -0.39 (0.20), residues: 629 loop : -1.25 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG X 451 TYR 0.032 0.001 TYR W 447 PHE 0.022 0.001 PHE W 121 TRP 0.017 0.001 TRP R 426 HIS 0.015 0.001 HIS Y 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (47358) covalent geometry : angle 0.64847 / 0.35 (65714) hydrogen bonds : bond 0.04861 / 3.23 ( 2153) hydrogen bonds : angle 4.74617 / 3.44 ( 5817) metal coordination : bond 0.00426 / 0.29 ( 8) metal coordination : angle 1.87245 / 1.18 ( 9) Misc. bond : bond 0.00142 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 147 MET cc_start: 0.9030 (mmm) cc_final: 0.8800 (mmm) REVERT: T 122 MET cc_start: 0.9068 (mmp) cc_final: 0.8850 (mmm) REVERT: U 94 LYS cc_start: 0.8859 (tptp) cc_final: 0.8458 (mmtt) REVERT: U 95 ASP cc_start: 0.8999 (m-30) cc_final: 0.8713 (m-30) REVERT: U 165 MET cc_start: 0.4389 (mpp) cc_final: 0.3291 (mmt) REVERT: V 315 MET cc_start: 0.8827 (tpt) cc_final: 0.8528 (tpp) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2558 time to fit residues: 89.7952 Evaluate side-chains 157 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 331 optimal weight: 5.9990 chunk 515 optimal weight: 9.9990 chunk 232 optimal weight: 0.0030 chunk 279 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 148 optimal weight: 50.0000 chunk 223 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 overall best weight: 5.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 115 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 969 GLN ** M1050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 436 ASN ** S 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 273 ASN ** T 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 190 GLN ** X 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.069126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.047565 restraints weight = 793059.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.048134 restraints weight = 663028.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.048630 restraints weight = 572064.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.049021 restraints weight = 504915.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.049348 restraints weight = 457826.239| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 47367 Z= 0.211 Angle : 0.706 9.261 65723 Z= 0.381 Chirality : 0.045 0.362 7657 Planarity : 0.005 0.101 6997 Dihedral : 25.351 169.866 9516 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.85 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.21 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.12), residues: 4788 helix: 0.22 (0.11), residues: 2225 sheet: -0.73 (0.20), residues: 612 loop : -1.29 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG T 342 TYR 0.023 0.002 TYR W 447 PHE 0.042 0.002 PHE R 233 TRP 0.027 0.002 TRP R 426 HIS 0.009 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 (47358) covalent geometry : angle 0.70582 / 0.38 (65714) hydrogen bonds : bond 0.05802 / 3.87 ( 2153) hydrogen bonds : angle 4.86393 / 3.51 ( 5817) metal coordination : bond 0.00787 / 0.51 ( 8) metal coordination : angle 2.58245 / 1.51 ( 9) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 147 MET cc_start: 0.9016 (mmm) cc_final: 0.8751 (mmm) REVERT: R 422 HIS cc_start: 0.8740 (m90) cc_final: 0.8534 (m90) REVERT: U 165 MET cc_start: 0.4556 (mpp) cc_final: 0.3512 (mmt) REVERT: V 315 MET cc_start: 0.8752 (tpt) cc_final: 0.8482 (tpp) REVERT: W 175 MET cc_start: 0.8235 (mpp) cc_final: 0.7901 (mpp) REVERT: X 70 MET cc_start: 0.6325 (mmt) cc_final: 0.6062 (mmt) REVERT: Y 86 MET cc_start: 0.9230 (mmp) cc_final: 0.8841 (ptm) REVERT: Y 265 ILE cc_start: 0.3755 (mt) cc_final: 0.3102 (mt) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2663 time to fit residues: 87.0505 Evaluate side-chains 150 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 471 optimal weight: 0.9980 chunk 482 optimal weight: 0.9990 chunk 302 optimal weight: 5.9990 chunk 296 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 438 optimal weight: 0.8980 chunk 58 optimal weight: 40.0000 chunk 107 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 chunk 390 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 29 HIS X 250 HIS ** X 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 325 ASN ** 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 = 0.3877 r_free = 0.3877 target = 0.069957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.048000 restraints weight = 779797.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.048624 restraints weight = 645045.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.049152 restraints weight = 552080.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.049582 restraints weight = 485923.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.049936 restraints weight = 437687.477| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 47367 Z= 0.142 Angle : 0.664 9.454 65723 Z= 0.354 Chirality : 0.045 0.367 7657 Planarity : 0.004 0.094 6997 Dihedral : 25.316 170.412 9516 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.41 % Favored : 94.49 % Rotamer: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.12), residues: 4788 helix: 0.31 (0.11), residues: 2221 sheet: -0.64 (0.20), residues: 622 loop : -1.33 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 342 TYR 0.019 0.001 TYR W 447 PHE 0.026 0.002 PHE M 869 TRP 0.021 0.001 TRP R 426 HIS 0.011 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (47358) covalent geometry : angle 0.66396 / 0.35 (65714) hydrogen bonds : bond 0.04670 / 3.11 ( 2153) hydrogen bonds : angle 4.71272 / 3.42 ( 5817) metal coordination : bond 0.00366 / 0.26 ( 8) metal coordination : angle 2.01970 / 1.26 ( 9) Misc. bond : bond 0.00106 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 147 MET cc_start: 0.9002 (mmm) cc_final: 0.8720 (mmm) REVERT: T 240 LYS cc_start: 0.9449 (pptt) cc_final: 0.9212 (ttpp) REVERT: U 165 MET cc_start: 0.5032 (mpp) cc_final: 0.4014 (mmt) REVERT: V 315 MET cc_start: 0.8734 (tpt) cc_final: 0.8412 (tpp) REVERT: W 175 MET cc_start: 0.8248 (mpp) cc_final: 0.7927 (mpp) REVERT: X 70 MET cc_start: 0.6501 (mmt) cc_final: 0.6230 (mmt) REVERT: Y 86 MET cc_start: 0.9315 (mmp) cc_final: 0.8930 (ptm) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.2410 time to fit residues: 81.3966 Evaluate side-chains 151 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 100 optimal weight: 10.0000 chunk 119 optimal weight: 40.0000 chunk 51 optimal weight: 7.9990 chunk 515 optimal weight: 6.9990 chunk 161 optimal weight: 0.4980 chunk 422 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 325 optimal weight: 4.9990 chunk 260 optimal weight: 20.0000 chunk 254 optimal weight: 30.0000 chunk 22 optimal weight: 9.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 804 GLN ** M 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 270 HIS ** S 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 248 ASN ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.068527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.047034 restraints weight = 794030.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.047605 restraints weight = 661700.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.048071 restraints weight = 571058.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.048460 restraints weight = 505262.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.048771 restraints weight = 457427.813| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 47367 Z= 0.204 Angle : 0.712 9.221 65723 Z= 0.381 Chirality : 0.046 0.395 7657 Planarity : 0.005 0.119 6997 Dihedral : 25.371 171.055 9516 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.89 % Favored : 94.01 % Rotamer: Outliers : 0.02 % Allowed : 3.05 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.12), residues: 4788 helix: 0.16 (0.11), residues: 2205 sheet: -0.79 (0.20), residues: 600 loop : -1.38 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 75 TYR 0.019 0.002 TYR X 323 PHE 0.025 0.002 PHE B 54 TRP 0.030 0.002 TRP R 426 HIS 0.011 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (47358) covalent geometry : angle 0.71119 / 0.38 (65714) hydrogen bonds : bond 0.05730 / 3.83 ( 2153) hydrogen bonds : angle 4.85460 / 3.51 ( 5817) metal coordination : bond 0.00763 / 0.51 ( 8) metal coordination : angle 2.46636 / 1.47 ( 9) Misc. bond : bond 0.00124 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 147 MET cc_start: 0.9058 (mmm) cc_final: 0.8768 (mmm) REVERT: R 422 HIS cc_start: 0.8759 (m90) cc_final: 0.8556 (m90) REVERT: S 174 GLU cc_start: 0.4809 (OUTLIER) cc_final: 0.4503 (pm20) REVERT: T 240 LYS cc_start: 0.9413 (pptt) cc_final: 0.9184 (ttpp) REVERT: U 165 MET cc_start: 0.5044 (mpp) cc_final: 0.4104 (mmt) REVERT: V 315 MET cc_start: 0.8625 (tpt) cc_final: 0.8325 (tpp) REVERT: W 175 MET cc_start: 0.8229 (mpp) cc_final: 0.7887 (mpp) REVERT: Y 86 MET cc_start: 0.9265 (mmp) cc_final: 0.8836 (ptm) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.2085 time to fit residues: 67.1611 Evaluate side-chains 141 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 27 optimal weight: 20.0000 chunk 448 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 435 optimal weight: 4.9990 chunk 485 optimal weight: 6.9990 chunk 437 optimal weight: 5.9990 chunk 371 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 356 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 27 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 808 GLN ** M 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1012 HIS ** M1050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1126 ASN ** M1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1302 GLN M1360 GLN ** S 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 248 ASN V 271 GLN ** W 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.067332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.046261 restraints weight = 806754.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.046801 restraints weight = 672374.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.047252 restraints weight = 579114.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.047620 restraints weight = 513305.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.047888 restraints weight = 464133.713| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 47367 Z= 0.244 Angle : 0.791 13.098 65723 Z= 0.422 Chirality : 0.048 0.370 7657 Planarity : 0.006 0.099 6997 Dihedral : 25.556 173.161 9516 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 26.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.50 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.12), residues: 4788 helix: -0.11 (0.11), residues: 2198 sheet: -1.07 (0.20), residues: 599 loop : -1.57 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG H 75 TYR 0.024 0.002 TYR S 234 PHE 0.034 0.002 PHE A 104 TRP 0.048 0.003 TRP R 426 HIS 0.017 0.002 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.24 (47358) covalent geometry : angle 0.79007 / 0.42 (65714) hydrogen bonds : bond 0.06200 / 4.15 ( 2153) hydrogen bonds : angle 5.14233 / 3.71 ( 5817) metal coordination : bond 0.00999 / 0.66 ( 8) metal coordination : angle 3.00753 / 1.77 ( 9) Misc. bond : bond 0.00126 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 240 LYS cc_start: 0.9340 (pptt) cc_final: 0.9094 (ttpp) REVERT: U 165 MET cc_start: 0.5529 (mpp) cc_final: 0.5046 (mpp) REVERT: W 175 MET cc_start: 0.8319 (mpp) cc_final: 0.7969 (mpp) REVERT: X 70 MET cc_start: 0.7237 (mmt) cc_final: 0.6486 (mmt) REVERT: Y 86 MET cc_start: 0.9185 (mmp) cc_final: 0.8682 (ptm) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2152 time to fit residues: 66.2802 Evaluate side-chains 136 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 470 optimal weight: 0.0570 chunk 44 optimal weight: 8.9990 chunk 333 optimal weight: 4.9990 chunk 346 optimal weight: 0.9980 chunk 349 optimal weight: 0.8980 chunk 210 optimal weight: 0.8980 chunk 329 optimal weight: 0.8980 chunk 301 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 16 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 270 HIS S 92 GLN ** S 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 153 HIS U 155 GLN ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 248 ASN ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.068882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.047037 restraints weight = 775486.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.047652 restraints weight = 640088.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.048168 restraints weight = 547827.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.048594 restraints weight = 482299.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.048905 restraints weight = 433774.223| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 47367 Z= 0.149 Angle : 0.717 10.239 65723 Z= 0.377 Chirality : 0.046 0.364 7657 Planarity : 0.004 0.080 6997 Dihedral : 25.440 172.048 9516 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.49 % Favored : 94.38 % Rotamer: Outliers : 0.02 % Allowed : 1.02 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.12), residues: 4788 helix: 0.18 (0.11), residues: 2197 sheet: -1.00 (0.20), residues: 608 loop : -1.43 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 75 TYR 0.037 0.002 TYR F 51 PHE 0.039 0.002 PHE B 67 TRP 0.028 0.002 TRP R 426 HIS 0.010 0.001 HIS S 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (47358) covalent geometry : angle 0.71612 / 0.38 (65714) hydrogen bonds : bond 0.04624 / 3.07 ( 2153) hydrogen bonds : angle 4.81706 / 3.50 ( 5817) metal coordination : bond 0.00388 / 0.28 ( 8) metal coordination : angle 2.40817 / 1.55 ( 9) Misc. bond : bond 0.00105 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 200 MET cc_start: 0.6389 (mmm) cc_final: 0.6165 (tpt) REVERT: T 240 LYS cc_start: 0.9411 (pptt) cc_final: 0.9178 (ttpp) REVERT: U 165 MET cc_start: 0.5400 (mpp) cc_final: 0.4831 (mpp) REVERT: U 294 PHE cc_start: 0.9346 (t80) cc_final: 0.9032 (t80) REVERT: U 323 MET cc_start: 0.9114 (mpp) cc_final: 0.8834 (mpp) REVERT: W 175 MET cc_start: 0.8235 (mpp) cc_final: 0.7884 (mpp) REVERT: X 70 MET cc_start: 0.7204 (mmt) cc_final: 0.6609 (mmt) REVERT: Y 86 MET cc_start: 0.9249 (mmp) cc_final: 0.8811 (ptm) outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.1829 time to fit residues: 60.3842 Evaluate side-chains 146 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 492 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 341 optimal weight: 10.0000 chunk 383 optimal weight: 6.9990 chunk 280 optimal weight: 8.9990 chunk 504 optimal weight: 0.0970 chunk 245 optimal weight: 0.8980 chunk 293 optimal weight: 1.9990 chunk 480 optimal weight: 9.9990 chunk 490 optimal weight: 5.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Z 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 455 GLN ** 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 = 0.3846 r_free = 0.3846 target = 0.068540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.046807 restraints weight = 786321.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.047403 restraints weight = 651129.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.047905 restraints weight = 557688.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.048315 restraints weight = 491731.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.048643 restraints weight = 443776.729| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 47367 Z= 0.153 Angle : 0.700 13.605 65723 Z= 0.371 Chirality : 0.045 0.360 7657 Planarity : 0.004 0.078 6997 Dihedral : 25.377 171.663 9516 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.70 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.12), residues: 4788 helix: 0.22 (0.11), residues: 2207 sheet: -1.00 (0.20), residues: 590 loop : -1.43 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 836 TYR 0.028 0.002 TYR F 51 PHE 0.024 0.002 PHE B 54 TRP 0.027 0.002 TRP R 426 HIS 0.009 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (47358) covalent geometry : angle 0.69975 / 0.37 (65714) hydrogen bonds : bond 0.04829 / 3.21 ( 2153) hydrogen bonds : angle 4.78011 / 3.47 ( 5817) metal coordination : bond 0.00479 / 0.33 ( 8) metal coordination : angle 2.13260 / 1.39 ( 9) Misc. bond : bond 0.00063 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 62 MET cc_start: 0.3871 (tpt) cc_final: 0.3582 (tpt) REVERT: Z 200 MET cc_start: 0.6267 (mmm) cc_final: 0.6019 (tpt) REVERT: T 122 MET cc_start: 0.8982 (mmp) cc_final: 0.8763 (mmm) REVERT: T 240 LYS cc_start: 0.9417 (pptt) cc_final: 0.9182 (ttpp) REVERT: U 165 MET cc_start: 0.5516 (mpp) cc_final: 0.4991 (mpp) REVERT: U 323 MET cc_start: 0.9089 (mpp) cc_final: 0.8877 (mpp) REVERT: V 315 MET cc_start: 0.8496 (tpt) cc_final: 0.8285 (tpp) REVERT: W 175 MET cc_start: 0.8278 (mpp) cc_final: 0.7923 (mpp) REVERT: X 70 MET cc_start: 0.7181 (mmt) cc_final: 0.6572 (mmt) REVERT: Y 86 MET cc_start: 0.9204 (mmp) cc_final: 0.8681 (ptm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1620 time to fit residues: 51.0435 Evaluate side-chains 143 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 45 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 134 optimal weight: 0.4980 chunk 133 optimal weight: 30.0000 chunk 258 optimal weight: 6.9990 chunk 412 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 328 optimal weight: 6.9990 chunk 308 optimal weight: 0.0040 chunk 508 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 63 ASN ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 341 HIS ** W 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 263 GLN ** 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 = 0.3839 r_free = 0.3839 target = 0.068356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.046722 restraints weight = 783370.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.047305 restraints weight = 651031.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.047788 restraints weight = 559326.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.048194 restraints weight = 493288.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.048533 restraints weight = 445239.069| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 47367 Z= 0.158 Angle : 0.696 12.725 65723 Z= 0.368 Chirality : 0.045 0.362 7657 Planarity : 0.004 0.075 6997 Dihedral : 25.340 172.162 9516 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.89 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.12), residues: 4788 helix: 0.20 (0.11), residues: 2211 sheet: -1.05 (0.20), residues: 593 loop : -1.46 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 836 TYR 0.027 0.002 TYR F 51 PHE 0.022 0.002 PHE M 869 TRP 0.028 0.002 TRP R 426 HIS 0.008 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (47358) covalent geometry : angle 0.69579 / 0.37 (65714) hydrogen bonds : bond 0.04747 / 3.16 ( 2153) hydrogen bonds : angle 4.76781 / 3.45 ( 5817) metal coordination : bond 0.00493 / 0.34 ( 8) metal coordination : angle 2.14005 / 1.41 ( 9) Misc. bond : bond 0.00058 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9990.90 seconds wall clock time: 172 minutes 31.48 seconds (10351.48 seconds total)