Starting phenix.real_space_refine on Wed Aug 27 02:22:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qkv_18472/08_2025/8qkv_18472.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qkv_18472/08_2025/8qkv_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qkv_18472/08_2025/8qkv_18472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qkv_18472/08_2025/8qkv_18472.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qkv_18472/08_2025/8qkv_18472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qkv_18472/08_2025/8qkv_18472.map" } 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-2.0-5787/lib/python3.9/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: 10.58, per 1000 atoms: 0.23 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: 4.04 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 1.2 microseconds 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: 6.10 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: 14.65 Time building geometry restraints manager: 5.46 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=" C THR Z 298 " pdb=" N PRO Z 299 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.47e+00 bond pdb=" C3' DG J -19 " pdb=" O3' DG J -19 " ideal model delta sigma weight residual 1.422 1.470 -0.048 3.00e-02 1.11e+03 2.56e+00 bond pdb=" CG1 ILE X 92 " pdb=" CD1 ILE X 92 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.07e+00 bond pdb=" CD GLU W 442 " pdb=" OE1 GLU W 442 " ideal model delta sigma weight residual 1.249 1.223 0.026 1.90e-02 2.77e+03 1.87e+00 ... (remaining 47353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 65035 2.48 - 4.95: 559 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=" N PHE E 26 " pdb=" CA PHE E 26 " pdb=" C PHE E 26 " ideal model delta sigma weight residual 109.60 114.85 -5.25 1.15e+00 7.56e-01 2.08e+01 angle pdb=" CB MET R 400 " pdb=" CG MET R 400 " pdb=" SD MET R 400 " ideal model delta sigma weight residual 112.70 125.00 -12.30 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C THR E 25 " pdb=" N PHE E 26 " pdb=" CA PHE E 26 " ideal model delta sigma weight residual 120.51 125.66 -5.15 1.45e+00 4.76e-01 1.26e+01 angle pdb=" CA LEU M 953 " pdb=" CB LEU M 953 " pdb=" CG LEU M 953 " ideal model delta sigma weight residual 116.30 127.93 -11.63 3.50e+00 8.16e-02 1.10e+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: 6593 0.058 - 0.117: 991 0.117 - 0.175: 70 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 57.370 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.130 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.003 0.056 47367 Z= 0.136 Angle : 0.638 12.383 65723 Z= 0.334 Chirality : 0.041 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 aren 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 covalent geometry : bond 0.00286 (47358) covalent geometry : angle 0.63827 (65714) hydrogen bonds : bond 0.14594 ( 2153) hydrogen bonds : angle 5.61851 ( 5817) metal coordination : bond 0.00925 ( 8) metal coordination : angle 1.56935 ( 9) Misc. bond : bond 0.00267 ( 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 : 1.701 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: 0.2359 (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: 0.2896 (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: 0.2785 time to fit residues: 103.1199 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 : 1.687 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 39 HIS ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN G 59 GLN E 105 GLN ** M 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 811 HIS ** M 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 969 GLN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 246 ASN ** T 271 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** ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.069569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.048036 restraints weight = 790825.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.048609 restraints weight = 663136.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.049081 restraints weight = 574590.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.049484 restraints weight = 508558.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.049808 restraints weight = 460443.224| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 47367 Z= 0.235 Angle : 0.710 9.156 65723 Z= 0.378 Chirality : 0.043 0.234 7657 Planarity : 0.005 0.088 6997 Dihedral : 25.226 164.705 9516 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 22.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.87 % Favored : 94.01 % Rotamer: Outliers : 0.22 % Allowed : 8.51 % Favored : 91.27 % 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 aren not related in a simple way. whole: -0.67 (0.12), residues: 4788 helix: 0.32 (0.11), residues: 2238 sheet: -0.35 (0.20), residues: 618 loop : -1.32 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M1169 TYR 0.022 0.002 TYR F 51 PHE 0.027 0.002 PHE B 54 TRP 0.025 0.002 TRP R 76 HIS 0.011 0.002 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00493 (47358) covalent geometry : angle 0.70882 (65714) hydrogen bonds : bond 0.06358 ( 2153) hydrogen bonds : angle 4.92483 ( 5817) metal coordination : bond 0.00856 ( 8) metal coordination : angle 2.76579 ( 9) Misc. bond : bond 0.00071 ( 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 205 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 196 time to evaluate : 1.490 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: U 94 LYS cc_start: 0.8880 (tptp) cc_final: 0.8517 (mmtt) REVERT: U 95 ASP cc_start: 0.9022 (m-30) cc_final: 0.8753 (m-30) REVERT: U 165 MET cc_start: 0.4789 (mpp) cc_final: 0.3855 (mmt) REVERT: V 315 MET cc_start: 0.8815 (tpt) cc_final: 0.8569 (tpp) REVERT: X 70 MET cc_start: 0.6717 (mmt) cc_final: 0.6260 (mmt) outliers start: 9 outliers final: 1 residues processed: 205 average time/residue: 0.2434 time to fit residues: 84.1890 Evaluate side-chains 156 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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: 10.0000 chunk 350 optimal weight: 0.9990 chunk 239 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 40.0000 chunk 6 optimal weight: 20.0000 chunk 180 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 288 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 430 optimal weight: 0.0570 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 828 ASN ** M 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** S 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 271 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** ** 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** ** 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 = 0.3879 r_free = 0.3879 target = 0.070176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.048294 restraints weight = 776408.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.048910 restraints weight = 644067.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.049430 restraints weight = 553941.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.049858 restraints weight = 487716.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.050200 restraints weight = 440617.621| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1704 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= 0.156 Angle : 0.638 9.358 65723 Z= 0.339 Chirality : 0.042 0.241 7657 Planarity : 0.004 0.097 6997 Dihedral : 25.225 165.392 9516 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.99 % Favored : 94.88 % Rotamer: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.86 % 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 aren not related in a simple way. whole: -0.61 (0.12), residues: 4788 helix: 0.39 (0.11), residues: 2218 sheet: -0.36 (0.20), residues: 615 loop : -1.27 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M1169 TYR 0.024 0.001 TYR W 447 PHE 0.022 0.001 PHE W 121 TRP 0.020 0.001 TRP R 426 HIS 0.007 0.001 HIS S 209 Details of bonding type rmsd covalent geometry : bond 0.00331 (47358) covalent geometry : angle 0.63791 (65714) hydrogen bonds : bond 0.04638 ( 2153) hydrogen bonds : angle 4.76666 ( 5817) metal coordination : bond 0.00477 ( 8) metal coordination : angle 2.17180 ( 9) Misc. bond : bond 0.00137 ( 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 207 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 204 time to evaluate : 1.381 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 238 MET cc_start: 0.2932 (mpp) cc_final: 0.2722 (mpp) REVERT: R 422 HIS cc_start: 0.8750 (m90) cc_final: 0.8540 (m90) REVERT: S 174 GLU cc_start: 0.5519 (OUTLIER) cc_final: 0.5316 (pm20) REVERT: U 94 LYS cc_start: 0.8887 (tptp) cc_final: 0.8511 (mmtt) REVERT: U 95 ASP cc_start: 0.9051 (m-30) cc_final: 0.8753 (m-30) REVERT: U 165 MET cc_start: 0.4765 (mpp) cc_final: 0.3866 (mmt) REVERT: V 315 MET cc_start: 0.8816 (tpt) cc_final: 0.8547 (tpp) REVERT: W 175 MET cc_start: 0.8234 (mpp) cc_final: 0.7928 (mpp) REVERT: X 70 MET cc_start: 0.6436 (mmt) cc_final: 0.6157 (mmt) outliers start: 3 outliers final: 0 residues processed: 207 average time/residue: 0.2688 time to fit residues: 93.0703 Evaluate side-chains 154 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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: 0.9980 chunk 127 optimal weight: 30.0000 chunk 273 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 456 optimal weight: 6.9990 chunk 238 optimal weight: 0.8980 chunk 459 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN ** 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 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** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 273 ASN ** T 314 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** ** U 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 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** X 29 HIS X 250 HIS ** X 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.070449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.048394 restraints weight = 775464.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.049031 restraints weight = 641621.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.049576 restraints weight = 550591.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.050023 restraints weight = 483397.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.050386 restraints weight = 435003.223| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1892 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= 0.142 Angle : 0.626 9.846 65723 Z= 0.330 Chirality : 0.041 0.273 7657 Planarity : 0.004 0.111 6997 Dihedral : 25.143 165.767 9516 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.12 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % 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 aren not related in a simple way. whole: -0.60 (0.12), residues: 4788 helix: 0.43 (0.11), residues: 2229 sheet: -0.43 (0.20), residues: 622 loop : -1.29 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 451 TYR 0.018 0.001 TYR W 447 PHE 0.023 0.001 PHE W 121 TRP 0.020 0.001 TRP R 426 HIS 0.011 0.001 HIS Y 23 Details of bonding type rmsd covalent geometry : bond 0.00302 (47358) covalent geometry : angle 0.62548 (65714) hydrogen bonds : bond 0.04308 ( 2153) hydrogen bonds : angle 4.59022 ( 5817) metal coordination : bond 0.00382 ( 8) metal coordination : angle 1.93076 ( 9) Misc. bond : bond 0.00110 ( 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 204 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.703 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: H 57 ILE cc_start: 0.4718 (tt) cc_final: 0.3980 (tt) REVERT: R 147 MET cc_start: 0.9060 (mmm) cc_final: 0.8809 (mmm) REVERT: R 238 MET cc_start: 0.2843 (mpp) cc_final: 0.2583 (mpp) REVERT: T 122 MET cc_start: 0.9028 (mmp) cc_final: 0.8824 (mmm) REVERT: U 94 LYS cc_start: 0.8882 (tptp) cc_final: 0.8495 (mmtt) REVERT: U 95 ASP cc_start: 0.9019 (m-30) cc_final: 0.8705 (m-30) REVERT: U 165 MET cc_start: 0.4848 (mpp) cc_final: 0.3929 (mmt) REVERT: V 315 MET cc_start: 0.8767 (tpt) cc_final: 0.8479 (tpp) REVERT: W 175 MET cc_start: 0.8148 (mpp) cc_final: 0.7816 (mpp) REVERT: Y 265 ILE cc_start: 0.3428 (mt) cc_final: 0.2628 (mt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2494 time to fit residues: 86.3844 Evaluate side-chains 154 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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: 8.9990 chunk 515 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 279 optimal weight: 7.9990 chunk 172 optimal weight: 20.0000 chunk 131 optimal weight: 8.9990 chunk 195 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 148 optimal weight: 50.0000 chunk 223 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS D 27 GLN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** 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 804 GLN M 808 GLN ** M 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 969 GLN M1012 HIS ** M1050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1126 ASN ** M1173 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** T 205 ASN ** T 271 GLN ** 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** ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN ** V 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** X 190 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 242 HIS ** Y 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.067371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.046378 restraints weight = 809840.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.046915 restraints weight = 676695.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.047359 restraints weight = 583776.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.047727 restraints weight = 517522.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.048027 restraints weight = 468176.064| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 47367 Z= 0.268 Angle : 0.775 9.098 65723 Z= 0.411 Chirality : 0.045 0.266 7657 Planarity : 0.006 0.088 6997 Dihedral : 25.372 168.401 9516 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 27.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 0.05 % Allowed : 6.05 % Favored : 93.91 % 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 aren not related in a simple way. whole: -1.18 (0.12), residues: 4788 helix: -0.07 (0.10), residues: 2209 sheet: -0.91 (0.20), residues: 594 loop : -1.48 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 410 TYR 0.024 0.002 TYR X 323 PHE 0.035 0.003 PHE M 869 TRP 0.020 0.002 TRP R 199 HIS 0.012 0.002 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00558 (47358) covalent geometry : angle 0.77434 (65714) hydrogen bonds : bond 0.06865 ( 2153) hydrogen bonds : angle 5.07555 ( 5817) metal coordination : bond 0.01010 ( 8) metal coordination : angle 3.65667 ( 9) Misc. bond : bond 0.00144 ( 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 185 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 1.495 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: H 62 MET cc_start: -0.1451 (tpt) cc_final: -0.1765 (tpt) REVERT: U 165 MET cc_start: 0.5152 (mpp) cc_final: 0.4621 (mpp) REVERT: V 315 MET cc_start: 0.8527 (tpt) cc_final: 0.8258 (tpp) REVERT: W 60 MET cc_start: 0.9635 (mmp) cc_final: 0.9417 (mmt) REVERT: W 175 MET cc_start: 0.8434 (mpp) cc_final: 0.8126 (mpp) REVERT: X 70 MET cc_start: 0.7047 (mmt) cc_final: 0.6408 (mmt) REVERT: Y 86 MET cc_start: 0.9180 (mmp) cc_final: 0.8686 (ptm) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.2666 time to fit residues: 83.1544 Evaluate side-chains 131 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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: 0.8980 chunk 482 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 292 optimal weight: 4.9990 chunk 438 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 346 optimal weight: 2.9990 chunk 390 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 702 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** M1302 GLN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1360 GLN ** R 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 205 ASN ** T 357 HIS ** 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** ** X 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** 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 = 0.3849 r_free = 0.3849 target = 0.068689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.046993 restraints weight = 784244.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.047570 restraints weight = 647734.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.048096 restraints weight = 556804.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.048506 restraints weight = 490693.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.048847 restraints weight = 441911.467| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 47367 Z= 0.156 Angle : 0.673 12.555 65723 Z= 0.353 Chirality : 0.043 0.321 7657 Planarity : 0.004 0.082 6997 Dihedral : 25.323 168.249 9516 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.30 % Favored : 94.59 % Rotamer: Outliers : 0.02 % Allowed : 3.00 % Favored : 96.98 % 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 aren not related in a simple way. whole: -0.91 (0.12), residues: 4788 helix: 0.20 (0.11), residues: 2220 sheet: -0.86 (0.20), residues: 612 loop : -1.37 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M1133 TYR 0.018 0.001 TYR Y 439 PHE 0.032 0.002 PHE U 254 TRP 0.014 0.001 TRP M1343 HIS 0.013 0.001 HIS Y 242 Details of bonding type rmsd covalent geometry : bond 0.00338 (47358) covalent geometry : angle 0.67253 (65714) hydrogen bonds : bond 0.04552 ( 2153) hydrogen bonds : angle 4.74127 ( 5817) metal coordination : bond 0.00480 ( 8) metal coordination : angle 2.33368 ( 9) Misc. bond : bond 0.00075 ( 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 187 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 1.110 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: M 941 MET cc_start: 0.9015 (tmm) cc_final: 0.8801 (tpt) REVERT: T 70 MET cc_start: 0.6284 (mtp) cc_final: 0.6047 (mmm) REVERT: T 240 LYS cc_start: 0.9426 (pptt) cc_final: 0.9185 (ttpp) REVERT: U 165 MET cc_start: 0.5260 (mpp) cc_final: 0.4623 (mpp) REVERT: V 315 MET cc_start: 0.8574 (tpt) cc_final: 0.8277 (tpp) REVERT: W 60 MET cc_start: 0.9706 (mmp) cc_final: 0.9505 (mmp) REVERT: X 70 MET cc_start: 0.7168 (mmt) cc_final: 0.6565 (mmt) REVERT: Y 86 MET cc_start: 0.9250 (mmp) cc_final: 0.8817 (ptm) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.2289 time to fit residues: 72.8830 Evaluate side-chains 144 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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: 6.9990 chunk 119 optimal weight: 30.0000 chunk 51 optimal weight: 6.9990 chunk 515 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 422 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 325 optimal weight: 2.9990 chunk 260 optimal weight: 9.9990 chunk 254 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS E 16 GLN ** 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** ** M1050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** 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 272 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** X 190 GLN ** X 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** 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 = 0.3828 r_free = 0.3828 target = 0.068000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.046518 restraints weight = 791624.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.047098 restraints weight = 656107.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.047577 restraints weight = 563769.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.047976 restraints weight = 496510.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.048242 restraints weight = 447711.058| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 47367 Z= 0.186 Angle : 0.682 9.660 65723 Z= 0.360 Chirality : 0.043 0.242 7657 Planarity : 0.004 0.077 6997 Dihedral : 25.299 168.168 9516 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.99 % Favored : 93.90 % Rotamer: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.34 % 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 aren not related in a simple way. whole: -0.97 (0.12), residues: 4788 helix: 0.18 (0.11), residues: 2216 sheet: -0.88 (0.20), residues: 587 loop : -1.44 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG T 258 TYR 0.025 0.002 TYR R 419 PHE 0.025 0.002 PHE M 869 TRP 0.027 0.002 TRP R 426 HIS 0.011 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00398 (47358) covalent geometry : angle 0.68140 (65714) hydrogen bonds : bond 0.05057 ( 2153) hydrogen bonds : angle 4.76952 ( 5817) metal coordination : bond 0.00588 ( 8) metal coordination : angle 2.24817 ( 9) Misc. bond : bond 0.00017 ( 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 186 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.997 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: T 70 MET cc_start: 0.6542 (mtp) cc_final: 0.6174 (mtp) REVERT: T 240 LYS cc_start: 0.9405 (pptt) cc_final: 0.9177 (ttpp) REVERT: U 165 MET cc_start: 0.6061 (mpp) cc_final: 0.5392 (mpp) REVERT: V 315 MET cc_start: 0.8473 (tpt) cc_final: 0.8128 (tpp) REVERT: W 175 MET cc_start: 0.8272 (mpp) cc_final: 0.7918 (mpp) REVERT: X 70 MET cc_start: 0.7316 (mmt) cc_final: 0.6691 (mmt) REVERT: Y 86 MET cc_start: 0.9152 (mmp) cc_final: 0.8607 (ptm) outliers start: 1 outliers final: 1 residues processed: 186 average time/residue: 0.1863 time to fit residues: 59.5185 Evaluate side-chains 135 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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: 4.9990 chunk 448 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 435 optimal weight: 0.9990 chunk 485 optimal weight: 10.0000 chunk 437 optimal weight: 1.9990 chunk 371 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 356 optimal weight: 10.0000 chunk 184 optimal weight: 0.3980 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 115 ASN ** 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** M 969 GLN ** 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** ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.068211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.046600 restraints weight = 788707.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.047187 restraints weight = 652292.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.047671 restraints weight = 558773.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.048063 restraints weight = 494646.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.048395 restraints weight = 446106.724| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 47367 Z= 0.165 Angle : 0.677 10.460 65723 Z= 0.355 Chirality : 0.043 0.365 7657 Planarity : 0.004 0.071 6997 Dihedral : 25.285 168.520 9516 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.49 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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 aren not related in a simple way. whole: -0.93 (0.12), residues: 4788 helix: 0.25 (0.11), residues: 2211 sheet: -0.92 (0.20), residues: 589 loop : -1.45 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 836 TYR 0.038 0.002 TYR F 51 PHE 0.025 0.002 PHE U 254 TRP 0.022 0.002 TRP R 426 HIS 0.010 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00358 (47358) covalent geometry : angle 0.67625 (65714) hydrogen bonds : bond 0.04583 ( 2153) hydrogen bonds : angle 4.71500 ( 5817) metal coordination : bond 0.00504 ( 8) metal coordination : angle 2.15061 ( 9) Misc. bond : bond 0.00016 ( 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 186 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.955 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: M 764 PHE cc_start: 0.9429 (m-10) cc_final: 0.9191 (m-10) REVERT: T 70 MET cc_start: 0.6566 (mtp) cc_final: 0.6201 (mtp) REVERT: T 240 LYS cc_start: 0.9410 (pptt) cc_final: 0.9188 (ttpp) REVERT: U 165 MET cc_start: 0.6547 (mpp) cc_final: 0.5818 (mpp) REVERT: W 175 MET cc_start: 0.8306 (mpp) cc_final: 0.7939 (mpp) REVERT: X 70 MET cc_start: 0.7344 (mmt) cc_final: 0.6709 (mmt) REVERT: Y 86 MET cc_start: 0.9181 (mmp) cc_final: 0.8650 (ptm) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1829 time to fit residues: 57.9178 Evaluate side-chains 141 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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: 0.5980 chunk 44 optimal weight: 20.0000 chunk 333 optimal weight: 4.9990 chunk 346 optimal weight: 6.9990 chunk 349 optimal weight: 1.9990 chunk 210 optimal weight: 0.7980 chunk 329 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 127 optimal weight: 30.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 702 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** ** 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 153 HIS U 155 GLN ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 248 ASN W 63 ASN ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 272 GLN ** 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 314 ASN ** 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 = 0.3854 r_free = 0.3854 target = 0.068753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.046906 restraints weight = 777739.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.047508 restraints weight = 642586.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.048019 restraints weight = 551413.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.048431 restraints weight = 486072.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.048784 restraints weight = 436364.202| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3647 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= 0.146 Angle : 0.674 10.488 65723 Z= 0.352 Chirality : 0.043 0.264 7657 Planarity : 0.004 0.133 6997 Dihedral : 25.198 168.316 9516 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.47 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.61 % 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 aren not related in a simple way. whole: -0.87 (0.12), residues: 4788 helix: 0.32 (0.11), residues: 2223 sheet: -0.87 (0.21), residues: 577 loop : -1.46 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 836 TYR 0.034 0.001 TYR X 414 PHE 0.025 0.002 PHE U 254 TRP 0.019 0.001 TRP R 426 HIS 0.019 0.001 HIS S 209 Details of bonding type rmsd covalent geometry : bond 0.00316 (47358) covalent geometry : angle 0.67397 (65714) hydrogen bonds : bond 0.04215 ( 2153) hydrogen bonds : angle 4.62240 ( 5817) metal coordination : bond 0.00532 ( 8) metal coordination : angle 2.29922 ( 9) Misc. bond : bond 0.00025 ( 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 189 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.962 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: T 70 MET cc_start: 0.6154 (mtp) cc_final: 0.5722 (mtp) REVERT: T 122 MET cc_start: 0.8974 (mmp) cc_final: 0.8743 (mmm) REVERT: T 240 LYS cc_start: 0.9388 (pptt) cc_final: 0.9160 (ttpp) REVERT: U 16 SER cc_start: 0.7127 (m) cc_final: 0.6893 (t) REVERT: U 165 MET cc_start: 0.6781 (mpp) cc_final: 0.6041 (mpp) REVERT: V 315 MET cc_start: 0.8029 (tpp) cc_final: 0.7813 (tpp) REVERT: W 175 MET cc_start: 0.8258 (mpp) cc_final: 0.7906 (mpp) REVERT: X 70 MET cc_start: 0.7371 (mmt) cc_final: 0.6720 (mmt) REVERT: Y 86 MET cc_start: 0.9173 (mmp) cc_final: 0.8648 (ptm) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1684 time to fit residues: 54.9585 Evaluate side-chains 144 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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: 8.9990 chunk 118 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 341 optimal weight: 8.9990 chunk 383 optimal weight: 0.0020 chunk 280 optimal weight: 8.9990 chunk 504 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 480 optimal weight: 7.9990 chunk 490 optimal weight: 5.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 279 GLN E 105 GLN ** E 113 HIS ** 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** ** 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** ** T 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 263 GLN ** 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 = 0.3804 r_free = 0.3804 target = 0.067001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.045724 restraints weight = 803545.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.046271 restraints weight = 668199.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.046722 restraints weight = 575961.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.047105 restraints weight = 508514.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.047420 restraints weight = 460119.592| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 47367 Z= 0.217 Angle : 0.731 10.575 65723 Z= 0.386 Chirality : 0.044 0.307 7657 Planarity : 0.005 0.113 6997 Dihedral : 25.314 169.947 9516 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.50 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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 aren not related in a simple way. whole: -1.12 (0.12), residues: 4788 helix: 0.11 (0.11), residues: 2229 sheet: -1.14 (0.20), residues: 592 loop : -1.53 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG X 73 TYR 0.034 0.002 TYR F 51 PHE 0.025 0.002 PHE M 869 TRP 0.031 0.002 TRP R 426 HIS 0.010 0.002 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00460 (47358) covalent geometry : angle 0.73034 (65714) hydrogen bonds : bond 0.05584 ( 2153) hydrogen bonds : angle 4.87030 ( 5817) metal coordination : bond 0.00647 ( 8) metal coordination : angle 2.48487 ( 9) Misc. bond : bond 0.00011 ( 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 : 0.969 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: M 980 MET cc_start: 0.7089 (mmp) cc_final: 0.6888 (mpp) REVERT: T 70 MET cc_start: 0.6403 (mtp) cc_final: 0.5871 (mtp) REVERT: T 240 LYS cc_start: 0.9329 (pptt) cc_final: 0.9102 (tmmt) REVERT: U 16 SER cc_start: 0.7198 (m) cc_final: 0.6968 (t) REVERT: W 175 MET cc_start: 0.8344 (mpp) cc_final: 0.7983 (mpp) REVERT: X 70 MET cc_start: 0.7452 (mmt) cc_final: 0.6817 (mmt) REVERT: Y 86 MET cc_start: 0.9160 (mmp) cc_final: 0.8631 (ptm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1709 time to fit residues: 54.4669 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 : 0.955 ------------------------------------------------------------------------------- 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: 10.0000 chunk 134 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 258 optimal weight: 7.9990 chunk 412 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 328 optimal weight: 5.9990 chunk 308 optimal weight: 0.0570 chunk 508 optimal weight: 0.9990 chunk 125 optimal weight: 20.0000 overall best weight: 2.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 ASN F 95 ASN ** 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** ** 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** ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 272 GLN ** 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 314 ASN ** 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 = 0.3826 r_free = 0.3826 target = 0.067616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.046061 restraints weight = 786540.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.046629 restraints weight = 652277.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.047108 restraints weight = 561102.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.047502 restraints weight = 495393.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.047823 restraints weight = 447213.965| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 47367 Z= 0.164 Angle : 0.685 10.626 65723 Z= 0.359 Chirality : 0.043 0.245 7657 Planarity : 0.004 0.100 6997 Dihedral : 25.308 170.293 9516 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.72 % Favored : 94.17 % 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 aren not related in a simple way. whole: -1.01 (0.12), residues: 4788 helix: 0.21 (0.11), residues: 2228 sheet: -1.02 (0.21), residues: 581 loop : -1.53 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 836 TYR 0.026 0.002 TYR F 51 PHE 0.024 0.002 PHE M 869 TRP 0.023 0.002 TRP R 426 HIS 0.009 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00357 (47358) covalent geometry : angle 0.68474 (65714) hydrogen bonds : bond 0.04508 ( 2153) hydrogen bonds : angle 4.73602 ( 5817) metal coordination : bond 0.00559 ( 8) metal coordination : angle 2.37724 ( 9) Misc. bond : bond 0.00022 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10409.79 seconds wall clock time: 179 minutes 33.59 seconds (10773.59 seconds total)