Starting phenix.real_space_refine on Wed Feb 21 20:32:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6poe_20413/02_2024/6poe_20413_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6poe_20413/02_2024/6poe_20413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6poe_20413/02_2024/6poe_20413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6poe_20413/02_2024/6poe_20413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6poe_20413/02_2024/6poe_20413_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6poe_20413/02_2024/6poe_20413_neut_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 180 5.16 5 C 20334 2.51 5 N 5387 2.21 5 O 5899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 128": "OE1" <-> "OE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A TYR 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 986": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A ARG 1045": "NH1" <-> "NH2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B GLU 781": "OE1" <-> "OE2" Residue "B PHE 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 966": "OE1" <-> "OE2" Residue "B ARG 986": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1045": "NH1" <-> "NH2" Residue "B ARG 1085": "NH1" <-> "NH2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C GLU 408": "OE1" <-> "OE2" Residue "C GLU 547": "OE1" <-> "OE2" Residue "C ARG 576": "NH1" <-> "NH2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "C GLU 683": "OE1" <-> "OE2" Residue "C GLU 770": "OE1" <-> "OE2" Residue "C PHE 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 861": "OE1" <-> "OE2" Residue "C GLU 865": "OE1" <-> "OE2" Residue "C ARG 986": "NH1" <-> "NH2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C GLU 1011": "OE1" <-> "OE2" Residue "C ARG 1045": "NH1" <-> "NH2" Residue "C ARG 1085": "NH1" <-> "NH2" Residue "C GLU 1097": "OE1" <-> "OE2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "D ARG 507": "NH1" <-> "NH2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "D GLU 603": "OE1" <-> "OE2" Residue "D TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 683": "OE1" <-> "OE2" Residue "D GLU 723": "OE1" <-> "OE2" Residue "D GLU 792": "OE1" <-> "OE2" Residue "D PHE 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 865": "OE1" <-> "OE2" Residue "D ARG 976": "NH1" <-> "NH2" Residue "D ARG 986": "NH1" <-> "NH2" Residue "D ARG 995": "NH1" <-> "NH2" Residue "D GLU 1011": "OE1" <-> "OE2" Residue "D PHE 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1045": "NH1" <-> "NH2" Residue "D ARG 1085": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31812 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "B" Number of atoms: 7903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7895 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7895 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8056 Chain: "C" Number of atoms: 7902 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7894 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7894 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8055 Chain: "D" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'COA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'COA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 31.18, per 1000 atoms: 0.98 Number of scatterers: 31812 At special positions: 0 Unit cell: (141.81, 163.56, 173.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 12 15.00 O 5899 8.00 N 5387 7.00 C 20334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.02 Conformation dependent library (CDL) restraints added in 11.6 seconds 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 153 helices and 33 sheets defined 38.3% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.19 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 78 through 84 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 178 through 195 removed outlier: 4.055A pdb=" N ALA A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 4.002A pdb=" N ASP A 226 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR A 227 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS A 230 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL A 231 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 283 through 295 removed outlier: 3.956A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 350 through 370 removed outlier: 3.611A pdb=" N TYR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLY A 366 " --> pdb=" O ARG A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 506 through 518 Processing helix chain 'A' and resid 556 through 562 Processing helix chain 'A' and resid 578 through 585 Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 643 through 648 Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 697 through 705 Processing helix chain 'A' and resid 724 through 732 Processing helix chain 'A' and resid 772 through 781 removed outlier: 3.943A pdb=" N GLU A 781 " --> pdb=" O GLN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 806 removed outlier: 3.721A pdb=" N LEU A 793 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLY A 794 " --> pdb=" O ASP A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 831 Processing helix chain 'A' and resid 859 through 864 Processing helix chain 'A' and resid 869 through 876 Processing helix chain 'A' and resid 884 through 896 removed outlier: 3.537A pdb=" N GLN A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 915 Processing helix chain 'A' and resid 920 through 930 removed outlier: 5.280A pdb=" N THR A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 951 removed outlier: 3.512A pdb=" N ALA A 942 " --> pdb=" O ALA A 938 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 950 " --> pdb=" O PHE A 946 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 962 Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1002 through 1014 Processing helix chain 'A' and resid 1025 through 1039 removed outlier: 3.786A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1054 Processing helix chain 'A' and resid 1056 through 1078 removed outlier: 4.259A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1090 No H-bonds generated for 'chain 'A' and resid 1088 through 1090' Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 49 through 52 Processing helix chain 'B' and resid 78 through 84 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 180 through 192 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 230 through 233 No H-bonds generated for 'chain 'B' and resid 230 through 233' Processing helix chain 'B' and resid 248 through 258 Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'B' and resid 350 through 371 removed outlier: 5.996A pdb=" N GLY B 366 " --> pdb=" O ARG B 362 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'B' and resid 384 through 396 Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 506 through 518 Processing helix chain 'B' and resid 556 through 562 Processing helix chain 'B' and resid 578 through 587 removed outlier: 4.114A pdb=" N ASN B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 616 Processing helix chain 'B' and resid 643 through 648 Processing helix chain 'B' and resid 665 through 677 removed outlier: 4.086A pdb=" N GLU B 669 " --> pdb=" O GLY B 665 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 670 " --> pdb=" O MET B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 706 removed outlier: 3.889A pdb=" N ARG B 703 " --> pdb=" O ASP B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 733 Processing helix chain 'B' and resid 772 through 782 removed outlier: 3.673A pdb=" N GLU B 781 " --> pdb=" O GLN B 777 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 782 " --> pdb=" O ALA B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 807 Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 859 through 864 Processing helix chain 'B' and resid 869 through 876 Processing helix chain 'B' and resid 884 through 896 removed outlier: 3.721A pdb=" N GLN B 888 " --> pdb=" O LYS B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 915 Processing helix chain 'B' and resid 920 through 930 removed outlier: 5.090A pdb=" N THR B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 948 removed outlier: 3.554A pdb=" N PHE B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 966 removed outlier: 3.508A pdb=" N ASN B 961 " --> pdb=" O MET B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 997 Processing helix chain 'B' and resid 1002 through 1017 Processing helix chain 'B' and resid 1025 through 1039 removed outlier: 4.433A pdb=" N GLY B1030 " --> pdb=" O ASP B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1053 No H-bonds generated for 'chain 'B' and resid 1050 through 1053' Processing helix chain 'B' and resid 1058 through 1078 removed outlier: 4.208A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1090 No H-bonds generated for 'chain 'B' and resid 1088 through 1090' Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 66 through 69 No H-bonds generated for 'chain 'C' and resid 66 through 69' Processing helix chain 'C' and resid 78 through 85 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 223 through 233 removed outlier: 3.558A pdb=" N ASP C 226 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR C 227 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 228 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LYS C 230 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL C 231 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP C 233 " --> pdb=" O LYS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 259 Processing helix chain 'C' and resid 282 through 294 removed outlier: 3.682A pdb=" N VAL C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 326 Processing helix chain 'C' and resid 350 through 363 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 397 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 506 through 518 Processing helix chain 'C' and resid 556 through 562 Processing helix chain 'C' and resid 578 through 587 removed outlier: 3.931A pdb=" N ASN C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 Processing helix chain 'C' and resid 643 through 648 Processing helix chain 'C' and resid 665 through 677 removed outlier: 4.216A pdb=" N GLU C 669 " --> pdb=" O GLY C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 705 removed outlier: 4.040A pdb=" N ARG C 703 " --> pdb=" O ASP C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 733 Processing helix chain 'C' and resid 772 through 782 removed outlier: 3.573A pdb=" N GLU C 781 " --> pdb=" O GLN C 777 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA C 782 " --> pdb=" O ALA C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 807 removed outlier: 3.645A pdb=" N ASN C 807 " --> pdb=" O ASP C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 831 Processing helix chain 'C' and resid 859 through 864 Processing helix chain 'C' and resid 869 through 878 Processing helix chain 'C' and resid 884 through 896 removed outlier: 3.502A pdb=" N GLN C 888 " --> pdb=" O LYS C 884 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 889 " --> pdb=" O TYR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 915 Processing helix chain 'C' and resid 920 through 930 removed outlier: 5.059A pdb=" N THR C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 948 removed outlier: 3.981A pdb=" N ALA C 943 " --> pdb=" O LEU C 939 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 965 removed outlier: 3.793A pdb=" N ASN C 961 " --> pdb=" O MET C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 994 removed outlier: 3.540A pdb=" N LEU C 990 " --> pdb=" O ARG C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1017 removed outlier: 3.991A pdb=" N LYS C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1038 removed outlier: 4.628A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1053 removed outlier: 4.129A pdb=" N ILE C1052 " --> pdb=" O ALA C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1078 removed outlier: 4.298A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1088 through 1090 No H-bonds generated for 'chain 'C' and resid 1088 through 1090' Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 66 through 69 No H-bonds generated for 'chain 'D' and resid 66 through 69' Processing helix chain 'D' and resid 78 through 84 Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 230 through 233 No H-bonds generated for 'chain 'D' and resid 230 through 233' Processing helix chain 'D' and resid 248 through 259 Processing helix chain 'D' and resid 282 through 294 removed outlier: 4.259A pdb=" N VAL D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 325 Processing helix chain 'D' and resid 350 through 370 removed outlier: 3.759A pdb=" N TYR D 364 " --> pdb=" O ALA D 360 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY D 366 " --> pdb=" O ARG D 362 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 385 through 398 Processing helix chain 'D' and resid 413 through 417 Processing helix chain 'D' and resid 506 through 518 Processing helix chain 'D' and resid 556 through 562 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 603 through 616 Processing helix chain 'D' and resid 643 through 648 Processing helix chain 'D' and resid 666 through 677 Processing helix chain 'D' and resid 697 through 706 removed outlier: 3.936A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 733 Processing helix chain 'D' and resid 772 through 780 Processing helix chain 'D' and resid 793 through 807 Processing helix chain 'D' and resid 826 through 830 Processing helix chain 'D' and resid 859 through 864 Processing helix chain 'D' and resid 869 through 878 Processing helix chain 'D' and resid 884 through 896 removed outlier: 3.592A pdb=" N GLN D 888 " --> pdb=" O LYS D 884 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE D 889 " --> pdb=" O TYR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 915 Processing helix chain 'D' and resid 920 through 930 removed outlier: 5.056A pdb=" N THR D 930 " --> pdb=" O SER D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 941 through 950 removed outlier: 4.024A pdb=" N PHE D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 965 removed outlier: 3.672A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 997 Processing helix chain 'D' and resid 1002 through 1016 removed outlier: 4.033A pdb=" N SER D1016 " --> pdb=" O LYS D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1025 through 1039 removed outlier: 4.496A pdb=" N GLY D1030 " --> pdb=" O ASP D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1054 No H-bonds generated for 'chain 'D' and resid 1051 through 1054' Processing helix chain 'D' and resid 1058 through 1078 removed outlier: 4.325A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1088 through 1090 No H-bonds generated for 'chain 'D' and resid 1088 through 1090' Processing sheet with id= A, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.421A pdb=" N ALA A 219 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR A 198 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 93 through 95 Processing sheet with id= D, first strand: chain 'A' and resid 205 through 207 Processing sheet with id= E, first strand: chain 'A' and resid 263 through 268 Processing sheet with id= F, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.226A pdb=" N ILE A 337 " --> pdb=" O TRP A 276 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL A 377 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N HIS A 403 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 537 through 543 Processing sheet with id= H, first strand: chain 'A' and resid 593 through 596 removed outlier: 7.589A pdb=" N LYS A 498 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 569 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 500 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASN A 571 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP A 502 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL A 501 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET A 529 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 739 through 744 removed outlier: 7.908A pdb=" N TYR A 659 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLY A 684 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N SER A 661 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA A 686 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 3 through 6 removed outlier: 4.819A pdb=" N ALA B 219 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR B 198 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.884A pdb=" N VAL B 57 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N VAL B 74 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N VAL B 72 " --> pdb=" O PRO B 59 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 93 through 95 Processing sheet with id= M, first strand: chain 'B' and resid 205 through 207 Processing sheet with id= N, first strand: chain 'B' and resid 263 through 268 Processing sheet with id= O, first strand: chain 'B' and resid 275 through 277 removed outlier: 6.278A pdb=" N ILE B 337 " --> pdb=" O TRP B 276 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THR B 374 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE B 340 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE B 376 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 593 through 596 removed outlier: 7.771A pdb=" N VAL B 501 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET B 529 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 14.178A pdb=" N ALA B 527 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N LEU B 549 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N MET B 529 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 739 through 745 removed outlier: 7.659A pdb=" N TYR B 659 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY B 684 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER B 661 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA B 686 " --> pdb=" O SER B 661 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 3 through 5 removed outlier: 5.153A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N THR C 198 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 31 through 34 Processing sheet with id= T, first strand: chain 'C' and resid 92 through 95 Processing sheet with id= U, first strand: chain 'C' and resid 205 through 208 Processing sheet with id= V, first strand: chain 'C' and resid 263 through 268 Processing sheet with id= W, first strand: chain 'C' and resid 275 through 277 removed outlier: 6.093A pdb=" N ILE C 337 " --> pdb=" O TRP C 276 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR C 374 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE C 340 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE C 376 " --> pdb=" O ILE C 340 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL C 377 " --> pdb=" O PRO C 401 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N HIS C 403 " --> pdb=" O VAL C 377 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'C' and resid 537 through 543 removed outlier: 8.200A pdb=" N ALA C 527 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA C 499 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET C 529 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL C 501 " --> pdb=" O MET C 529 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE C 500 " --> pdb=" O ASP C 567 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU C 569 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP C 502 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASN C 571 " --> pdb=" O TRP C 502 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR C 593 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASN C 571 " --> pdb=" O THR C 593 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA C 595 " --> pdb=" O ASN C 571 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 627 through 629 removed outlier: 4.464A pdb=" N GLY C 627 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 657 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLY C 684 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR C 659 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ALA C 686 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER C 661 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N MET C 712 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N VAL C 660 " --> pdb=" O MET C 712 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL C 714 " --> pdb=" O VAL C 660 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL C 715 " --> pdb=" O PRO C 739 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL C 741 " --> pdb=" O VAL C 715 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLY C 717 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TRP C 743 " --> pdb=" O GLY C 717 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.121A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR D 198 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 32 through 34 Processing sheet with id= AB, first strand: chain 'D' and resid 93 through 95 Processing sheet with id= AC, first strand: chain 'D' and resid 205 through 207 Processing sheet with id= AD, first strand: chain 'D' and resid 263 through 268 Processing sheet with id= AE, first strand: chain 'D' and resid 275 through 277 removed outlier: 6.353A pdb=" N ILE D 337 " --> pdb=" O TRP D 276 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR D 374 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE D 340 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE D 376 " --> pdb=" O ILE D 340 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 593 through 596 removed outlier: 7.761A pdb=" N VAL D 501 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET D 529 " --> pdb=" O VAL D 501 " (cutoff:3.500A) removed outlier: 14.211A pdb=" N ALA D 527 " --> pdb=" O GLU D 547 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N LEU D 549 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N MET D 529 " --> pdb=" O LEU D 549 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 739 through 745 removed outlier: 3.685A pdb=" N ILE D 713 " --> pdb=" O PRO D 739 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR D 659 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLY D 684 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N SER D 661 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA D 686 " --> pdb=" O SER D 661 " (cutoff:3.500A) 1161 hydrogen bonds defined for protein. 3312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.95 Time building geometry restraints manager: 12.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.79: 32291 1.79 - 2.40: 210 2.40 - 3.01: 0 3.01 - 3.63: 2 3.63 - 4.24: 6 Bond restraints: 32509 Sorted by residual: bond pdb=" AP1 COA C1202 " pdb="AO5* COA C1202 " ideal model delta sigma weight residual 1.610 4.244 -2.634 2.00e-02 2.50e+03 1.73e+04 bond pdb=" AO6 COA B1202 " pdb=" AP2 COA B1202 " ideal model delta sigma weight residual 1.610 4.175 -2.565 2.00e-02 2.50e+03 1.64e+04 bond pdb=" AP1 COA B1201 " pdb="AO5* COA B1201 " ideal model delta sigma weight residual 1.610 4.151 -2.541 2.00e-02 2.50e+03 1.61e+04 bond pdb=" AO6 COA C1201 " pdb=" AP2 COA C1201 " ideal model delta sigma weight residual 1.610 4.051 -2.441 2.00e-02 2.50e+03 1.49e+04 bond pdb=" AO6 COA C1202 " pdb=" AP2 COA C1202 " ideal model delta sigma weight residual 1.610 3.958 -2.348 2.00e-02 2.50e+03 1.38e+04 ... (remaining 32504 not shown) Histogram of bond angle deviations from ideal: 14.02 - 46.86: 6 46.86 - 79.70: 5 79.70 - 112.54: 17298 112.54 - 145.38: 26740 145.38 - 178.22: 3 Bond angle restraints: 44052 Sorted by residual: angle pdb=" AO3 COA C1202 " pdb=" AP1 COA C1202 " pdb="AO5* COA C1202 " ideal model delta sigma weight residual 102.60 14.02 88.58 3.00e+00 1.11e-01 8.72e+02 angle pdb=" AO3 COA B1202 " pdb=" AP2 COA B1202 " pdb=" AO6 COA B1202 " ideal model delta sigma weight residual 102.60 22.00 80.60 3.00e+00 1.11e-01 7.22e+02 angle pdb=" AO3 COA B1201 " pdb=" AP1 COA B1201 " pdb="AO5* COA B1201 " ideal model delta sigma weight residual 102.60 23.48 79.12 3.00e+00 1.11e-01 6.96e+02 angle pdb=" AO3 COA C1201 " pdb=" AP2 COA C1201 " pdb=" AO6 COA C1201 " ideal model delta sigma weight residual 102.60 26.70 75.90 3.00e+00 1.11e-01 6.40e+02 angle pdb=" AO3 COA C1202 " pdb=" AP2 COA C1202 " pdb=" AO6 COA C1202 " ideal model delta sigma weight residual 102.60 31.86 70.74 3.00e+00 1.11e-01 5.56e+02 ... (remaining 44047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 18757 35.63 - 71.27: 592 71.27 - 106.90: 46 106.90 - 142.54: 6 142.54 - 178.17: 5 Dihedral angle restraints: 19406 sinusoidal: 7766 harmonic: 11640 Sorted by residual: dihedral pdb=" CA GLY B 622 " pdb=" C GLY B 622 " pdb=" N PRO B 623 " pdb=" CA PRO B 623 " ideal model delta harmonic sigma weight residual -180.00 -133.44 -46.56 0 5.00e+00 4.00e-02 8.67e+01 dihedral pdb=" CA GLY C 622 " pdb=" C GLY C 622 " pdb=" N PRO C 623 " pdb=" CA PRO C 623 " ideal model delta harmonic sigma weight residual -180.00 -136.12 -43.88 0 5.00e+00 4.00e-02 7.70e+01 dihedral pdb=" CA GLY D 622 " pdb=" C GLY D 622 " pdb=" N PRO D 623 " pdb=" CA PRO D 623 " ideal model delta harmonic sigma weight residual -180.00 -138.37 -41.63 0 5.00e+00 4.00e-02 6.93e+01 ... (remaining 19403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4531 0.099 - 0.197: 353 0.197 - 0.296: 16 0.296 - 0.395: 6 0.395 - 0.494: 1 Chirality restraints: 4907 Sorted by residual: chirality pdb=" CB ILE B 834 " pdb=" CA ILE B 834 " pdb=" CG1 ILE B 834 " pdb=" CG2 ILE B 834 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.09e+00 chirality pdb=" CB VAL C1094 " pdb=" CA VAL C1094 " pdb=" CG1 VAL C1094 " pdb=" CG2 VAL C1094 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA THR A 842 " pdb=" N THR A 842 " pdb=" C THR A 842 " pdb=" CB THR A 842 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 4904 not shown) Planarity restraints: 5624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 854 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C TYR A 854 " -0.052 2.00e-02 2.50e+03 pdb=" O TYR A 854 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 855 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B1018 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO B1019 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B1019 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B1019 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 601 " 0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO D 602 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 602 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 602 " 0.038 5.00e-02 4.00e+02 ... (remaining 5621 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 22 2.31 - 2.96: 14230 2.96 - 3.60: 45774 3.60 - 4.25: 74396 4.25 - 4.90: 126137 Nonbonded interactions: 260559 Sorted by model distance: nonbonded pdb=" AP2 COA C1201 " pdb="AO5* COA C1201 " model vdw 1.661 2.720 nonbonded pdb=" AP2 COA B1202 " pdb="AO5* COA B1202 " model vdw 1.663 2.720 nonbonded pdb=" AP2 COA C1202 " pdb="AO5* COA C1202 " model vdw 1.665 2.720 nonbonded pdb=" AO6 COA B1202 " pdb=" AP1 COA B1202 " model vdw 1.666 2.720 nonbonded pdb=" AO6 COA C1202 " pdb=" AP1 COA C1202 " model vdw 1.666 2.720 ... (remaining 260554 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 979 or (resid 980 and (name N or name CA or name C or name O or name CB )) or re \ sid 981 through 1016 or (resid 1017 and (name N or name CA or name C or name O o \ r name CB )) or resid 1018 through 1099)) selection = (chain 'B' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1016 or (resid 1017 and (name N or name CA or name C or name O or name CB )) or \ resid 1018 through 1099)) selection = (chain 'C' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 979 or (resid 980 and (name N or name CA or name C or name O or name CB )) or re \ sid 981 through 1099)) selection = (chain 'D' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 979 or (resid 980 and (name N or name CA or name C or name O or name CB )) or re \ sid 981 through 1016 or (resid 1017 and (name N or name CA or name C or name O o \ r name CB )) or resid 1018 through 1099)) } 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=0.40 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 4.110 Check model and map are aligned: 0.490 Set scattering table: 0.280 Process input model: 107.170 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.180 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 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 : 0.037 2.634 32509 Z= 2.480 Angle : 1.464 88.583 44052 Z= 0.629 Chirality : 0.057 0.494 4907 Planarity : 0.007 0.070 5624 Dihedral : 16.735 178.173 12014 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.24 % Favored : 92.61 % Rotamer: Outliers : 11.53 % Allowed : 11.56 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.10), residues: 4068 helix: -2.67 (0.09), residues: 1761 sheet: -2.53 (0.18), residues: 637 loop : -3.00 (0.13), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 84 HIS 0.008 0.001 HIS A 537 PHE 0.022 0.002 PHE A 191 TYR 0.025 0.002 TYR C 213 ARG 0.004 0.001 ARG D 848 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 923 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 537 time to evaluate : 3.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8425 (tp) cc_final: 0.8205 (pt) REVERT: A 97 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7711 (tmmt) REVERT: A 175 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6486 (tp30) REVERT: A 190 ASN cc_start: 0.7242 (t0) cc_final: 0.6850 (t0) REVERT: A 409 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8703 (m) REVERT: A 507 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7721 (ttm170) REVERT: A 666 MET cc_start: 0.8200 (mmm) cc_final: 0.7860 (mmt) REVERT: A 1001 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8230 (t) REVERT: A 1035 ASP cc_start: 0.7824 (t70) cc_final: 0.7434 (t0) REVERT: A 1036 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.8019 (ttm) REVERT: A 1075 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8196 (t0) REVERT: B 25 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6612 (tp) REVERT: B 386 GLU cc_start: 0.7804 (tt0) cc_final: 0.7474 (tm-30) REVERT: B 391 MET cc_start: 0.8813 (tpp) cc_final: 0.8538 (tpt) REVERT: B 411 MET cc_start: 0.8584 (ttt) cc_final: 0.8232 (ttt) REVERT: B 567 ASP cc_start: 0.8149 (t70) cc_final: 0.7795 (t0) REVERT: B 965 LYS cc_start: 0.8752 (tptt) cc_final: 0.8519 (mttm) REVERT: B 1075 ASP cc_start: 0.8450 (t0) cc_final: 0.8224 (t0) REVERT: C 29 PHE cc_start: 0.5855 (OUTLIER) cc_final: 0.5557 (m-10) REVERT: C 391 MET cc_start: 0.8250 (tpp) cc_final: 0.7712 (tpt) REVERT: C 393 GLU cc_start: 0.6674 (tm-30) cc_final: 0.6436 (tm-30) REVERT: C 516 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: C 597 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8862 (mm) REVERT: C 729 ARG cc_start: 0.7025 (mtm-85) cc_final: 0.6775 (mtt180) REVERT: C 866 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: C 873 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8587 (mp) REVERT: C 1051 TYR cc_start: 0.8766 (m-80) cc_final: 0.8456 (m-80) REVERT: C 1054 ILE cc_start: 0.8604 (mm) cc_final: 0.8309 (pt) REVERT: C 1075 ASP cc_start: 0.8459 (t0) cc_final: 0.8128 (t0) REVERT: D 91 GLN cc_start: 0.4845 (OUTLIER) cc_final: 0.4560 (mp10) REVERT: D 106 LEU cc_start: 0.2269 (OUTLIER) cc_final: 0.1843 (tp) REVERT: D 154 VAL cc_start: 0.2869 (OUTLIER) cc_final: 0.2624 (p) REVERT: D 242 PHE cc_start: 0.2716 (OUTLIER) cc_final: 0.1236 (t80) REVERT: D 274 ARG cc_start: 0.5225 (OUTLIER) cc_final: 0.3658 (ptm-80) REVERT: D 389 ARG cc_start: 0.6216 (ttp80) cc_final: 0.5852 (ttm-80) REVERT: D 869 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8721 (mp) REVERT: D 1035 ASP cc_start: 0.7619 (t0) cc_final: 0.7211 (t0) REVERT: D 1036 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8220 (ttm) REVERT: D 1050 GLU cc_start: 0.7442 (tt0) cc_final: 0.6836 (mt-10) outliers start: 386 outliers final: 153 residues processed: 871 average time/residue: 0.4600 time to fit residues: 638.6280 Evaluate side-chains 562 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 390 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1009 GLU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 829 ARG Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 897 THR Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 921 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 TYR Chi-restraints excluded: chain D residue 546 LYS Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 567 ASP Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 712 MET Chi-restraints excluded: chain D residue 839 SER Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 872 VAL Chi-restraints excluded: chain D residue 921 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1025 VAL Chi-restraints excluded: chain D residue 1036 MET Chi-restraints excluded: chain D residue 1040 CYS Chi-restraints excluded: chain D residue 1075 ASP Chi-restraints excluded: chain D residue 1095 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 7.9990 chunk 309 optimal weight: 50.0000 chunk 171 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 319 optimal weight: 30.0000 chunk 123 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 238 optimal weight: 0.0030 chunk 370 optimal weight: 7.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 45 GLN A 332 HIS A 555 ASN A 587 ASN A 638 ASN A 705 GLN A 807 ASN A 908 HIS A 961 ASN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 161 ASN B 403 HIS B 571 ASN B 587 ASN B 638 ASN B 767 GLN B 777 GLN B 850 GLN B 908 HIS B 988 GLN C 410 HIS ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN C 705 GLN C 767 GLN C 888 GLN C 900 HIS C 908 HIS C 975 HIS C 988 GLN C1086 HIS D 47 HIS D 54 ASN D 75 ASN D 203 ASN ** D 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN D 410 HIS D 545 HIS D 645 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 GLN D 908 HIS D 961 ASN ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 988 GLN D1020 ASN D1086 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32509 Z= 0.287 Angle : 0.747 39.962 44052 Z= 0.358 Chirality : 0.047 0.326 4907 Planarity : 0.005 0.061 5624 Dihedral : 11.655 172.706 4809 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.77 % Favored : 93.20 % Rotamer: Outliers : 6.18 % Allowed : 17.62 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.12), residues: 4068 helix: -1.32 (0.11), residues: 1756 sheet: -2.28 (0.19), residues: 637 loop : -2.71 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 49 HIS 0.005 0.001 HIS C 537 PHE 0.026 0.001 PHE B 110 TYR 0.021 0.002 TYR C 213 ARG 0.006 0.000 ARG C 662 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 613 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 407 time to evaluate : 3.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7712 (tmmt) REVERT: A 151 LYS cc_start: 0.7370 (mttm) cc_final: 0.7158 (mttt) REVERT: A 175 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6239 (mp0) REVERT: A 190 ASN cc_start: 0.7240 (t0) cc_final: 0.6881 (t0) REVERT: A 385 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7944 (mm-40) REVERT: A 666 MET cc_start: 0.8254 (mmm) cc_final: 0.8025 (mmp) REVERT: A 847 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7893 (pt0) REVERT: A 888 GLN cc_start: 0.7420 (tt0) cc_final: 0.7069 (tp-100) REVERT: A 1001 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8242 (t) REVERT: A 1035 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7236 (t0) REVERT: B 25 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6651 (tp) REVERT: B 339 ILE cc_start: 0.8725 (mm) cc_final: 0.8453 (mt) REVERT: B 386 GLU cc_start: 0.7827 (tt0) cc_final: 0.7511 (tm-30) REVERT: B 391 MET cc_start: 0.8878 (tpp) cc_final: 0.8596 (tpt) REVERT: B 411 MET cc_start: 0.8447 (ttt) cc_final: 0.8064 (ttt) REVERT: B 560 MET cc_start: 0.8855 (mmm) cc_final: 0.8121 (mmm) REVERT: B 567 ASP cc_start: 0.8181 (t70) cc_final: 0.7817 (t0) REVERT: B 963 MET cc_start: 0.8277 (tpp) cc_final: 0.7833 (mmm) REVERT: B 1075 ASP cc_start: 0.8370 (t0) cc_final: 0.8166 (t0) REVERT: C 391 MET cc_start: 0.8271 (tpp) cc_final: 0.8038 (tpt) REVERT: C 848 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8094 (pmt-80) REVERT: C 866 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: C 873 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8410 (mp) REVERT: C 1075 ASP cc_start: 0.8405 (t0) cc_final: 0.8097 (t0) REVERT: D 91 GLN cc_start: 0.4907 (OUTLIER) cc_final: 0.4567 (mp10) REVERT: D 106 LEU cc_start: 0.2283 (OUTLIER) cc_final: 0.1866 (tp) REVERT: D 154 VAL cc_start: 0.2816 (OUTLIER) cc_final: 0.2546 (p) REVERT: D 242 PHE cc_start: 0.2304 (OUTLIER) cc_final: 0.0837 (t80) REVERT: D 274 ARG cc_start: 0.5060 (OUTLIER) cc_final: 0.3577 (ptm-80) REVERT: D 389 ARG cc_start: 0.6331 (ttp80) cc_final: 0.5898 (ttm-80) REVERT: D 1011 GLU cc_start: 0.8112 (tt0) cc_final: 0.7847 (tt0) REVERT: D 1035 ASP cc_start: 0.7423 (t0) cc_final: 0.7127 (t0) REVERT: D 1050 GLU cc_start: 0.7386 (tt0) cc_final: 0.7022 (mt-10) outliers start: 206 outliers final: 144 residues processed: 582 average time/residue: 0.4222 time to fit residues: 401.6821 Evaluate side-chains 526 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 368 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 675 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 767 GLN Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 767 GLN Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 829 ARG Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 897 THR Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 921 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 546 LYS Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 567 ASP Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 712 MET Chi-restraints excluded: chain D residue 839 SER Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 897 THR Chi-restraints excluded: chain D residue 921 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1025 VAL Chi-restraints excluded: chain D residue 1075 ASP Chi-restraints excluded: chain D residue 1095 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 308 optimal weight: 50.0000 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 371 optimal weight: 9.9990 chunk 400 optimal weight: 8.9990 chunk 330 optimal weight: 20.0000 chunk 368 optimal weight: 30.0000 chunk 126 optimal weight: 20.0000 chunk 297 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 410 HIS B 767 GLN B1086 HIS ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN C1024 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS ** D 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS D 638 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 32509 Z= 0.570 Angle : 0.831 30.763 44052 Z= 0.409 Chirality : 0.052 0.284 4907 Planarity : 0.005 0.073 5624 Dihedral : 10.863 174.617 4732 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.45 % Favored : 91.53 % Rotamer: Outliers : 7.07 % Allowed : 17.26 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.12), residues: 4068 helix: -0.97 (0.12), residues: 1751 sheet: -2.21 (0.19), residues: 634 loop : -2.62 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 49 HIS 0.008 0.001 HIS C 537 PHE 0.022 0.002 PHE B 110 TYR 0.026 0.002 TYR C 213 ARG 0.007 0.001 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 614 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 378 time to evaluate : 3.749 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: A 97 LYS cc_start: 0.8105 (ttmm) cc_final: 0.7720 (tmmt) REVERT: A 151 LYS cc_start: 0.7343 (mttm) cc_final: 0.7141 (mttm) REVERT: A 175 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: A 190 ASN cc_start: 0.7371 (t0) cc_final: 0.7045 (t0) REVERT: A 330 GLU cc_start: 0.6259 (mp0) cc_final: 0.5555 (pm20) REVERT: A 385 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8034 (mm-40) REVERT: A 824 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7099 (m-30) REVERT: A 921 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.9076 (p) REVERT: A 1001 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.7992 (t) REVERT: A 1035 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7385 (t0) REVERT: A 1075 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8116 (t0) REVERT: B 386 GLU cc_start: 0.7895 (tt0) cc_final: 0.7630 (tm-30) REVERT: B 391 MET cc_start: 0.8890 (tpp) cc_final: 0.8650 (tpt) REVERT: B 560 MET cc_start: 0.8720 (mmm) cc_final: 0.8115 (mmm) REVERT: B 567 ASP cc_start: 0.8312 (t70) cc_final: 0.7754 (t0) REVERT: B 669 GLU cc_start: 0.7909 (tp30) cc_final: 0.7626 (tp30) REVERT: B 779 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7954 (mp) REVERT: C 560 MET cc_start: 0.8516 (mmt) cc_final: 0.7649 (mmt) REVERT: C 866 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: C 1075 ASP cc_start: 0.8560 (t0) cc_final: 0.8192 (t0) REVERT: D 106 LEU cc_start: 0.2255 (OUTLIER) cc_final: 0.1929 (tp) REVERT: D 154 VAL cc_start: 0.3136 (OUTLIER) cc_final: 0.2892 (p) REVERT: D 242 PHE cc_start: 0.2272 (OUTLIER) cc_final: 0.0696 (t80) REVERT: D 274 ARG cc_start: 0.5215 (OUTLIER) cc_final: 0.3593 (ptm-80) REVERT: D 389 ARG cc_start: 0.6546 (ttp80) cc_final: 0.5974 (ttm-80) REVERT: D 940 ASP cc_start: 0.8412 (t0) cc_final: 0.8194 (t0) REVERT: D 1011 GLU cc_start: 0.8123 (tt0) cc_final: 0.7889 (tt0) REVERT: D 1035 ASP cc_start: 0.7469 (t0) cc_final: 0.7253 (t0) outliers start: 236 outliers final: 177 residues processed: 580 average time/residue: 0.4156 time to fit residues: 397.9019 Evaluate side-chains 544 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 354 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 675 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 945 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 829 ARG Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 921 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 391 MET Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 TYR Chi-restraints excluded: chain D residue 546 LYS Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 567 ASP Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 712 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 839 SER Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 897 THR Chi-restraints excluded: chain D residue 921 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1025 VAL Chi-restraints excluded: chain D residue 1075 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 20.0000 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 177 optimal weight: 0.2980 chunk 249 optimal weight: 0.9980 chunk 372 optimal weight: 40.0000 chunk 394 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 353 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 332 HIS ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS D 587 ASN D 638 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32509 Z= 0.233 Angle : 0.693 29.187 44052 Z= 0.331 Chirality : 0.046 0.281 4907 Planarity : 0.004 0.063 5624 Dihedral : 9.981 179.998 4718 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.65 % Favored : 93.33 % Rotamer: Outliers : 5.61 % Allowed : 19.01 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.13), residues: 4068 helix: -0.50 (0.12), residues: 1760 sheet: -1.99 (0.19), residues: 634 loop : -2.38 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 49 HIS 0.005 0.001 HIS A 537 PHE 0.018 0.001 PHE C 347 TYR 0.028 0.001 TYR D 692 ARG 0.007 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 584 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 397 time to evaluate : 3.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7311 (mm) cc_final: 0.7015 (mt) REVERT: A 97 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7732 (tmmt) REVERT: A 175 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: A 190 ASN cc_start: 0.7304 (t0) cc_final: 0.6969 (t0) REVERT: A 330 GLU cc_start: 0.6134 (mp0) cc_final: 0.5899 (pm20) REVERT: A 385 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7930 (mm-40) REVERT: A 507 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7741 (ttm170) REVERT: A 1001 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8083 (t) REVERT: A 1035 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7204 (t0) REVERT: A 1075 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8099 (t0) REVERT: B 25 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6878 (pp) REVERT: B 339 ILE cc_start: 0.8706 (mm) cc_final: 0.8438 (mt) REVERT: B 386 GLU cc_start: 0.7868 (tt0) cc_final: 0.7592 (tm-30) REVERT: B 391 MET cc_start: 0.8868 (tpp) cc_final: 0.8600 (tpt) REVERT: B 560 MET cc_start: 0.8593 (mmm) cc_final: 0.8073 (mmm) REVERT: B 567 ASP cc_start: 0.8205 (t70) cc_final: 0.7665 (t0) REVERT: B 669 GLU cc_start: 0.7722 (tp30) cc_final: 0.7513 (tp30) REVERT: B 779 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7678 (mp) REVERT: C 29 PHE cc_start: 0.5671 (OUTLIER) cc_final: 0.5226 (m-10) REVERT: C 560 MET cc_start: 0.8538 (mmt) cc_final: 0.7710 (mmt) REVERT: C 848 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8049 (pmt-80) REVERT: C 866 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: C 873 LEU cc_start: 0.9260 (tp) cc_final: 0.8737 (mt) REVERT: D 106 LEU cc_start: 0.2295 (OUTLIER) cc_final: 0.1978 (tp) REVERT: D 154 VAL cc_start: 0.3288 (OUTLIER) cc_final: 0.3051 (p) REVERT: D 242 PHE cc_start: 0.2204 (OUTLIER) cc_final: 0.0705 (t80) REVERT: D 274 ARG cc_start: 0.5176 (OUTLIER) cc_final: 0.3525 (ptm-80) REVERT: D 368 LEU cc_start: 0.5603 (OUTLIER) cc_final: 0.5237 (mm) REVERT: D 389 ARG cc_start: 0.6485 (ttp80) cc_final: 0.5899 (ttm-80) REVERT: D 1011 GLU cc_start: 0.8163 (tt0) cc_final: 0.7916 (tt0) REVERT: D 1035 ASP cc_start: 0.7315 (t0) cc_final: 0.7068 (t0) outliers start: 187 outliers final: 135 residues processed: 561 average time/residue: 0.4094 time to fit residues: 375.8479 Evaluate side-chains 523 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 372 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 675 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 829 ARG Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 546 LYS Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 712 MET Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 897 THR Chi-restraints excluded: chain D residue 921 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1075 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 3.9990 chunk 223 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 336 optimal weight: 50.0000 chunk 272 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 353 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS D 638 ASN D 671 ASN ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32509 Z= 0.360 Angle : 0.725 28.983 44052 Z= 0.349 Chirality : 0.048 0.276 4907 Planarity : 0.005 0.065 5624 Dihedral : 9.769 175.674 4690 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.54 % Favored : 92.44 % Rotamer: Outliers : 6.18 % Allowed : 18.72 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.13), residues: 4068 helix: -0.36 (0.12), residues: 1748 sheet: -1.91 (0.20), residues: 634 loop : -2.29 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 49 HIS 0.005 0.001 HIS C1086 PHE 0.014 0.001 PHE C 191 TYR 0.019 0.002 TYR B 192 ARG 0.008 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 590 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 384 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7367 (mm) cc_final: 0.7067 (mt) REVERT: A 97 LYS cc_start: 0.8104 (ttmm) cc_final: 0.7719 (tmmt) REVERT: A 175 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6222 (mp0) REVERT: A 190 ASN cc_start: 0.7341 (t0) cc_final: 0.7007 (t0) REVERT: A 330 GLU cc_start: 0.6180 (mp0) cc_final: 0.5939 (pm20) REVERT: A 385 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7970 (mm-40) REVERT: A 507 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7769 (ttm170) REVERT: A 1001 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8041 (t) REVERT: A 1035 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7250 (t0) REVERT: A 1075 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8120 (t0) REVERT: B 25 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6951 (pp) REVERT: B 339 ILE cc_start: 0.8719 (mm) cc_final: 0.8450 (mt) REVERT: B 386 GLU cc_start: 0.7889 (tt0) cc_final: 0.7612 (tm-30) REVERT: B 391 MET cc_start: 0.8897 (tpp) cc_final: 0.8638 (tpt) REVERT: B 560 MET cc_start: 0.8614 (mmm) cc_final: 0.8064 (mmm) REVERT: B 567 ASP cc_start: 0.8251 (t70) cc_final: 0.7702 (t0) REVERT: B 669 GLU cc_start: 0.7801 (tp30) cc_final: 0.7504 (tp30) REVERT: B 779 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7896 (mp) REVERT: C 29 PHE cc_start: 0.5684 (OUTLIER) cc_final: 0.5211 (m-10) REVERT: C 50 LEU cc_start: 0.5762 (OUTLIER) cc_final: 0.5446 (mt) REVERT: C 77 THR cc_start: 0.6403 (t) cc_final: 0.6155 (t) REVERT: C 391 MET cc_start: 0.8239 (tpp) cc_final: 0.8020 (mmm) REVERT: C 848 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8180 (pmt-80) REVERT: C 866 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7701 (mt-10) REVERT: C 1075 ASP cc_start: 0.8426 (t0) cc_final: 0.8171 (t0) REVERT: D 91 GLN cc_start: 0.5069 (OUTLIER) cc_final: 0.4848 (mp10) REVERT: D 106 LEU cc_start: 0.2339 (OUTLIER) cc_final: 0.2017 (tp) REVERT: D 154 VAL cc_start: 0.3368 (OUTLIER) cc_final: 0.3129 (p) REVERT: D 242 PHE cc_start: 0.2249 (OUTLIER) cc_final: 0.0641 (t80) REVERT: D 274 ARG cc_start: 0.5180 (OUTLIER) cc_final: 0.3492 (ptm-80) REVERT: D 368 LEU cc_start: 0.5597 (OUTLIER) cc_final: 0.5203 (mm) REVERT: D 389 ARG cc_start: 0.6547 (ttp80) cc_final: 0.5927 (ttm-80) REVERT: D 940 ASP cc_start: 0.8312 (t0) cc_final: 0.7963 (t0) REVERT: D 1011 GLU cc_start: 0.8151 (tt0) cc_final: 0.7907 (tt0) REVERT: D 1035 ASP cc_start: 0.7384 (t0) cc_final: 0.7153 (t0) outliers start: 206 outliers final: 154 residues processed: 559 average time/residue: 0.4148 time to fit residues: 380.1660 Evaluate side-chains 543 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 371 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 675 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 829 ARG Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 546 LYS Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 712 MET Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 897 THR Chi-restraints excluded: chain D residue 921 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1075 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 9.9990 chunk 355 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 394 optimal weight: 0.9990 chunk 327 optimal weight: 30.0000 chunk 182 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 168 HIS ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS C 135 HIS C 505 GLN ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN D 638 ASN D 671 ASN ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32509 Z= 0.226 Angle : 0.677 29.341 44052 Z= 0.322 Chirality : 0.046 0.274 4907 Planarity : 0.004 0.060 5624 Dihedral : 9.287 171.305 4681 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.77 % Favored : 93.20 % Rotamer: Outliers : 5.26 % Allowed : 20.02 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.13), residues: 4068 helix: -0.14 (0.12), residues: 1752 sheet: -1.76 (0.20), residues: 635 loop : -2.17 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 49 HIS 0.005 0.001 HIS A 537 PHE 0.012 0.001 PHE B 110 TYR 0.026 0.001 TYR D 692 ARG 0.008 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 566 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 391 time to evaluate : 3.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7295 (mm) cc_final: 0.6984 (mt) REVERT: A 97 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7734 (tmmt) REVERT: A 175 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6236 (mp0) REVERT: A 190 ASN cc_start: 0.7307 (t0) cc_final: 0.6965 (t0) REVERT: A 385 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7958 (mm-40) REVERT: A 507 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7725 (ttm170) REVERT: A 921 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.8988 (p) REVERT: A 961 ASN cc_start: 0.8499 (m-40) cc_final: 0.8263 (m110) REVERT: A 1001 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.7997 (t) REVERT: A 1035 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7170 (t0) REVERT: A 1075 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8106 (t0) REVERT: B 25 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.7005 (pp) REVERT: B 339 ILE cc_start: 0.8654 (mm) cc_final: 0.8406 (mt) REVERT: B 386 GLU cc_start: 0.7851 (tt0) cc_final: 0.7584 (tm-30) REVERT: B 391 MET cc_start: 0.8942 (tpp) cc_final: 0.8685 (tpt) REVERT: B 560 MET cc_start: 0.8550 (mmm) cc_final: 0.8053 (mmm) REVERT: B 567 ASP cc_start: 0.8201 (t70) cc_final: 0.7657 (t0) REVERT: B 669 GLU cc_start: 0.7696 (tp30) cc_final: 0.7403 (tp30) REVERT: B 779 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7673 (mp) REVERT: B 973 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7651 (mm) REVERT: C 29 PHE cc_start: 0.5833 (OUTLIER) cc_final: 0.5340 (m-10) REVERT: C 50 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5400 (mt) REVERT: C 77 THR cc_start: 0.6408 (t) cc_final: 0.6184 (t) REVERT: C 866 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: D 106 LEU cc_start: 0.2458 (OUTLIER) cc_final: 0.2110 (tp) REVERT: D 154 VAL cc_start: 0.3409 (OUTLIER) cc_final: 0.3198 (p) REVERT: D 242 PHE cc_start: 0.2173 (OUTLIER) cc_final: 0.0643 (t80) REVERT: D 274 ARG cc_start: 0.5196 (OUTLIER) cc_final: 0.3563 (ptm-80) REVERT: D 368 LEU cc_start: 0.5490 (OUTLIER) cc_final: 0.5131 (mm) REVERT: D 389 ARG cc_start: 0.6400 (ttp80) cc_final: 0.5825 (ttm-80) REVERT: D 1011 GLU cc_start: 0.8159 (tt0) cc_final: 0.7906 (tt0) REVERT: D 1035 ASP cc_start: 0.7306 (t0) cc_final: 0.7049 (t0) outliers start: 175 outliers final: 138 residues processed: 535 average time/residue: 0.4166 time to fit residues: 365.1530 Evaluate side-chains 528 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 372 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 675 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 829 ARG Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 546 LYS Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 897 THR Chi-restraints excluded: chain D residue 921 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1075 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 224 optimal weight: 0.0980 chunk 288 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 332 optimal weight: 40.0000 chunk 220 optimal weight: 0.4980 chunk 393 optimal weight: 8.9990 chunk 246 optimal weight: 0.0670 chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 0.6980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 ASN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 HIS ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 ASN ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32509 Z= 0.150 Angle : 0.648 33.422 44052 Z= 0.305 Chirality : 0.044 0.270 4907 Planarity : 0.004 0.063 5624 Dihedral : 8.618 167.677 4662 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.35 % Favored : 93.62 % Rotamer: Outliers : 4.19 % Allowed : 21.33 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 4068 helix: 0.15 (0.13), residues: 1748 sheet: -1.45 (0.22), residues: 558 loop : -2.10 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 49 HIS 0.011 0.001 HIS D 168 PHE 0.028 0.001 PHE B 110 TYR 0.017 0.001 TYR D 307 ARG 0.009 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 557 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 418 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7288 (mm) cc_final: 0.6932 (mt) REVERT: A 97 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7695 (tmmt) REVERT: A 101 PHE cc_start: 0.6681 (OUTLIER) cc_final: 0.6462 (m-80) REVERT: A 175 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: A 190 ASN cc_start: 0.7277 (t0) cc_final: 0.6922 (t0) REVERT: A 507 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7672 (ttm170) REVERT: A 961 ASN cc_start: 0.8456 (m-40) cc_final: 0.8226 (m-40) REVERT: A 1001 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7823 (t) REVERT: A 1035 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7011 (t0) REVERT: B 25 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6953 (pp) REVERT: B 386 GLU cc_start: 0.7833 (tt0) cc_final: 0.7560 (tm-30) REVERT: B 391 MET cc_start: 0.8974 (tpp) cc_final: 0.8694 (tpt) REVERT: B 560 MET cc_start: 0.8513 (mmm) cc_final: 0.8031 (mmm) REVERT: B 567 ASP cc_start: 0.8127 (t70) cc_final: 0.7559 (t0) REVERT: B 973 ILE cc_start: 0.8020 (mm) cc_final: 0.7713 (mm) REVERT: C 29 PHE cc_start: 0.5797 (OUTLIER) cc_final: 0.5335 (m-10) REVERT: C 50 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.5146 (mt) REVERT: C 77 THR cc_start: 0.6464 (t) cc_final: 0.6247 (t) REVERT: C 560 MET cc_start: 0.8527 (mmt) cc_final: 0.7828 (mmt) REVERT: C 848 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8065 (pmt-80) REVERT: C 857 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7732 (mtp) REVERT: C 866 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7754 (mt-10) REVERT: C 1051 TYR cc_start: 0.8600 (m-80) cc_final: 0.8392 (m-80) REVERT: D 106 LEU cc_start: 0.2513 (OUTLIER) cc_final: 0.2217 (tp) REVERT: D 242 PHE cc_start: 0.2282 (OUTLIER) cc_final: 0.0646 (t80) REVERT: D 274 ARG cc_start: 0.5138 (OUTLIER) cc_final: 0.3578 (ptm-80) REVERT: D 389 ARG cc_start: 0.6390 (ttp80) cc_final: 0.5856 (ttm-80) REVERT: D 496 HIS cc_start: 0.6747 (m90) cc_final: 0.6052 (t-90) REVERT: D 504 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6852 (tpp) REVERT: D 1035 ASP cc_start: 0.7210 (t0) cc_final: 0.6903 (t0) outliers start: 139 outliers final: 97 residues processed: 527 average time/residue: 0.4047 time to fit residues: 348.8148 Evaluate side-chains 491 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 379 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 857 MET Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 897 THR Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 504 MET Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 897 THR Chi-restraints excluded: chain D residue 921 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 234 optimal weight: 40.0000 chunk 118 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 309 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 ASN ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32509 Z= 0.154 Angle : 0.651 33.455 44052 Z= 0.306 Chirality : 0.044 0.308 4907 Planarity : 0.004 0.066 5624 Dihedral : 8.180 164.281 4616 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.99 % Favored : 93.99 % Rotamer: Outliers : 3.65 % Allowed : 22.10 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.13), residues: 4068 helix: 0.30 (0.13), residues: 1755 sheet: -1.41 (0.22), residues: 564 loop : -2.01 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 49 HIS 0.010 0.001 HIS D 332 PHE 0.026 0.001 PHE C 110 TYR 0.021 0.001 TYR C 16 ARG 0.009 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 522 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 401 time to evaluate : 3.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7244 (mm) cc_final: 0.6861 (mt) REVERT: A 97 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7714 (tmmt) REVERT: A 175 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6198 (mp0) REVERT: A 190 ASN cc_start: 0.7263 (t0) cc_final: 0.6924 (t0) REVERT: A 507 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7659 (ttm170) REVERT: A 841 MET cc_start: 0.7856 (mtp) cc_final: 0.7645 (mtt) REVERT: A 961 ASN cc_start: 0.8448 (m-40) cc_final: 0.8239 (m-40) REVERT: A 1001 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.7796 (t) REVERT: A 1035 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6976 (t0) REVERT: B 25 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.7021 (pp) REVERT: B 386 GLU cc_start: 0.7809 (tt0) cc_final: 0.7551 (tm-30) REVERT: B 391 MET cc_start: 0.8976 (tpp) cc_final: 0.8669 (tpt) REVERT: B 567 ASP cc_start: 0.8097 (t70) cc_final: 0.7872 (t70) REVERT: B 973 ILE cc_start: 0.7994 (mm) cc_final: 0.7672 (mm) REVERT: C 29 PHE cc_start: 0.5780 (OUTLIER) cc_final: 0.5338 (m-10) REVERT: C 50 LEU cc_start: 0.5489 (OUTLIER) cc_final: 0.5248 (mt) REVERT: C 560 MET cc_start: 0.8499 (mmt) cc_final: 0.7834 (mmt) REVERT: C 848 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8103 (pmt-80) REVERT: C 1051 TYR cc_start: 0.8625 (m-80) cc_final: 0.8409 (m-80) REVERT: D 106 LEU cc_start: 0.2829 (OUTLIER) cc_final: 0.2567 (tp) REVERT: D 242 PHE cc_start: 0.2237 (OUTLIER) cc_final: 0.0613 (t80) REVERT: D 389 ARG cc_start: 0.6528 (ttp80) cc_final: 0.5965 (ttm-80) REVERT: D 496 HIS cc_start: 0.6779 (m90) cc_final: 0.6083 (t-90) REVERT: D 1035 ASP cc_start: 0.7160 (t0) cc_final: 0.6889 (t0) outliers start: 121 outliers final: 95 residues processed: 491 average time/residue: 0.4223 time to fit residues: 338.8327 Evaluate side-chains 488 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 383 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 857 MET Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 857 MET Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 921 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.0000 chunk 376 optimal weight: 0.0970 chunk 343 optimal weight: 10.0000 chunk 366 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 287 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 331 optimal weight: 8.9990 chunk 346 optimal weight: 9.9990 chunk 365 optimal weight: 6.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS A1081 GLN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 ASN ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32509 Z= 0.236 Angle : 0.672 34.323 44052 Z= 0.318 Chirality : 0.046 0.339 4907 Planarity : 0.004 0.066 5624 Dihedral : 8.001 160.156 4597 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.53 % Favored : 93.45 % Rotamer: Outliers : 3.36 % Allowed : 22.52 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.13), residues: 4068 helix: 0.30 (0.12), residues: 1762 sheet: -1.38 (0.21), residues: 594 loop : -2.00 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 49 HIS 0.010 0.001 HIS A 421 PHE 0.027 0.001 PHE B 110 TYR 0.020 0.001 TYR D 307 ARG 0.009 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 504 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 393 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7283 (mm) cc_final: 0.6915 (mt) REVERT: A 97 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7700 (tmmt) REVERT: A 175 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6237 (mp0) REVERT: A 190 ASN cc_start: 0.7303 (t0) cc_final: 0.6965 (t0) REVERT: A 507 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7694 (ttm170) REVERT: A 961 ASN cc_start: 0.8418 (m-40) cc_final: 0.8193 (m-40) REVERT: A 1001 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.7830 (t) REVERT: A 1035 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7058 (t0) REVERT: B 25 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.7099 (pp) REVERT: B 391 MET cc_start: 0.8998 (tpp) cc_final: 0.8711 (tpt) REVERT: B 560 MET cc_start: 0.8762 (mmm) cc_final: 0.8150 (mmm) REVERT: B 567 ASP cc_start: 0.8151 (t70) cc_final: 0.7624 (t0) REVERT: B 973 ILE cc_start: 0.8058 (mm) cc_final: 0.7688 (mm) REVERT: C 29 PHE cc_start: 0.5805 (OUTLIER) cc_final: 0.5326 (m-10) REVERT: C 50 LEU cc_start: 0.5457 (OUTLIER) cc_final: 0.5151 (mt) REVERT: C 848 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8003 (pmt-80) REVERT: C 873 LEU cc_start: 0.9174 (tp) cc_final: 0.8744 (mt) REVERT: D 106 LEU cc_start: 0.2842 (OUTLIER) cc_final: 0.2536 (tp) REVERT: D 242 PHE cc_start: 0.2047 (OUTLIER) cc_final: 0.0324 (t80) REVERT: D 389 ARG cc_start: 0.6477 (ttp80) cc_final: 0.5975 (ttm-80) REVERT: D 496 HIS cc_start: 0.6811 (m90) cc_final: 0.6103 (t-90) REVERT: D 1035 ASP cc_start: 0.7250 (t0) cc_final: 0.6976 (t0) outliers start: 111 outliers final: 95 residues processed: 476 average time/residue: 0.4411 time to fit residues: 343.0815 Evaluate side-chains 483 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 378 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 857 MET Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 897 THR Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 0.0670 chunk 387 optimal weight: 0.2980 chunk 236 optimal weight: 9.9990 chunk 183 optimal weight: 0.3980 chunk 269 optimal weight: 40.0000 chunk 406 optimal weight: 3.9990 chunk 374 optimal weight: 40.0000 chunk 323 optimal weight: 40.0000 chunk 33 optimal weight: 0.1980 chunk 250 optimal weight: 1.9990 chunk 198 optimal weight: 0.1980 overall best weight: 0.2318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN C 798 GLN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 ASN ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32509 Z= 0.146 Angle : 0.650 32.628 44052 Z= 0.305 Chirality : 0.044 0.281 4907 Planarity : 0.004 0.065 5624 Dihedral : 7.735 156.570 4595 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 2.85 % Allowed : 23.17 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 4068 helix: 0.51 (0.13), residues: 1752 sheet: -1.25 (0.22), residues: 569 loop : -1.91 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 49 HIS 0.006 0.001 HIS A 537 PHE 0.026 0.001 PHE C 110 TYR 0.019 0.001 TYR D 307 ARG 0.014 0.000 ARG C 561 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 505 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 411 time to evaluate : 3.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7229 (mm) cc_final: 0.6828 (mt) REVERT: A 97 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7725 (tmmt) REVERT: A 190 ASN cc_start: 0.7262 (t0) cc_final: 0.6921 (t0) REVERT: A 507 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7559 (ttm170) REVERT: A 1001 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7726 (t) REVERT: A 1035 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6902 (t0) REVERT: B 25 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.7085 (pp) REVERT: B 101 PHE cc_start: 0.8422 (m-10) cc_final: 0.8124 (m-80) REVERT: B 391 MET cc_start: 0.8954 (tpp) cc_final: 0.8661 (tpt) REVERT: B 560 MET cc_start: 0.8792 (mmm) cc_final: 0.8297 (mmt) REVERT: B 567 ASP cc_start: 0.8073 (t70) cc_final: 0.7859 (t70) REVERT: B 973 ILE cc_start: 0.8020 (mm) cc_final: 0.7715 (mm) REVERT: C 29 PHE cc_start: 0.5701 (OUTLIER) cc_final: 0.5312 (m-10) REVERT: C 75 ASN cc_start: 0.5393 (OUTLIER) cc_final: 0.4931 (p0) REVERT: C 326 LEU cc_start: 0.7710 (tp) cc_final: 0.7360 (tp) REVERT: C 560 MET cc_start: 0.8509 (mmt) cc_final: 0.7821 (mmt) REVERT: C 797 ILE cc_start: 0.7770 (mt) cc_final: 0.7551 (mt) REVERT: C 1051 TYR cc_start: 0.8617 (m-80) cc_final: 0.8412 (m-80) REVERT: D 242 PHE cc_start: 0.2320 (OUTLIER) cc_final: 0.0614 (t80) REVERT: D 389 ARG cc_start: 0.6542 (ttp80) cc_final: 0.6232 (mmt-90) REVERT: D 496 HIS cc_start: 0.6660 (m90) cc_final: 0.6004 (t-90) REVERT: D 1035 ASP cc_start: 0.7137 (t0) cc_final: 0.6828 (t0) outliers start: 94 outliers final: 77 residues processed: 480 average time/residue: 0.4218 time to fit residues: 330.4430 Evaluate side-chains 469 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 385 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 897 THR Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 977 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 10.0000 chunk 344 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 chunk 47 optimal weight: 0.2980 chunk 89 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 50.0000 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS A 590 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS C 172 HIS ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN ** D 981 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 = 0.4038 r_free = 0.4038 target = 0.174944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142918 restraints weight = 52967.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138185 restraints weight = 70472.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136687 restraints weight = 62972.687| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32509 Z= 0.288 Angle : 0.698 35.208 44052 Z= 0.333 Chirality : 0.046 0.263 4907 Planarity : 0.004 0.066 5624 Dihedral : 7.764 153.852 4577 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.70 % Favored : 93.28 % Rotamer: Outliers : 3.09 % Allowed : 22.85 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 4068 helix: 0.40 (0.12), residues: 1753 sheet: -1.27 (0.21), residues: 598 loop : -1.89 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 49 HIS 0.009 0.001 HIS A 421 PHE 0.026 0.002 PHE B 110 TYR 0.019 0.002 TYR D 307 ARG 0.015 0.000 ARG C 561 =============================================================================== Job complete usr+sys time: 7878.79 seconds wall clock time: 143 minutes 28.79 seconds (8608.79 seconds total)