Starting phenix.real_space_refine on Sun Apr 14 14:20:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uuz_20903/04_2024/6uuz_20903_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uuz_20903/04_2024/6uuz_20903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uuz_20903/04_2024/6uuz_20903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uuz_20903/04_2024/6uuz_20903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uuz_20903/04_2024/6uuz_20903_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uuz_20903/04_2024/6uuz_20903_neut_updated.pdb" } resolution = 3.0 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= 0.006 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 20340 2.51 5 N 5388 2.21 5 O 5898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A GLU 865": "OE1" <-> "OE2" Residue "A TYR 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 976": "NH1" <-> "NH2" Residue "A ARG 986": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1045": "NH1" <-> "NH2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A GLU 1097": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B GLU 724": "OE1" <-> "OE2" Residue "B GLU 865": "OE1" <-> "OE2" Residue "B TYR 885": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "B GLU 1097": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C GLU 408": "OE1" <-> "OE2" Residue "C ARG 576": "NH1" <-> "NH2" Residue "C TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 669": "OE1" <-> "OE2" Residue "C GLU 724": "OE1" <-> "OE2" Residue "C GLU 865": "OE1" <-> "OE2" Residue "C TYR 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 986": "NH1" <-> "NH2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1045": "NH1" <-> "NH2" Residue "C ARG 1085": "NH1" <-> "NH2" Residue "C GLU 1097": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "D TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 669": "OE1" <-> "OE2" Residue "D GLU 724": "OE1" <-> "OE2" Residue "D GLU 865": "OE1" <-> "OE2" Residue "D TYR 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 986": "NH1" <-> "NH2" Residue "D ARG 995": "NH1" <-> "NH2" Residue "D ARG 1045": "NH1" <-> "NH2" Residue "D ARG 1085": "NH1" <-> "NH2" Residue "D GLU 1097": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31818 Number of models: 1 Model: "" Number of chains: 10 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: 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: "C" 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: "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: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 29.81, per 1000 atoms: 0.94 Number of scatterers: 31818 At special positions: 0 Unit cell: (140.07, 162.69, 167.91, 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 5898 8.00 N 5388 7.00 C 20340 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: 12.75 Conformation dependent library (CDL) restraints added in 11.4 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: 152 helices and 32 sheets defined 38.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.54 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 175 through 193 removed outlier: 5.167A pdb=" N GLU A 179 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 180 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 181 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A 182 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU A 193 " --> pdb=" O ASN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 removed outlier: 4.724A pdb=" N TYR A 227 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 259 Processing helix chain 'A' and resid 282 through 294 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 350 through 361 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 411 through 418 removed outlier: 4.364A pdb=" N ILE A 414 " --> pdb=" O MET A 411 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 415 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 417 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 418 " --> pdb=" O VAL A 415 " (cutoff:3.500A) 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 706 removed outlier: 3.748A pdb=" N ARG A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 732 Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 793 through 806 Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 859 through 864 Processing helix chain 'A' and resid 869 through 877 Processing helix chain 'A' and resid 884 through 896 removed outlier: 3.623A 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: 4.965A pdb=" N THR A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 950 removed outlier: 3.553A pdb=" N ALA A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 964 removed outlier: 4.053A pdb=" N ASN A 961 " --> pdb=" O MET A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 996 removed outlier: 3.721A pdb=" N GLN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1017 removed outlier: 3.790A pdb=" N SER A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1039 removed outlier: 4.185A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1054 removed outlier: 3.621A pdb=" N ILE A1052 " --> pdb=" O ALA A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1078 removed outlier: 4.156A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 3.976A 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 41 through 45 Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 175 through 193 removed outlier: 5.167A pdb=" N GLU B 179 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 180 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU B 181 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA B 182 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU B 193 " --> pdb=" O ASN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 removed outlier: 4.723A pdb=" N TYR B 227 " --> pdb=" O THR B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 259 Processing helix chain 'B' and resid 282 through 294 Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'B' and resid 350 through 361 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 398 Processing helix chain 'B' and resid 411 through 418 removed outlier: 4.364A pdb=" N ILE B 414 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 415 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET B 417 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 418 " --> pdb=" O VAL B 415 " (cutoff:3.500A) 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 585 Processing helix chain 'B' and resid 603 through 616 Processing helix chain 'B' and resid 643 through 648 Processing helix chain 'B' and resid 667 through 677 Processing helix chain 'B' and resid 697 through 706 removed outlier: 3.748A pdb=" N ARG B 703 " --> pdb=" O ASP B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 732 Processing helix chain 'B' and resid 772 through 780 Processing helix chain 'B' and resid 793 through 806 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 877 Processing helix chain 'B' and resid 884 through 896 removed outlier: 3.621A 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: 4.965A pdb=" N THR B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 950 removed outlier: 3.553A pdb=" N ALA B 943 " --> pdb=" O LEU B 939 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 964 removed outlier: 4.053A pdb=" N ASN B 961 " --> pdb=" O MET B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 996 removed outlier: 3.720A pdb=" N GLN B 996 " --> pdb=" O ASP B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1017 removed outlier: 3.790A pdb=" N SER B1016 " --> pdb=" O LYS B1012 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1039 removed outlier: 4.183A pdb=" N GLY B1030 " --> pdb=" O ASP B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1054 removed outlier: 3.627A pdb=" N ILE B1052 " --> pdb=" O ALA B1048 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1078 removed outlier: 4.157A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 3.976A 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 41 through 45 Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'C' and resid 78 through 86 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 175 through 193 removed outlier: 5.166A pdb=" N GLU C 179 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 181 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA C 182 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU C 193 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 removed outlier: 4.724A pdb=" N TYR C 227 " --> pdb=" O THR C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 259 Processing helix chain 'C' and resid 282 through 294 Processing helix chain 'C' and resid 313 through 326 Processing helix chain 'C' and resid 350 through 361 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 398 Processing helix chain 'C' and resid 411 through 418 removed outlier: 4.365A pdb=" N ILE C 414 " --> pdb=" O MET C 411 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 415 " --> pdb=" O THR C 412 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET C 417 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA C 418 " --> pdb=" O VAL C 415 " (cutoff:3.500A) 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 585 Processing helix chain 'C' and resid 603 through 616 Processing helix chain 'C' and resid 643 through 648 Processing helix chain 'C' and resid 667 through 677 Processing helix chain 'C' and resid 697 through 706 removed outlier: 3.749A pdb=" N ARG C 703 " --> pdb=" O ASP C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 732 Processing helix chain 'C' and resid 772 through 780 Processing helix chain 'C' and resid 793 through 806 Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 859 through 864 Processing helix chain 'C' and resid 869 through 877 Processing helix chain 'C' and resid 884 through 896 removed outlier: 3.622A pdb=" N GLN C 888 " --> pdb=" O LYS C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 915 Processing helix chain 'C' and resid 920 through 930 removed outlier: 4.965A pdb=" N THR C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 950 removed outlier: 3.553A pdb=" N ALA C 943 " --> pdb=" O LEU C 939 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 964 removed outlier: 4.053A pdb=" N ASN C 961 " --> pdb=" O MET C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 996 removed outlier: 3.721A pdb=" N GLN C 996 " --> pdb=" O ASP C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1017 removed outlier: 3.790A pdb=" N SER C1016 " --> pdb=" O LYS C1012 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1039 removed outlier: 4.184A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1054 removed outlier: 3.628A pdb=" N ILE C1052 " --> pdb=" O ALA C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1078 removed outlier: 4.156A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.975A 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 18 Processing helix chain 'D' and resid 41 through 45 Processing helix chain 'D' and resid 48 through 51 Processing helix chain 'D' and resid 78 through 86 Processing helix chain 'D' and resid 162 through 168 Processing helix chain 'D' and resid 175 through 193 removed outlier: 5.166A pdb=" N GLU D 179 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D 180 " --> pdb=" O LYS D 177 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU D 181 " --> pdb=" O LYS D 178 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA D 182 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU D 193 " --> pdb=" O ASN D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 removed outlier: 4.724A pdb=" N TYR D 227 " --> pdb=" O THR D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 259 Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 313 through 326 Processing helix chain 'D' and resid 350 through 361 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 384 through 398 Processing helix chain 'D' and resid 411 through 418 removed outlier: 4.364A pdb=" N ILE D 414 " --> pdb=" O MET D 411 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 415 " --> pdb=" O THR D 412 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET D 417 " --> pdb=" O ILE D 414 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA D 418 " --> pdb=" O VAL D 415 " (cutoff:3.500A) 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 585 Processing helix chain 'D' and resid 603 through 616 Processing helix chain 'D' and resid 643 through 648 Processing helix chain 'D' and resid 667 through 677 Processing helix chain 'D' and resid 697 through 706 removed outlier: 3.749A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 772 through 780 Processing helix chain 'D' and resid 793 through 806 Processing helix chain 'D' and resid 825 through 830 Processing helix chain 'D' and resid 859 through 864 Processing helix chain 'D' and resid 869 through 877 Processing helix chain 'D' and resid 884 through 896 removed outlier: 3.621A pdb=" N GLN D 888 " --> pdb=" O LYS D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 915 Processing helix chain 'D' and resid 920 through 930 removed outlier: 4.965A pdb=" N THR D 930 " --> pdb=" O SER D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 950 removed outlier: 3.553A pdb=" N ALA D 943 " --> pdb=" O LEU D 939 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 964 removed outlier: 4.053A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 996 removed outlier: 3.720A pdb=" N GLN D 996 " --> pdb=" O ASP D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1017 removed outlier: 3.790A pdb=" N SER D1016 " --> pdb=" O LYS D1012 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS D1017 " --> pdb=" O ILE D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1025 through 1039 removed outlier: 4.184A pdb=" N GLY D1030 " --> pdb=" O ASP D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1046 through 1054 removed outlier: 3.627A pdb=" N ILE D1052 " --> pdb=" O ALA D1048 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1078 removed outlier: 4.156A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 3.975A 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 5 removed outlier: 5.350A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N THR A 198 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.427A pdb=" N VAL A 57 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL A 74 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 92 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: 6.035A pdb=" N ILE A 337 " --> pdb=" O TRP A 276 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL A 377 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 6.216A 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 removed outlier: 8.045A pdb=" N ALA A 527 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA A 499 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET A 529 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 501 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE A 500 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A 569 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TRP A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASN A 571 " --> pdb=" O TRP A 502 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR A 593 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASN A 571 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA A 595 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR A 619 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE A 596 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE A 621 " --> pdb=" O ILE A 596 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 739 through 745 removed outlier: 7.795A pdb=" N TYR A 659 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY A 684 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N SER A 661 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A 686 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 3 through 5 removed outlier: 5.349A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N THR B 198 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.426A pdb=" N VAL B 57 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL B 74 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 92 through 95 Processing sheet with id= L, first strand: chain 'B' and resid 205 through 207 Processing sheet with id= M, first strand: chain 'B' and resid 263 through 268 Processing sheet with id= N, first strand: chain 'B' and resid 275 through 277 removed outlier: 6.035A pdb=" N ILE B 337 " --> pdb=" O TRP B 276 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL B 377 " --> pdb=" O PRO B 401 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS B 403 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 537 through 543 removed outlier: 8.045A pdb=" N ALA B 527 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA B 499 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET B 529 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 501 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE B 500 " --> pdb=" O ASP B 567 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU B 569 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TRP B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASN B 571 " --> pdb=" O TRP B 502 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR B 593 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASN B 571 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 595 " --> pdb=" O ASN B 571 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR B 619 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE B 596 " --> pdb=" O THR B 619 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE B 621 " --> pdb=" O ILE B 596 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 739 through 745 removed outlier: 7.795A pdb=" N TYR B 659 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY B 684 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N SER B 661 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA B 686 " --> pdb=" O SER B 661 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 3 through 5 removed outlier: 5.350A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N THR C 198 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.426A pdb=" N VAL C 57 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL C 74 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 92 through 95 Processing sheet with id= T, first strand: chain 'C' and resid 205 through 207 Processing sheet with id= U, first strand: chain 'C' and resid 263 through 268 Processing sheet with id= V, first strand: chain 'C' and resid 275 through 277 removed outlier: 6.035A pdb=" N ILE C 337 " --> pdb=" O TRP C 276 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL C 377 " --> pdb=" O PRO C 401 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N HIS C 403 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 537 through 543 removed outlier: 8.045A pdb=" N ALA C 527 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA C 499 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET C 529 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL C 501 " --> pdb=" O MET C 529 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE C 500 " --> pdb=" O ASP C 567 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU C 569 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TRP C 502 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASN C 571 " --> pdb=" O TRP C 502 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR C 593 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASN C 571 " --> pdb=" O THR C 593 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA C 595 " --> pdb=" O ASN C 571 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR C 619 " --> pdb=" O ILE C 594 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE C 596 " --> pdb=" O THR C 619 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE C 621 " --> pdb=" O ILE C 596 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 739 through 745 removed outlier: 7.795A pdb=" N TYR C 659 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY C 684 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N SER C 661 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA C 686 " --> pdb=" O SER C 661 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 3 through 5 removed outlier: 5.350A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N THR D 198 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 32 through 34 removed outlier: 7.426A pdb=" N VAL D 57 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL D 74 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 92 through 95 Processing sheet with id= AB, first strand: chain 'D' and resid 205 through 207 Processing sheet with id= AC, first strand: chain 'D' and resid 263 through 268 Processing sheet with id= AD, first strand: chain 'D' and resid 275 through 277 removed outlier: 6.035A pdb=" N ILE D 337 " --> pdb=" O TRP D 276 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL D 377 " --> pdb=" O PRO D 401 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N HIS D 403 " --> pdb=" O VAL D 377 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 537 through 543 removed outlier: 8.046A pdb=" N ALA D 527 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA D 499 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET D 529 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL D 501 " --> pdb=" O MET D 529 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE D 500 " --> pdb=" O ASP D 567 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU D 569 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TRP D 502 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASN D 571 " --> pdb=" O TRP D 502 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR D 593 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASN D 571 " --> pdb=" O THR D 593 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA D 595 " --> pdb=" O ASN D 571 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR D 619 " --> pdb=" O ILE D 594 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE D 596 " --> pdb=" O THR D 619 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE D 621 " --> pdb=" O ILE D 596 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 739 through 745 removed outlier: 7.795A pdb=" N TYR D 659 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY D 684 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N SER D 661 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA D 686 " --> pdb=" O SER D 661 " (cutoff:3.500A) 1188 hydrogen bonds defined for protein. 3264 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: 13.31 Time building geometry restraints manager: 13.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 32220 1.76 - 2.31: 288 2.31 - 2.86: 0 2.86 - 3.41: 6 3.41 - 3.96: 2 Bond restraints: 32516 Sorted by residual: bond pdb=" AO6 COA A1201 " pdb=" AP2 COA A1201 " ideal model delta sigma weight residual 1.610 3.957 -2.347 2.00e-02 2.50e+03 1.38e+04 bond pdb=" AO6 COA D1201 " pdb=" AP2 COA D1201 " ideal model delta sigma weight residual 1.610 3.818 -2.208 2.00e-02 2.50e+03 1.22e+04 bond pdb=" AP1 COA C1201 " pdb="AO5* COA C1201 " ideal model delta sigma weight residual 1.610 3.312 -1.702 2.00e-02 2.50e+03 7.24e+03 bond pdb=" AP1 COA B1201 " pdb="AO5* COA B1201 " ideal model delta sigma weight residual 1.610 3.225 -1.615 2.00e-02 2.50e+03 6.52e+03 bond pdb=" AP1 COA A1201 " pdb="AO5* COA A1201 " ideal model delta sigma weight residual 1.610 3.195 -1.585 2.00e-02 2.50e+03 6.28e+03 ... (remaining 32511 not shown) Histogram of bond angle deviations from ideal: 21.21 - 50.93: 5 50.93 - 80.66: 9 80.66 - 110.38: 8174 110.38 - 140.10: 35867 140.10 - 169.82: 5 Bond angle restraints: 44060 Sorted by residual: angle pdb=" AO3 COA A1201 " pdb=" AP2 COA A1201 " pdb=" AO6 COA A1201 " ideal model delta sigma weight residual 102.60 21.21 81.39 3.00e+00 1.11e-01 7.36e+02 angle pdb=" AO3 COA D1201 " pdb=" AP2 COA D1201 " pdb=" AO6 COA D1201 " ideal model delta sigma weight residual 102.60 27.95 74.65 3.00e+00 1.11e-01 6.19e+02 angle pdb=" AO3 COA C1201 " pdb=" AP1 COA C1201 " pdb="AO5* COA C1201 " ideal model delta sigma weight residual 102.60 46.99 55.61 3.00e+00 1.11e-01 3.44e+02 angle pdb=" AO3 COA B1201 " pdb=" AP1 COA B1201 " pdb="AO5* COA B1201 " ideal model delta sigma weight residual 102.60 49.93 52.67 3.00e+00 1.11e-01 3.08e+02 angle pdb=" AO5 COA C1201 " pdb=" AP2 COA C1201 " pdb=" AO6 COA C1201 " ideal model delta sigma weight residual 109.50 57.55 51.95 3.00e+00 1.11e-01 3.00e+02 ... (remaining 44055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 18439 24.42 - 48.83: 861 48.83 - 73.25: 93 73.25 - 97.66: 15 97.66 - 122.08: 4 Dihedral angle restraints: 19412 sinusoidal: 7772 harmonic: 11640 Sorted by residual: dihedral pdb=" AO6 COA B1201 " pdb="PC11 COA B1201 " pdb="PC12 COA B1201 " pdb="PC10 COA B1201 " ideal model delta sinusoidal sigma weight residual 291.50 169.42 122.08 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" AO6 COA D1201 " pdb="PC11 COA D1201 " pdb="PC12 COA D1201 " pdb="PC10 COA D1201 " ideal model delta sinusoidal sigma weight residual -68.50 -172.83 104.33 1 2.00e+01 2.50e-03 2.99e+01 dihedral pdb=" AO3 COA A1201 " pdb=" AO6 COA A1201 " pdb=" AP2 COA A1201 " pdb="PC12 COA A1201 " ideal model delta sinusoidal sigma weight residual 278.38 177.34 101.04 1 2.00e+01 2.50e-03 2.86e+01 ... (remaining 19409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3822 0.072 - 0.145: 945 0.145 - 0.217: 101 0.217 - 0.290: 20 0.290 - 0.362: 20 Chirality restraints: 4908 Sorted by residual: chirality pdb=" CB VAL B 904 " pdb=" CA VAL B 904 " pdb=" CG1 VAL B 904 " pdb=" CG2 VAL B 904 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CB VAL A 904 " pdb=" CA VAL A 904 " pdb=" CG1 VAL A 904 " pdb=" CG2 VAL A 904 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CB VAL D 904 " pdb=" CA VAL D 904 " pdb=" CG1 VAL D 904 " pdb=" CG2 VAL D 904 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 4905 not shown) Planarity restraints: 5624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 854 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C TYR C 854 " -0.059 2.00e-02 2.50e+03 pdb=" O TYR C 854 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA C 855 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 854 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C TYR A 854 " -0.059 2.00e-02 2.50e+03 pdb=" O TYR A 854 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA A 855 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 854 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C TYR B 854 " 0.059 2.00e-02 2.50e+03 pdb=" O TYR B 854 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA B 855 " -0.020 2.00e-02 2.50e+03 ... (remaining 5621 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 9 2.27 - 2.93: 12628 2.93 - 3.58: 44634 3.58 - 4.24: 76551 4.24 - 4.90: 128385 Nonbonded interactions: 262207 Sorted by model distance: nonbonded pdb=" AP2 COA C1201 " pdb="AO5* COA C1201 " model vdw 1.608 2.720 nonbonded pdb=" AP2 COA A1201 " pdb="AO5* COA A1201 " model vdw 1.609 2.720 nonbonded pdb=" AP2 COA D1201 " pdb="AO5* COA D1201 " model vdw 1.609 2.720 nonbonded pdb=" AP2 COA B1201 " pdb="AO5* COA B1201 " model vdw 1.609 2.720 nonbonded pdb=" AO6 COA A1201 " pdb=" AP1 COA A1201 " model vdw 1.609 2.720 ... (remaining 262202 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 \ 1099 or resid 1201)) selection = (chain 'B' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099 or resid 1201)) selection = (chain 'C' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099 or resid 1201)) selection = (chain 'D' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099 or resid 1201)) } 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 individual isotropic 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.170 Check model and map are aligned: 0.450 Set scattering table: 0.250 Process input model: 106.950 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.240 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:15.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 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 : 0.029 2.347 32516 Z= 2.020 Angle : 1.524 81.390 44060 Z= 0.676 Chirality : 0.065 0.362 4908 Planarity : 0.008 0.065 5624 Dihedral : 13.556 122.081 12020 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.62 % Favored : 94.19 % Rotamer: Outliers : 1.45 % Allowed : 3.36 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -4.07 (0.10), residues: 4068 helix: -2.84 (0.09), residues: 1716 sheet: -1.85 (0.20), residues: 524 loop : -2.71 (0.12), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 877 HIS 0.014 0.002 HIS A 332 PHE 0.029 0.003 PHE C 376 TYR 0.020 0.003 TYR C 288 ARG 0.006 0.001 ARG D1085 *********************** 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 629 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 584 time to evaluate : 3.409 Fit side-chains REVERT: A 259 LYS cc_start: 0.6356 (pttp) cc_final: 0.5553 (mppt) REVERT: A 504 MET cc_start: 0.8634 (tpt) cc_final: 0.8422 (tpt) REVERT: A 895 MET cc_start: 0.8391 (mtm) cc_final: 0.7951 (mtp) REVERT: A 995 ARG cc_start: 0.6763 (mtt-85) cc_final: 0.6327 (mtt90) REVERT: A 996 GLN cc_start: 0.7335 (mt0) cc_final: 0.6927 (tm-30) REVERT: B 259 LYS cc_start: 0.6337 (pttp) cc_final: 0.5531 (mppt) REVERT: B 504 MET cc_start: 0.8659 (tpt) cc_final: 0.8438 (tpt) REVERT: B 835 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8514 (ptt180) REVERT: B 895 MET cc_start: 0.8383 (mtm) cc_final: 0.7914 (mtp) REVERT: B 996 GLN cc_start: 0.7363 (mt0) cc_final: 0.6968 (tm-30) REVERT: C 259 LYS cc_start: 0.6357 (pttp) cc_final: 0.5556 (mppt) REVERT: C 504 MET cc_start: 0.8657 (tpt) cc_final: 0.8435 (tpt) REVERT: C 835 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8537 (ptt180) REVERT: C 895 MET cc_start: 0.8388 (mtm) cc_final: 0.7934 (mtp) REVERT: C 995 ARG cc_start: 0.6761 (mtt-85) cc_final: 0.6349 (mtt90) REVERT: C 996 GLN cc_start: 0.7362 (mt0) cc_final: 0.6972 (tm-30) REVERT: D 259 LYS cc_start: 0.6311 (pttp) cc_final: 0.5525 (mppt) REVERT: D 504 MET cc_start: 0.8641 (tpt) cc_final: 0.8423 (tpt) REVERT: D 835 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8540 (ptt180) REVERT: D 895 MET cc_start: 0.8387 (mtm) cc_final: 0.7970 (mtp) REVERT: D 995 ARG cc_start: 0.6763 (mtt-85) cc_final: 0.6323 (mtt90) REVERT: D 996 GLN cc_start: 0.7348 (mt0) cc_final: 0.6919 (tm-30) outliers start: 45 outliers final: 14 residues processed: 623 average time/residue: 1.3966 time to fit residues: 1036.8977 Evaluate side-chains 407 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 390 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 913 CYS Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 913 CYS Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 913 CYS Chi-restraints excluded: chain D residue 1021 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 4.9990 chunk 309 optimal weight: 0.2980 chunk 171 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 208 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 319 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 194 optimal weight: 0.9990 chunk 238 optimal weight: 20.0000 chunk 370 optimal weight: 10.0000 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 61 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN A 371 HIS A 638 ASN A 850 GLN A 888 GLN A 900 HIS A 908 HIS ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 HIS B 61 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 638 ASN B 850 GLN B 900 HIS B 908 HIS ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 ASN B1098 HIS C 61 GLN ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 638 ASN C 850 GLN C 900 HIS C 908 HIS ** C 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 HIS D 61 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 638 ASN D 850 GLN D 900 HIS D 908 HIS ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 32516 Z= 0.320 Angle : 0.677 8.405 44060 Z= 0.345 Chirality : 0.048 0.207 4908 Planarity : 0.005 0.076 5624 Dihedral : 8.629 164.203 4559 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.93 % Allowed : 11.82 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.01 (0.11), residues: 4068 helix: -1.53 (0.11), residues: 1740 sheet: -1.70 (0.20), residues: 560 loop : -2.50 (0.12), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 84 HIS 0.005 0.001 HIS D1086 PHE 0.014 0.002 PHE A 959 TYR 0.016 0.002 TYR D 196 ARG 0.009 0.001 ARG B 995 *********************** 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 465 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 404 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.6343 (pttp) cc_final: 0.5602 (mtmt) REVERT: A 326 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.7024 (tp) REVERT: A 678 THR cc_start: 0.8021 (OUTLIER) cc_final: 0.7814 (m) REVERT: A 895 MET cc_start: 0.8259 (mtm) cc_final: 0.7862 (mtp) REVERT: A 992 ASP cc_start: 0.7058 (m-30) cc_final: 0.6597 (m-30) REVERT: A 995 ARG cc_start: 0.6746 (mtt-85) cc_final: 0.6202 (mtm110) REVERT: A 996 GLN cc_start: 0.7281 (mt0) cc_final: 0.6866 (mp10) REVERT: B 259 LYS cc_start: 0.6375 (pttp) cc_final: 0.5645 (mtmt) REVERT: B 326 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7058 (tp) REVERT: B 678 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7803 (m) REVERT: B 895 MET cc_start: 0.8256 (mtm) cc_final: 0.7856 (mtp) REVERT: B 992 ASP cc_start: 0.6919 (m-30) cc_final: 0.6369 (m-30) REVERT: B 996 GLN cc_start: 0.7268 (mt0) cc_final: 0.6859 (mp10) REVERT: C 259 LYS cc_start: 0.6395 (pttp) cc_final: 0.5655 (mtmt) REVERT: C 678 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7808 (m) REVERT: C 895 MET cc_start: 0.8259 (mtm) cc_final: 0.7855 (mtp) REVERT: C 992 ASP cc_start: 0.7054 (m-30) cc_final: 0.6589 (m-30) REVERT: C 995 ARG cc_start: 0.6749 (mtt-85) cc_final: 0.6272 (mtm110) REVERT: C 996 GLN cc_start: 0.7265 (mt0) cc_final: 0.6874 (mp10) REVERT: D 259 LYS cc_start: 0.6385 (pttp) cc_final: 0.5633 (mtmt) REVERT: D 326 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.7030 (tp) REVERT: D 678 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7812 (m) REVERT: D 895 MET cc_start: 0.8258 (mtm) cc_final: 0.7870 (mtp) REVERT: D 992 ASP cc_start: 0.7051 (m-30) cc_final: 0.6595 (m-30) REVERT: D 995 ARG cc_start: 0.6726 (mtt-85) cc_final: 0.6190 (mtm110) REVERT: D 996 GLN cc_start: 0.7290 (mt0) cc_final: 0.6893 (mp10) outliers start: 61 outliers final: 21 residues processed: 443 average time/residue: 1.2961 time to fit residues: 695.2981 Evaluate side-chains 392 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 364 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 ARG 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: 30.0000 chunk 308 optimal weight: 30.0000 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 40.0000 chunk 371 optimal weight: 20.0000 chunk 400 optimal weight: 4.9990 chunk 330 optimal weight: 40.0000 chunk 368 optimal weight: 5.9990 chunk 126 optimal weight: 30.0000 chunk 297 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 GLN ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS ** C 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1081 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 32516 Z= 0.501 Angle : 0.748 8.788 44060 Z= 0.384 Chirality : 0.052 0.256 4908 Planarity : 0.006 0.086 5624 Dihedral : 8.130 149.405 4544 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.89 % Favored : 94.01 % Rotamer: Outliers : 3.47 % Allowed : 12.59 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.62 (0.12), residues: 4068 helix: -1.13 (0.12), residues: 1756 sheet: -1.61 (0.21), residues: 560 loop : -2.34 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D1088 HIS 0.006 0.001 HIS B1086 PHE 0.028 0.002 PHE B 998 TYR 0.019 0.002 TYR A 993 ARG 0.010 0.001 ARG B 995 *********************** 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 519 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 406 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.6512 (pttp) cc_final: 0.5544 (mtmt) REVERT: A 326 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7208 (tp) REVERT: A 678 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7976 (m) REVERT: A 777 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7242 (tp40) REVERT: A 895 MET cc_start: 0.8310 (mtm) cc_final: 0.7960 (mtp) REVERT: A 945 MET cc_start: 0.7917 (ttm) cc_final: 0.7664 (ttm) REVERT: A 995 ARG cc_start: 0.6830 (mtt-85) cc_final: 0.6382 (mtm110) REVERT: A 996 GLN cc_start: 0.7213 (mt0) cc_final: 0.6849 (mp10) REVERT: A 998 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6454 (t80) REVERT: B 259 LYS cc_start: 0.6503 (pttp) cc_final: 0.5555 (mtmt) REVERT: B 326 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7135 (tp) REVERT: B 678 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7987 (m) REVERT: B 777 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7212 (tp40) REVERT: B 895 MET cc_start: 0.8306 (mtm) cc_final: 0.7949 (mtp) REVERT: B 976 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7678 (ptp90) REVERT: B 996 GLN cc_start: 0.7214 (mt0) cc_final: 0.6861 (mp10) REVERT: B 998 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6464 (t80) REVERT: B 1081 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7842 (mm-40) REVERT: C 259 LYS cc_start: 0.6502 (pttp) cc_final: 0.5550 (mtmt) REVERT: C 678 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7989 (m) REVERT: C 777 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7204 (tp40) REVERT: C 895 MET cc_start: 0.8314 (mtm) cc_final: 0.7962 (mtp) REVERT: C 945 MET cc_start: 0.7908 (ttm) cc_final: 0.7656 (ttm) REVERT: C 976 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7668 (ptp90) REVERT: C 995 ARG cc_start: 0.6834 (mtt-85) cc_final: 0.6389 (mtm110) REVERT: C 996 GLN cc_start: 0.7213 (mt0) cc_final: 0.6864 (mp10) REVERT: C 998 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6457 (t80) REVERT: C 1081 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7859 (mm-40) REVERT: D 259 LYS cc_start: 0.6485 (pttp) cc_final: 0.5529 (mtmt) REVERT: D 326 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7119 (tp) REVERT: D 678 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.8006 (m) REVERT: D 777 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7205 (tp40) REVERT: D 895 MET cc_start: 0.8314 (mtm) cc_final: 0.7963 (mtp) REVERT: D 945 MET cc_start: 0.7906 (ttm) cc_final: 0.7655 (ttm) REVERT: D 976 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7681 (ptp90) REVERT: D 995 ARG cc_start: 0.6838 (mtt-85) cc_final: 0.6385 (mtm110) REVERT: D 996 GLN cc_start: 0.7221 (mt0) cc_final: 0.6862 (mp10) REVERT: D 998 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6462 (t80) REVERT: D 1081 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7918 (mm-40) outliers start: 113 outliers final: 30 residues processed: 461 average time/residue: 1.2921 time to fit residues: 719.5415 Evaluate side-chains 419 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 368 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 777 GLN Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 913 CYS Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1081 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 777 GLN Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 913 CYS Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 998 PHE Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 777 GLN Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 913 CYS Chi-restraints excluded: chain D residue 976 ARG Chi-restraints excluded: chain D residue 998 PHE Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1081 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 10.0000 chunk 279 optimal weight: 0.9990 chunk 192 optimal weight: 9.9990 chunk 41 optimal weight: 30.0000 chunk 177 optimal weight: 0.4980 chunk 249 optimal weight: 2.9990 chunk 372 optimal weight: 10.0000 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 353 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS A 545 HIS ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN B 371 HIS B 545 HIS ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 GLN ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN C 371 HIS C 545 HIS ** C 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1081 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN D 371 HIS D 545 HIS ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1098 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32516 Z= 0.188 Angle : 0.583 7.277 44060 Z= 0.296 Chirality : 0.044 0.169 4908 Planarity : 0.004 0.073 5624 Dihedral : 7.161 124.335 4544 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.40 % Allowed : 15.50 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.13 (0.12), residues: 4068 helix: -0.57 (0.12), residues: 1764 sheet: -1.35 (0.20), residues: 588 loop : -2.27 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 84 HIS 0.004 0.001 HIS C1086 PHE 0.016 0.001 PHE A 405 TYR 0.012 0.001 TYR C 196 ARG 0.007 0.000 ARG B 995 *********************** 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 468 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 391 time to evaluate : 3.282 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 259 LYS cc_start: 0.6392 (pttp) cc_final: 0.5559 (mtmt) REVERT: A 892 MET cc_start: 0.7454 (mtp) cc_final: 0.7112 (mtp) REVERT: A 895 MET cc_start: 0.8116 (mtm) cc_final: 0.7716 (mtp) REVERT: A 945 MET cc_start: 0.7933 (ttm) cc_final: 0.7643 (ttm) REVERT: A 992 ASP cc_start: 0.7035 (m-30) cc_final: 0.6486 (m-30) REVERT: A 995 ARG cc_start: 0.6560 (mtt-85) cc_final: 0.5984 (mtm110) REVERT: A 996 GLN cc_start: 0.7243 (mt0) cc_final: 0.6814 (mp10) REVERT: A 998 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6936 (t80) REVERT: B 259 LYS cc_start: 0.6284 (pttp) cc_final: 0.5502 (mtmt) REVERT: B 326 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7060 (tp) REVERT: B 575 LEU cc_start: 0.8989 (pp) cc_final: 0.8692 (pp) REVERT: B 892 MET cc_start: 0.7464 (mtp) cc_final: 0.7219 (mtp) REVERT: B 895 MET cc_start: 0.8109 (mtm) cc_final: 0.7708 (mtp) REVERT: B 976 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7618 (ptp90) REVERT: B 992 ASP cc_start: 0.7035 (m-30) cc_final: 0.6450 (m-30) REVERT: B 996 GLN cc_start: 0.7228 (mt0) cc_final: 0.6811 (mp10) REVERT: B 998 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6821 (m-80) REVERT: C 259 LYS cc_start: 0.6346 (pttp) cc_final: 0.5550 (mtmt) REVERT: C 892 MET cc_start: 0.7462 (mtp) cc_final: 0.7134 (mtp) REVERT: C 895 MET cc_start: 0.8115 (mtm) cc_final: 0.7715 (mtp) REVERT: C 945 MET cc_start: 0.7919 (ttm) cc_final: 0.7689 (ttm) REVERT: C 976 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7582 (ptp90) REVERT: C 992 ASP cc_start: 0.7022 (m-30) cc_final: 0.6475 (m-30) REVERT: C 995 ARG cc_start: 0.6563 (mtt-85) cc_final: 0.5990 (mtm110) REVERT: C 996 GLN cc_start: 0.7246 (mt0) cc_final: 0.6817 (mp10) REVERT: D 259 LYS cc_start: 0.6374 (pttp) cc_final: 0.5536 (mtmt) REVERT: D 326 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7049 (tp) REVERT: D 599 GLU cc_start: 0.7855 (tp30) cc_final: 0.7425 (tt0) REVERT: D 892 MET cc_start: 0.7454 (mtp) cc_final: 0.7135 (mtp) REVERT: D 895 MET cc_start: 0.8128 (mtm) cc_final: 0.7719 (mtp) REVERT: D 945 MET cc_start: 0.7910 (ttm) cc_final: 0.7621 (ttm) REVERT: D 976 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7593 (ptp90) REVERT: D 992 ASP cc_start: 0.7016 (m-30) cc_final: 0.6484 (m-30) REVERT: D 995 ARG cc_start: 0.6574 (mtt-85) cc_final: 0.5989 (mtm110) REVERT: D 996 GLN cc_start: 0.7247 (mt0) cc_final: 0.6822 (mp10) REVERT: D 998 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.6951 (t80) REVERT: D 1081 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7707 (mm-40) outliers start: 77 outliers final: 18 residues processed: 431 average time/residue: 1.2157 time to fit residues: 641.8117 Evaluate side-chains 397 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 370 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 644 ASP Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 976 ARG Chi-restraints excluded: chain D residue 998 PHE Chi-restraints excluded: chain D residue 1081 GLN 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: 8.9990 chunk 293 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 336 optimal weight: 20.0000 chunk 272 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 201 optimal weight: 4.9990 chunk 353 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS A 545 HIS ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 545 HIS ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 545 HIS ** C 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 545 HIS ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 32516 Z= 0.384 Angle : 0.668 7.721 44060 Z= 0.339 Chirality : 0.048 0.227 4908 Planarity : 0.005 0.081 5624 Dihedral : 6.949 93.887 4528 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.62 % Favored : 94.29 % Rotamer: Outliers : 3.30 % Allowed : 16.75 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.99 (0.12), residues: 4068 helix: -0.46 (0.12), residues: 1756 sheet: -1.39 (0.20), residues: 580 loop : -2.15 (0.13), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 84 HIS 0.006 0.001 HIS B1086 PHE 0.024 0.002 PHE C 998 TYR 0.017 0.002 TYR D 993 ARG 0.007 0.001 ARG B 995 *********************** 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 480 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 373 time to evaluate : 3.489 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 259 LYS cc_start: 0.6417 (pttp) cc_final: 0.5515 (mtmt) REVERT: A 278 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.6087 (tmm) REVERT: A 512 MET cc_start: 0.8327 (mtp) cc_final: 0.8106 (mtp) REVERT: A 678 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7919 (m) REVERT: A 777 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7195 (tp40) REVERT: A 895 MET cc_start: 0.8261 (mtm) cc_final: 0.7907 (mtp) REVERT: A 995 ARG cc_start: 0.6746 (mtt-85) cc_final: 0.6243 (mtm110) REVERT: A 996 GLN cc_start: 0.7276 (mt0) cc_final: 0.6868 (mp10) REVERT: A 998 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6427 (t80) REVERT: B 259 LYS cc_start: 0.6419 (pttp) cc_final: 0.5529 (mtmt) REVERT: B 278 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.6068 (tmm) REVERT: B 575 LEU cc_start: 0.9048 (pp) cc_final: 0.8777 (pp) REVERT: B 678 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7941 (m) REVERT: B 777 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7259 (tp40) REVERT: B 895 MET cc_start: 0.8258 (mtm) cc_final: 0.7899 (mtp) REVERT: B 976 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7608 (ptp90) REVERT: B 996 GLN cc_start: 0.7259 (mt0) cc_final: 0.6858 (mp10) REVERT: B 998 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6429 (t80) REVERT: C 259 LYS cc_start: 0.6430 (pttp) cc_final: 0.5544 (mtmt) REVERT: C 278 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.6069 (tmm) REVERT: C 678 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7952 (m) REVERT: C 777 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7235 (tp40) REVERT: C 895 MET cc_start: 0.8244 (mtm) cc_final: 0.7899 (mtp) REVERT: C 976 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7647 (ptp90) REVERT: C 995 ARG cc_start: 0.6745 (mtt-85) cc_final: 0.6138 (mtm110) REVERT: C 996 GLN cc_start: 0.7275 (mt0) cc_final: 0.6866 (mp10) REVERT: C 998 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6246 (t80) REVERT: D 259 LYS cc_start: 0.6420 (pttp) cc_final: 0.5524 (mtmt) REVERT: D 278 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.6066 (tmm) REVERT: D 599 GLU cc_start: 0.8066 (tp30) cc_final: 0.7634 (tt0) REVERT: D 678 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7945 (m) REVERT: D 777 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7229 (tp40) REVERT: D 895 MET cc_start: 0.8246 (mtm) cc_final: 0.7895 (mtp) REVERT: D 976 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7617 (ptp90) REVERT: D 995 ARG cc_start: 0.6756 (mtt-85) cc_final: 0.6247 (mtm110) REVERT: D 996 GLN cc_start: 0.7280 (mt0) cc_final: 0.6873 (mp10) REVERT: D 998 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6430 (t80) REVERT: D 1081 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7792 (mm-40) outliers start: 107 outliers final: 43 residues processed: 423 average time/residue: 1.2464 time to fit residues: 652.5884 Evaluate side-chains 417 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 354 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 777 GLN Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 777 GLN Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 998 PHE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 644 ASP Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 712 MET Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 777 GLN Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 976 ARG Chi-restraints excluded: chain D residue 998 PHE Chi-restraints excluded: chain D residue 1022 ILE Chi-restraints excluded: chain D residue 1081 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 30.0000 chunk 355 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 231 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 394 optimal weight: 1.9990 chunk 327 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 207 optimal weight: 0.1980 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS A 545 HIS ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 545 HIS ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 545 HIS ** C 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 545 HIS ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32516 Z= 0.195 Angle : 0.574 7.620 44060 Z= 0.290 Chirality : 0.044 0.173 4908 Planarity : 0.004 0.068 5624 Dihedral : 6.416 87.103 4528 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.43 % Allowed : 17.16 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.65 (0.13), residues: 4068 helix: -0.12 (0.12), residues: 1760 sheet: -1.02 (0.21), residues: 600 loop : -2.13 (0.13), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 276 HIS 0.005 0.001 HIS B1086 PHE 0.016 0.001 PHE A 347 TYR 0.012 0.001 TYR D 124 ARG 0.007 0.000 ARG B 995 *********************** 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 458 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 380 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.6310 (pttp) cc_final: 0.5497 (mtmt) REVERT: A 678 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7798 (m) REVERT: A 892 MET cc_start: 0.7511 (mtp) cc_final: 0.7221 (mtp) REVERT: A 895 MET cc_start: 0.8142 (mtm) cc_final: 0.7724 (mtp) REVERT: A 995 ARG cc_start: 0.6551 (mtt-85) cc_final: 0.5932 (mtm110) REVERT: A 996 GLN cc_start: 0.7296 (mt0) cc_final: 0.6795 (mp10) REVERT: A 998 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6752 (t80) REVERT: B 259 LYS cc_start: 0.6289 (pttp) cc_final: 0.5507 (mtmt) REVERT: B 391 MET cc_start: 0.3967 (ttt) cc_final: 0.3389 (ttp) REVERT: B 678 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7808 (m) REVERT: B 892 MET cc_start: 0.7510 (mtp) cc_final: 0.7198 (mtp) REVERT: B 895 MET cc_start: 0.8142 (mtm) cc_final: 0.7724 (mtp) REVERT: B 976 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7529 (ptp90) REVERT: B 995 ARG cc_start: 0.6704 (mtt-85) cc_final: 0.5915 (mtm110) REVERT: B 996 GLN cc_start: 0.7254 (mt0) cc_final: 0.6928 (tm-30) REVERT: B 998 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6812 (t80) REVERT: C 259 LYS cc_start: 0.6290 (pttp) cc_final: 0.5478 (mtmt) REVERT: C 678 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7809 (m) REVERT: C 892 MET cc_start: 0.7529 (mtp) cc_final: 0.7178 (mtp) REVERT: C 895 MET cc_start: 0.8157 (mtm) cc_final: 0.7725 (mtp) REVERT: C 976 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7564 (ptp90) REVERT: C 995 ARG cc_start: 0.6550 (mtt-85) cc_final: 0.5922 (mtm110) REVERT: C 996 GLN cc_start: 0.7301 (mt0) cc_final: 0.6794 (mp10) REVERT: C 998 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6873 (m-80) REVERT: D 259 LYS cc_start: 0.6291 (pttp) cc_final: 0.5487 (mtmt) REVERT: D 599 GLU cc_start: 0.7968 (tp30) cc_final: 0.7470 (tt0) REVERT: D 678 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7810 (m) REVERT: D 892 MET cc_start: 0.7514 (mtp) cc_final: 0.7202 (mtp) REVERT: D 895 MET cc_start: 0.8148 (mtm) cc_final: 0.7737 (mtp) REVERT: D 976 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7501 (ptp90) REVERT: D 995 ARG cc_start: 0.6565 (mtt-85) cc_final: 0.5939 (mtm110) REVERT: D 996 GLN cc_start: 0.7295 (mt0) cc_final: 0.6798 (mp10) REVERT: D 998 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6760 (t80) REVERT: D 1081 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7800 (mm-40) outliers start: 78 outliers final: 32 residues processed: 426 average time/residue: 1.2758 time to fit residues: 661.6325 Evaluate side-chains 402 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 358 time to evaluate : 3.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 998 PHE Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 644 ASP Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 712 MET Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 976 ARG Chi-restraints excluded: chain D residue 998 PHE Chi-restraints excluded: chain D residue 1081 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 chunk 224 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 332 optimal weight: 20.0000 chunk 220 optimal weight: 0.0050 chunk 393 optimal weight: 0.1980 chunk 246 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS A 545 HIS ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 545 HIS ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 545 HIS ** C 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 545 HIS ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 32516 Z= 0.146 Angle : 0.547 8.856 44060 Z= 0.273 Chirality : 0.043 0.165 4908 Planarity : 0.004 0.054 5624 Dihedral : 6.036 81.331 4528 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.78 % Allowed : 18.62 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.26 (0.13), residues: 4068 helix: 0.23 (0.13), residues: 1732 sheet: -0.69 (0.21), residues: 592 loop : -1.98 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 276 HIS 0.002 0.000 HIS B 332 PHE 0.014 0.001 PHE A 347 TYR 0.012 0.001 TYR C 124 ARG 0.007 0.000 ARG B 995 *********************** 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 466 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 410 time to evaluate : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.6095 (pttp) cc_final: 0.5371 (mtmt) REVERT: A 278 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.5725 (tmm) REVERT: A 678 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7703 (m) REVERT: A 892 MET cc_start: 0.7518 (mtp) cc_final: 0.7228 (mtp) REVERT: A 895 MET cc_start: 0.8097 (mtm) cc_final: 0.7697 (mtp) REVERT: A 980 ILE cc_start: 0.6401 (OUTLIER) cc_final: 0.6176 (tp) REVERT: A 995 ARG cc_start: 0.6347 (mtt-85) cc_final: 0.5865 (mtm110) REVERT: A 996 GLN cc_start: 0.7302 (mt0) cc_final: 0.6918 (tm-30) REVERT: A 998 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6837 (m-80) REVERT: B 259 LYS cc_start: 0.6097 (pttp) cc_final: 0.5377 (mtmt) REVERT: B 278 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.5680 (tmm) REVERT: B 307 TYR cc_start: 0.6863 (p90) cc_final: 0.6583 (p90) REVERT: B 575 LEU cc_start: 0.8947 (pp) cc_final: 0.8675 (pp) REVERT: B 678 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7692 (m) REVERT: B 892 MET cc_start: 0.7541 (mtp) cc_final: 0.7232 (mtp) REVERT: B 895 MET cc_start: 0.8095 (mtm) cc_final: 0.7653 (mtp) REVERT: B 976 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7557 (ptp90) REVERT: B 995 ARG cc_start: 0.6447 (mtt-85) cc_final: 0.5736 (mtm110) REVERT: B 996 GLN cc_start: 0.7321 (mt0) cc_final: 0.6923 (tm-30) REVERT: B 1090 ASP cc_start: 0.7459 (t70) cc_final: 0.7183 (t0) REVERT: C 259 LYS cc_start: 0.6052 (pttp) cc_final: 0.5357 (mtmt) REVERT: C 599 GLU cc_start: 0.7748 (tp30) cc_final: 0.7147 (tt0) REVERT: C 678 THR cc_start: 0.7973 (OUTLIER) cc_final: 0.7689 (m) REVERT: C 888 GLN cc_start: 0.7165 (tp40) cc_final: 0.6943 (mm110) REVERT: C 892 MET cc_start: 0.7468 (mtp) cc_final: 0.7167 (mtp) REVERT: C 895 MET cc_start: 0.8092 (mtm) cc_final: 0.7658 (mtp) REVERT: C 976 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7576 (ptp90) REVERT: C 995 ARG cc_start: 0.6340 (mtt-85) cc_final: 0.5839 (mtm110) REVERT: C 996 GLN cc_start: 0.7295 (mt0) cc_final: 0.6914 (tm-30) REVERT: D 259 LYS cc_start: 0.6098 (pttp) cc_final: 0.5364 (mtmt) REVERT: D 278 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.5689 (tmm) REVERT: D 307 TYR cc_start: 0.6859 (p90) cc_final: 0.6579 (p90) REVERT: D 678 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7692 (m) REVERT: D 698 MET cc_start: 0.6925 (tpp) cc_final: 0.6635 (tpp) REVERT: D 888 GLN cc_start: 0.7010 (tp40) cc_final: 0.6779 (mm110) REVERT: D 892 MET cc_start: 0.7551 (mtp) cc_final: 0.7239 (mtp) REVERT: D 895 MET cc_start: 0.8077 (mtm) cc_final: 0.7652 (mtp) REVERT: D 976 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7502 (ptp90) REVERT: D 995 ARG cc_start: 0.6359 (mtt-85) cc_final: 0.5874 (mtm110) REVERT: D 996 GLN cc_start: 0.7302 (mt0) cc_final: 0.6927 (tm-30) REVERT: D 998 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6853 (m-80) REVERT: D 1081 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7640 (mm-40) outliers start: 56 outliers final: 22 residues processed: 440 average time/residue: 1.2657 time to fit residues: 681.0862 Evaluate side-chains 419 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 383 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 976 ARG Chi-restraints excluded: chain D residue 998 PHE Chi-restraints excluded: chain D residue 1081 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 234 optimal weight: 40.0000 chunk 118 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 76 optimal weight: 0.0570 chunk 250 optimal weight: 3.9990 chunk 267 optimal weight: 10.0000 chunk 194 optimal weight: 0.0570 chunk 36 optimal weight: 1.9990 chunk 309 optimal weight: 8.9990 overall best weight: 1.3820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS A 545 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 545 HIS B 888 GLN ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 545 HIS ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 545 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32516 Z= 0.179 Angle : 0.560 10.290 44060 Z= 0.280 Chirality : 0.044 0.176 4908 Planarity : 0.004 0.056 5624 Dihedral : 5.945 74.495 4528 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.63 % Allowed : 19.21 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.08 (0.13), residues: 4068 helix: 0.32 (0.13), residues: 1744 sheet: -0.55 (0.21), residues: 592 loop : -1.84 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 84 HIS 0.004 0.001 HIS B1086 PHE 0.013 0.001 PHE A 347 TYR 0.014 0.001 TYR B 993 ARG 0.009 0.000 ARG B 995 *********************** 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 462 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 411 time to evaluate : 3.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.6081 (pttp) cc_final: 0.5333 (mtmt) REVERT: A 678 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7716 (m) REVERT: A 892 MET cc_start: 0.7415 (mtp) cc_final: 0.7202 (mtp) REVERT: A 895 MET cc_start: 0.8129 (mtm) cc_final: 0.7774 (mtp) REVERT: A 995 ARG cc_start: 0.6386 (mtt-85) cc_final: 0.5882 (mtm110) REVERT: A 996 GLN cc_start: 0.7343 (mt0) cc_final: 0.6909 (tm-30) REVERT: A 998 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: A 1090 ASP cc_start: 0.7498 (t70) cc_final: 0.7261 (t0) REVERT: B 259 LYS cc_start: 0.6087 (pttp) cc_final: 0.5339 (mtmt) REVERT: B 575 LEU cc_start: 0.8975 (pp) cc_final: 0.8702 (pp) REVERT: B 678 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7721 (m) REVERT: B 892 MET cc_start: 0.7421 (mtp) cc_final: 0.7142 (mtp) REVERT: B 895 MET cc_start: 0.8121 (mtm) cc_final: 0.7704 (mtp) REVERT: B 976 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7585 (ptp90) REVERT: B 995 ARG cc_start: 0.6676 (mtt-85) cc_final: 0.5907 (mtm110) REVERT: B 996 GLN cc_start: 0.7306 (mt0) cc_final: 0.6935 (tm-30) REVERT: B 1090 ASP cc_start: 0.7490 (t70) cc_final: 0.7258 (t0) REVERT: C 259 LYS cc_start: 0.6063 (pttp) cc_final: 0.5348 (mtmt) REVERT: C 278 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.5820 (tmm) REVERT: C 599 GLU cc_start: 0.7631 (tp30) cc_final: 0.7033 (tt0) REVERT: C 678 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7716 (m) REVERT: C 892 MET cc_start: 0.7406 (mtp) cc_final: 0.7124 (mtp) REVERT: C 895 MET cc_start: 0.8136 (mtm) cc_final: 0.7713 (mtp) REVERT: C 976 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7603 (ptp90) REVERT: C 995 ARG cc_start: 0.6403 (mtt-85) cc_final: 0.5888 (mtm110) REVERT: C 996 GLN cc_start: 0.7357 (mt0) cc_final: 0.6920 (tm-30) REVERT: C 1090 ASP cc_start: 0.7500 (t70) cc_final: 0.7272 (t0) REVERT: D 259 LYS cc_start: 0.6064 (pttp) cc_final: 0.5329 (mtmt) REVERT: D 678 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7702 (m) REVERT: D 892 MET cc_start: 0.7421 (mtp) cc_final: 0.7135 (mtp) REVERT: D 895 MET cc_start: 0.8110 (mtm) cc_final: 0.7711 (mtp) REVERT: D 976 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7503 (ptp90) REVERT: D 995 ARG cc_start: 0.6397 (mtt-85) cc_final: 0.5884 (mtm110) REVERT: D 996 GLN cc_start: 0.7345 (mt0) cc_final: 0.6917 (tm-30) REVERT: D 998 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.6875 (m-80) REVERT: D 1081 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7573 (mm-40) REVERT: D 1090 ASP cc_start: 0.7498 (t70) cc_final: 0.7268 (t0) outliers start: 51 outliers final: 33 residues processed: 444 average time/residue: 1.2019 time to fit residues: 660.2012 Evaluate side-chains 439 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 395 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 976 ARG Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 998 PHE Chi-restraints excluded: chain D residue 1081 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 10.0000 chunk 376 optimal weight: 10.0000 chunk 343 optimal weight: 20.0000 chunk 366 optimal weight: 0.0270 chunk 220 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 331 optimal weight: 5.9990 chunk 346 optimal weight: 9.9990 chunk 365 optimal weight: 2.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS A 545 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 545 HIS ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 545 HIS ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 545 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32516 Z= 0.208 Angle : 0.571 10.180 44060 Z= 0.285 Chirality : 0.044 0.180 4908 Planarity : 0.004 0.066 5624 Dihedral : 5.940 67.588 4528 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.75 % Allowed : 19.42 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.02 (0.13), residues: 4068 helix: 0.34 (0.13), residues: 1744 sheet: -0.50 (0.22), residues: 592 loop : -1.78 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 276 HIS 0.005 0.001 HIS B1086 PHE 0.016 0.001 PHE C 998 TYR 0.014 0.001 TYR B 993 ARG 0.006 0.000 ARG B 995 *********************** 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 435 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 380 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.6103 (pttp) cc_final: 0.5342 (mtmt) REVERT: A 599 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7451 (tp30) REVERT: A 678 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7716 (m) REVERT: A 892 MET cc_start: 0.7434 (mtp) cc_final: 0.7212 (mtp) REVERT: A 895 MET cc_start: 0.8143 (mtm) cc_final: 0.7722 (mtp) REVERT: A 995 ARG cc_start: 0.6410 (mtt-85) cc_final: 0.5903 (mtm110) REVERT: A 996 GLN cc_start: 0.7352 (mt0) cc_final: 0.6883 (tm-30) REVERT: A 998 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6293 (t80) REVERT: A 1090 ASP cc_start: 0.7536 (t70) cc_final: 0.7282 (t0) REVERT: B 259 LYS cc_start: 0.6099 (pttp) cc_final: 0.5329 (mtmt) REVERT: B 575 LEU cc_start: 0.8984 (pp) cc_final: 0.8710 (pp) REVERT: B 678 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7715 (m) REVERT: B 895 MET cc_start: 0.8145 (mtm) cc_final: 0.7723 (mtp) REVERT: B 976 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7581 (ptp90) REVERT: B 995 ARG cc_start: 0.6683 (mtt-85) cc_final: 0.5877 (mtm110) REVERT: B 996 GLN cc_start: 0.7349 (mt0) cc_final: 0.6896 (tm-30) REVERT: B 1090 ASP cc_start: 0.7575 (t70) cc_final: 0.7321 (t0) REVERT: C 259 LYS cc_start: 0.6074 (pttp) cc_final: 0.5311 (mtmt) REVERT: C 278 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.5855 (tmm) REVERT: C 307 TYR cc_start: 0.7027 (p90) cc_final: 0.6735 (p90) REVERT: C 599 GLU cc_start: 0.7615 (tp30) cc_final: 0.6975 (tt0) REVERT: C 678 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7721 (m) REVERT: C 892 MET cc_start: 0.7405 (mtp) cc_final: 0.7114 (mtp) REVERT: C 895 MET cc_start: 0.8148 (mtm) cc_final: 0.7724 (mtp) REVERT: C 976 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7543 (ptp90) REVERT: C 995 ARG cc_start: 0.6465 (mtt-85) cc_final: 0.5945 (mtm110) REVERT: C 996 GLN cc_start: 0.7360 (mt0) cc_final: 0.6857 (tm-30) REVERT: C 1090 ASP cc_start: 0.7581 (t70) cc_final: 0.7335 (t0) REVERT: D 259 LYS cc_start: 0.6094 (pttp) cc_final: 0.5320 (mtmt) REVERT: D 599 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7786 (tp30) REVERT: D 678 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7711 (m) REVERT: D 892 MET cc_start: 0.7418 (mtp) cc_final: 0.7136 (mtp) REVERT: D 895 MET cc_start: 0.8147 (mtm) cc_final: 0.7757 (mtp) REVERT: D 976 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7520 (ptp90) REVERT: D 995 ARG cc_start: 0.6419 (mtt-85) cc_final: 0.5906 (mtm110) REVERT: D 996 GLN cc_start: 0.7359 (mt0) cc_final: 0.6891 (tm-30) REVERT: D 998 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6296 (t80) REVERT: D 1081 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7804 (mm110) REVERT: D 1090 ASP cc_start: 0.7583 (t70) cc_final: 0.7332 (t0) outliers start: 55 outliers final: 39 residues processed: 422 average time/residue: 1.2423 time to fit residues: 659.0932 Evaluate side-chains 427 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 377 time to evaluate : 3.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 683 GLU Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 976 ARG Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 998 PHE Chi-restraints excluded: chain D residue 1081 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 20.0000 chunk 387 optimal weight: 0.4980 chunk 236 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 269 optimal weight: 10.0000 chunk 406 optimal weight: 3.9990 chunk 374 optimal weight: 1.9990 chunk 323 optimal weight: 40.0000 chunk 33 optimal weight: 20.0000 chunk 250 optimal weight: 0.1980 chunk 198 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 32516 Z= 0.148 Angle : 0.544 10.555 44060 Z= 0.269 Chirality : 0.043 0.207 4908 Planarity : 0.004 0.057 5624 Dihedral : 5.659 60.674 4528 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.43 % Allowed : 20.19 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.88 (0.13), residues: 4068 helix: 0.43 (0.13), residues: 1744 sheet: -0.36 (0.22), residues: 592 loop : -1.70 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 84 HIS 0.003 0.000 HIS C1086 PHE 0.015 0.001 PHE A 347 TYR 0.011 0.001 TYR C 124 ARG 0.008 0.000 ARG B 676 ********************** 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 448 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 404 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.6144 (pttp) cc_final: 0.5388 (mtmt) REVERT: A 512 MET cc_start: 0.8062 (mtp) cc_final: 0.7860 (mtp) REVERT: A 599 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7394 (tp30) REVERT: A 638 ASN cc_start: 0.8599 (m-40) cc_final: 0.8335 (m110) REVERT: A 678 THR cc_start: 0.7920 (OUTLIER) cc_final: 0.7613 (m) REVERT: A 892 MET cc_start: 0.7426 (mtp) cc_final: 0.7151 (mtp) REVERT: A 895 MET cc_start: 0.8108 (mtm) cc_final: 0.7677 (mtp) REVERT: A 995 ARG cc_start: 0.6377 (mtt-85) cc_final: 0.5873 (mtm110) REVERT: A 996 GLN cc_start: 0.7395 (mt0) cc_final: 0.6864 (tm-30) REVERT: A 1090 ASP cc_start: 0.7477 (t70) cc_final: 0.7219 (t0) REVERT: B 259 LYS cc_start: 0.6144 (pttp) cc_final: 0.5396 (mtmt) REVERT: B 575 LEU cc_start: 0.8942 (pp) cc_final: 0.8656 (pp) REVERT: B 678 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7567 (m) REVERT: B 892 MET cc_start: 0.7500 (mtp) cc_final: 0.7226 (mtp) REVERT: B 895 MET cc_start: 0.8112 (mtm) cc_final: 0.7679 (mtp) REVERT: B 976 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7547 (ptp90) REVERT: B 995 ARG cc_start: 0.6518 (mtt-85) cc_final: 0.5758 (mtm110) REVERT: B 996 GLN cc_start: 0.7503 (mt0) cc_final: 0.6934 (tm-30) REVERT: B 1090 ASP cc_start: 0.7513 (t70) cc_final: 0.7266 (t0) REVERT: C 259 LYS cc_start: 0.6115 (pttp) cc_final: 0.5390 (mtmt) REVERT: C 278 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.5556 (tmm) REVERT: C 307 TYR cc_start: 0.6995 (p90) cc_final: 0.6757 (p90) REVERT: C 678 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7639 (m) REVERT: C 888 GLN cc_start: 0.7028 (tp40) cc_final: 0.6797 (mm110) REVERT: C 892 MET cc_start: 0.7530 (mtp) cc_final: 0.7249 (mtp) REVERT: C 895 MET cc_start: 0.8107 (mtm) cc_final: 0.7675 (mtp) REVERT: C 976 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7566 (ptp90) REVERT: C 995 ARG cc_start: 0.6428 (mtt-85) cc_final: 0.5909 (mtm110) REVERT: C 996 GLN cc_start: 0.7376 (mt0) cc_final: 0.6866 (tm-30) REVERT: C 1090 ASP cc_start: 0.7515 (t70) cc_final: 0.7269 (t0) REVERT: D 259 LYS cc_start: 0.6143 (pttp) cc_final: 0.5379 (mtmt) REVERT: D 678 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7592 (m) REVERT: D 888 GLN cc_start: 0.6994 (tp40) cc_final: 0.6751 (mm110) REVERT: D 892 MET cc_start: 0.7541 (mtp) cc_final: 0.7254 (mtp) REVERT: D 895 MET cc_start: 0.8115 (mtm) cc_final: 0.7715 (mtp) REVERT: D 976 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7545 (ptp90) REVERT: D 995 ARG cc_start: 0.6402 (mtt-85) cc_final: 0.5896 (mtm110) REVERT: D 996 GLN cc_start: 0.7399 (mt0) cc_final: 0.6871 (tm-30) REVERT: D 1090 ASP cc_start: 0.7510 (t70) cc_final: 0.7265 (t0) outliers start: 44 outliers final: 34 residues processed: 440 average time/residue: 1.2342 time to fit residues: 662.3292 Evaluate side-chains 422 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 380 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 683 GLU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 976 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 20.0000 chunk 344 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 89 optimal weight: 0.0670 chunk 324 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 332 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 59 optimal weight: 0.4980 overall best weight: 2.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 545 HIS ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 545 HIS ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 545 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.234509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.215399 restraints weight = 66787.980| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 1.54 r_work: 0.4106 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4075 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4051 r_free = 0.4051 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4050 r_free = 0.4050 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32516 Z= 0.230 Angle : 0.594 12.175 44060 Z= 0.298 Chirality : 0.045 0.249 4908 Planarity : 0.005 0.059 5624 Dihedral : 5.761 62.893 4528 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.69 % Allowed : 20.25 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.87 (0.13), residues: 4068 helix: 0.39 (0.13), residues: 1748 sheet: -0.24 (0.23), residues: 572 loop : -1.68 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 84 HIS 0.005 0.001 HIS B1086 PHE 0.035 0.002 PHE D 959 TYR 0.037 0.001 TYR C 579 ARG 0.008 0.000 ARG B 676 =============================================================================== Job complete usr+sys time: 11399.27 seconds wall clock time: 206 minutes 1.49 seconds (12361.49 seconds total)