Starting phenix.real_space_refine on Wed Feb 21 21:12:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ui9_20783/02_2024/6ui9_20783_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ui9_20783/02_2024/6ui9_20783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ui9_20783/02_2024/6ui9_20783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ui9_20783/02_2024/6ui9_20783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ui9_20783/02_2024/6ui9_20783_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ui9_20783/02_2024/6ui9_20783_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 180 5.16 5 C 20380 2.51 5 N 5388 2.21 5 O 5952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "C GLU 523": "OE1" <-> "OE2" Residue "C GLU 547": "OE1" <-> "OE2" Residue "C GLU 584": "OE1" <-> "OE2" Residue "C GLU 891": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 523": "OE1" <-> "OE2" Residue "D GLU 669": "OE1" <-> "OE2" Residue "D ASP 933": "OD1" <-> "OD2" Residue "D TYR 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1006": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1026": "OD1" <-> "OD2" Residue "D PHE 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1047": "OE1" <-> "OE2" Residue "D TYR 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31912 Number of models: 1 Model: "" Number of chains: 12 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: {'PTRANS': 49, '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: {'PTRANS': 49, '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': 2, 'PTRANS': 47, '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': 2, 'PTRANS': 47, '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': 2, 'PTRANS': 47, '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': 2, 'PTRANS': 47, '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: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'ACO': 2, 'OAA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'ACO': 1, 'OAA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'OAA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'ACO': 1, 'OAA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 31.49, per 1000 atoms: 0.99 Number of scatterers: 31912 At special positions: 0 Unit cell: (140.07, 162.69, 171.39, 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 5952 8.00 N 5388 7.00 C 20380 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: 12.22 Conformation dependent library (CDL) restraints added in 11.3 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: 162 helices and 32 sheets defined 40.1% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.78 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 48 through 51 removed outlier: 4.209A pdb=" N LEU A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 178 through 194 Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.701A pdb=" N ASP A 226 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR A 227 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS A 230 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL A 231 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP A 233 " --> pdb=" O LYS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 282 through 294 Processing helix chain 'A' and resid 313 through 325 Processing helix chain 'A' and resid 350 through 363 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: 3.976A pdb=" N ILE A 414 " --> pdb=" O MET A 411 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 415 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 3.887A 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 586 Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 643 through 648 Processing helix chain 'A' and resid 665 through 677 removed outlier: 4.477A pdb=" N GLU A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 removed outlier: 3.724A pdb=" N ARG A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 733 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 772 through 782 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 876 Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 905 through 914 Processing helix chain 'A' and resid 920 through 930 removed outlier: 4.312A pdb=" N THR A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 951 Processing helix chain 'A' and resid 956 through 965 removed outlier: 3.587A pdb=" N ASN A 961 " --> pdb=" O MET A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1002 through 1017 removed outlier: 3.502A pdb=" N TYR A1006 " --> pdb=" O PRO A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1039 removed outlier: 3.816A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1054 removed outlier: 3.578A pdb=" N ILE A1052 " --> pdb=" O ALA A1048 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP A1053 " --> pdb=" O ASP A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1078 removed outlier: 4.034A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.067A 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 46 Processing helix chain 'B' and resid 48 through 51 removed outlier: 4.216A pdb=" N LEU B 51 " --> pdb=" O PRO B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 66 through 69 No H-bonds generated for 'chain 'B' and resid 66 through 69' Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 178 through 194 Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.705A pdb=" N ASP B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR B 227 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS B 230 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL B 231 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP B 233 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 258 Processing helix chain 'B' and resid 282 through 294 Processing helix chain 'B' and resid 313 through 327 removed outlier: 3.565A pdb=" N MET B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 397 Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.821A pdb=" N ILE B 414 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 415 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 3.835A 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 586 Processing helix chain 'B' and resid 603 through 616 Processing helix chain 'B' and resid 643 through 648 Processing helix chain 'B' and resid 665 through 677 removed outlier: 4.409A pdb=" N GLU B 669 " --> pdb=" O GLY B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 706 removed outlier: 3.753A pdb=" N ARG B 703 " --> pdb=" O ASP B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 733 Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 772 through 782 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 876 Processing helix chain 'B' and resid 884 through 896 Processing helix chain 'B' and resid 905 through 914 Processing helix chain 'B' and resid 920 through 930 removed outlier: 4.315A pdb=" N THR B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 951 Processing helix chain 'B' and resid 956 through 965 removed outlier: 3.577A pdb=" N ASN B 961 " --> pdb=" O MET B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 997 Processing helix chain 'B' and resid 1002 through 1017 Processing helix chain 'B' and resid 1025 through 1039 removed outlier: 3.825A pdb=" N GLY B1030 " --> pdb=" O ASP B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1054 removed outlier: 3.593A pdb=" N ILE B1052 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP B1053 " --> pdb=" O ASP B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1078 removed outlier: 4.049A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.075A 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 46 Processing helix chain 'C' and resid 48 through 51 removed outlier: 4.246A pdb=" N LEU C 51 " --> pdb=" O PRO C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 66 through 69 No H-bonds generated for 'chain 'C' and resid 66 through 69' Processing helix chain 'C' and resid 78 through 86 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 178 through 194 Processing helix chain 'C' and resid 223 through 233 removed outlier: 3.723A pdb=" N ASP C 226 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR C 227 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS C 230 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL C 231 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TRP C 233 " --> pdb=" O LYS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 258 Processing helix chain 'C' and resid 282 through 294 Processing helix chain 'C' and resid 313 through 325 Processing helix chain 'C' and resid 350 through 363 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 398 Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.773A pdb=" N ILE C 414 " --> pdb=" O MET C 411 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 415 " --> pdb=" O THR C 412 " (cutoff:3.500A) removed outlier: 3.704A 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 586 Processing helix chain 'C' and resid 603 through 616 Processing helix chain 'C' and resid 643 through 648 Processing helix chain 'C' and resid 665 through 677 removed outlier: 4.520A pdb=" N GLU C 669 " --> pdb=" O GLY C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 706 removed outlier: 3.761A pdb=" N ARG C 703 " --> pdb=" O ASP C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 733 Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 772 through 782 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 876 Processing helix chain 'C' and resid 884 through 896 Processing helix chain 'C' and resid 905 through 914 Processing helix chain 'C' and resid 920 through 930 removed outlier: 4.309A pdb=" N THR C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 951 Processing helix chain 'C' and resid 956 through 965 removed outlier: 3.613A pdb=" N ASN C 961 " --> pdb=" O MET C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 997 Processing helix chain 'C' and resid 1002 through 1017 Processing helix chain 'C' and resid 1025 through 1039 removed outlier: 3.812A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1048 through 1054 removed outlier: 3.583A pdb=" N ILE C1052 " --> pdb=" O ALA C1048 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C1053 " --> pdb=" O ASP C1049 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1078 removed outlier: 4.038A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.068A 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 46 Processing helix chain 'D' and resid 48 through 51 removed outlier: 4.236A pdb=" N LEU D 51 " --> pdb=" O PRO D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 66 through 69 No H-bonds generated for 'chain 'D' and resid 66 through 69' Processing helix chain 'D' and resid 78 through 86 Processing helix chain 'D' and resid 162 through 168 Processing helix chain 'D' and resid 178 through 194 removed outlier: 3.614A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.739A pdb=" N ASP D 226 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR D 227 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS D 230 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL D 231 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP D 233 " --> pdb=" O LYS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 258 removed outlier: 3.500A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 313 through 327 removed outlier: 3.554A pdb=" N MET D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 363 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 384 through 397 Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.834A pdb=" N ILE D 414 " --> pdb=" O MET D 411 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 415 " --> pdb=" O THR D 412 " (cutoff:3.500A) removed outlier: 3.862A 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 586 Processing helix chain 'D' and resid 603 through 616 Processing helix chain 'D' and resid 643 through 648 Processing helix chain 'D' and resid 665 through 677 removed outlier: 4.463A pdb=" N GLU D 669 " --> pdb=" O GLY D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 706 removed outlier: 3.756A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 733 Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 772 through 782 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 876 Processing helix chain 'D' and resid 884 through 896 Processing helix chain 'D' and resid 905 through 916 removed outlier: 3.735A pdb=" N ALA D 916 " --> pdb=" O ILE D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 930 removed outlier: 3.825A pdb=" N GLY D 927 " --> pdb=" O SER D 923 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 950 removed outlier: 3.717A pdb=" N LYS D 948 " --> pdb=" O LYS D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 965 removed outlier: 3.595A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 991 Processing helix chain 'D' and resid 993 through 996 No H-bonds generated for 'chain 'D' and resid 993 through 996' Processing helix chain 'D' and resid 1002 through 1017 removed outlier: 4.159A pdb=" N LYS D1012 " --> pdb=" O LEU D1008 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS D1017 " --> pdb=" O ILE D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1025 through 1037 Processing helix chain 'D' and resid 1047 through 1049 No H-bonds generated for 'chain 'D' and resid 1047 through 1049' Processing helix chain 'D' and resid 1051 through 1054 No H-bonds generated for 'chain 'D' and resid 1051 through 1054' Processing helix chain 'D' and resid 1058 through 1072 removed outlier: 3.591A pdb=" N VAL D1062 " --> pdb=" O ASN D1058 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1088 through 1090 No H-bonds generated for 'chain 'D' and resid 1088 through 1090' Processing sheet with id= A, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.819A pdb=" N ALA A 219 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR A 198 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 121 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 32 through 35 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 removed outlier: 3.533A pdb=" N THR A 267 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.489A pdb=" N ILE A 337 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 593 through 596 removed outlier: 7.747A pdb=" N VAL A 501 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET A 529 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 14.003A pdb=" N ALA A 527 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N LEU A 549 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N MET A 529 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 739 through 742 removed outlier: 7.672A pdb=" N TYR A 659 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY A 684 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 7.317A 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: 5.712A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 7.538A 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 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: 6.468A pdb=" N ILE B 337 " --> pdb=" O TRP B 276 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 619 through 621 removed outlier: 7.718A pdb=" N VAL B 501 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 529 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 14.018A pdb=" N ALA B 527 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N LEU B 549 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N MET B 529 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 739 through 742 removed outlier: 7.626A pdb=" N TYR B 659 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY B 684 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N SER B 661 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 4.267A 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: 5.749A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR C 198 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 121 " --> pdb=" O ILE C 202 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 32 through 35 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: 6.499A pdb=" N ILE C 337 " --> pdb=" O TRP C 276 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 619 through 621 removed outlier: 7.692A pdb=" N VAL C 501 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET C 529 " --> pdb=" O VAL C 501 " (cutoff:3.500A) removed outlier: 14.078A pdb=" N ALA C 527 " --> pdb=" O GLU C 547 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N LEU C 549 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N MET C 529 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 627 through 629 removed outlier: 4.326A pdb=" N GLY C 627 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL C 657 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLY C 684 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR C 659 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ALA C 686 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER C 661 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET C 712 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N VAL C 660 " --> pdb=" O MET C 712 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 714 " --> pdb=" O VAL C 660 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL C 715 " --> pdb=" O PRO C 739 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 741 " --> pdb=" O VAL C 715 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 3 through 5 removed outlier: 5.733A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 7.386A 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 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: 6.469A pdb=" N ILE D 337 " --> pdb=" O TRP D 276 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 619 through 621 removed outlier: 7.720A pdb=" N VAL D 501 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET D 529 " --> pdb=" O VAL D 501 " (cutoff:3.500A) removed outlier: 14.023A pdb=" N ALA D 527 " --> pdb=" O GLU D 547 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N LEU D 549 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N MET D 529 " --> pdb=" O LEU D 549 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 739 through 742 removed outlier: 7.622A pdb=" N TYR D 659 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY D 684 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER D 661 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA D 686 " --> pdb=" O SER D 661 " (cutoff:3.500A) 1237 hydrogen bonds defined for protein. 3549 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: 13.21 Time building geometry restraints manager: 13.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 5300 1.27 - 1.41: 7824 1.41 - 1.54: 19093 1.54 - 1.68: 83 1.68 - 1.82: 292 Bond restraints: 32592 Sorted by residual: bond pdb=" CA TYR D1073 " pdb=" C TYR D1073 " ideal model delta sigma weight residual 1.524 1.426 0.098 1.16e-02 7.43e+03 7.10e+01 bond pdb=" CA MET D 945 " pdb=" C MET D 945 " ideal model delta sigma weight residual 1.525 1.425 0.100 1.29e-02 6.01e+03 5.99e+01 bond pdb=" C HIS D1072 " pdb=" O HIS D1072 " ideal model delta sigma weight residual 1.235 1.135 0.100 1.38e-02 5.25e+03 5.20e+01 bond pdb=" C PHE D 935 " pdb=" O PHE D 935 " ideal model delta sigma weight residual 1.236 1.153 0.083 1.17e-02 7.31e+03 5.01e+01 bond pdb=" CA ALA D 943 " pdb=" C ALA D 943 " ideal model delta sigma weight residual 1.523 1.426 0.097 1.37e-02 5.33e+03 4.97e+01 ... (remaining 32587 not shown) Histogram of bond angle deviations from ideal: 97.35 - 105.13: 761 105.13 - 112.90: 17454 112.90 - 120.68: 14839 120.68 - 128.46: 10888 128.46 - 136.24: 214 Bond angle restraints: 44156 Sorted by residual: angle pdb=" N GLU D1046 " pdb=" CA GLU D1046 " pdb=" C GLU D1046 " ideal model delta sigma weight residual 114.62 97.53 17.09 1.14e+00 7.69e-01 2.25e+02 angle pdb=" N GLU D1050 " pdb=" CA GLU D1050 " pdb=" C GLU D1050 " ideal model delta sigma weight residual 113.55 97.55 16.00 1.26e+00 6.30e-01 1.61e+02 angle pdb=" P1A ACO B1203 " pdb=" O3A ACO B1203 " pdb=" P2A ACO B1203 " ideal model delta sigma weight residual 136.83 124.38 12.45 1.00e+00 1.00e+00 1.55e+02 angle pdb=" P1A ACO D1201 " pdb=" O3A ACO D1201 " pdb=" P2A ACO D1201 " ideal model delta sigma weight residual 136.83 124.50 12.33 1.00e+00 1.00e+00 1.52e+02 angle pdb=" P1A ACO A1204 " pdb=" O3A ACO A1204 " pdb=" P2A ACO A1204 " ideal model delta sigma weight residual 136.83 124.54 12.29 1.00e+00 1.00e+00 1.51e+02 ... (remaining 44151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 18070 22.40 - 44.80: 1257 44.80 - 67.20: 185 67.20 - 89.60: 36 89.60 - 112.00: 4 Dihedral angle restraints: 19552 sinusoidal: 7912 harmonic: 11640 Sorted by residual: dihedral pdb=" C GLU D1050 " pdb=" N GLU D1050 " pdb=" CA GLU D1050 " pdb=" CB GLU D1050 " ideal model delta harmonic sigma weight residual -122.60 -108.89 -13.71 0 2.50e+00 1.60e-01 3.01e+01 dihedral pdb=" C ARG B 848 " pdb=" N ARG B 848 " pdb=" CA ARG B 848 " pdb=" CB ARG B 848 " ideal model delta harmonic sigma weight residual -122.60 -109.02 -13.58 0 2.50e+00 1.60e-01 2.95e+01 dihedral pdb=" CA ILE A 621 " pdb=" C ILE A 621 " pdb=" N GLY A 622 " pdb=" CA GLY A 622 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 19549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4388 0.084 - 0.169: 466 0.169 - 0.253: 36 0.253 - 0.337: 16 0.337 - 0.421: 6 Chirality restraints: 4912 Sorted by residual: chirality pdb=" CA ARG D1038 " pdb=" N ARG D1038 " pdb=" C ARG D1038 " pdb=" CB ARG D1038 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA MET D 985 " pdb=" N MET D 985 " pdb=" C MET D 985 " pdb=" CB MET D 985 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CA TYR D1051 " pdb=" N TYR D1051 " pdb=" C TYR D1051 " pdb=" CB TYR D1051 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 4909 not shown) Planarity restraints: 5652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P ACO A1204 " 0.173 2.00e-02 2.50e+03 1.41e-01 2.49e+02 pdb=" C9P ACO A1204 " -0.056 2.00e-02 2.50e+03 pdb=" CAP ACO A1204 " 0.130 2.00e-02 2.50e+03 pdb=" N8P ACO A1204 " -0.221 2.00e-02 2.50e+03 pdb=" O9P ACO A1204 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO D1201 " 0.164 2.00e-02 2.50e+03 1.34e-01 2.23e+02 pdb=" C9P ACO D1201 " -0.053 2.00e-02 2.50e+03 pdb=" CAP ACO D1201 " 0.123 2.00e-02 2.50e+03 pdb=" N8P ACO D1201 " -0.209 2.00e-02 2.50e+03 pdb=" O9P ACO D1201 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO B1203 " -0.164 2.00e-02 2.50e+03 1.33e-01 2.21e+02 pdb=" C9P ACO B1203 " 0.053 2.00e-02 2.50e+03 pdb=" CAP ACO B1203 " -0.123 2.00e-02 2.50e+03 pdb=" N8P ACO B1203 " 0.208 2.00e-02 2.50e+03 pdb=" O9P ACO B1203 " 0.026 2.00e-02 2.50e+03 ... (remaining 5649 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3109 2.74 - 3.28: 32288 3.28 - 3.82: 54147 3.82 - 4.36: 66176 4.36 - 4.90: 112972 Nonbonded interactions: 268692 Sorted by model distance: nonbonded pdb=" OG1 THR C 625 " pdb=" O ALA C 686 " model vdw 2.199 2.440 nonbonded pdb=" OE2 GLU B 306 " pdb=" OG SER B 308 " model vdw 2.208 2.440 nonbonded pdb=" O ALA C 838 " pdb=" NZ LYS D 540 " model vdw 2.246 2.520 nonbonded pdb=" NZ LYS A 540 " pdb=" O ALA B 838 " model vdw 2.255 2.520 nonbonded pdb=" O SER C 343 " pdb=" NH1 ARG C 379 " model vdw 2.256 2.520 ... (remaining 268687 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 1202)) selection = (chain 'B' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099 or resid 1202)) selection = (chain 'C' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099 or resid 1202)) selection = (chain 'D' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099 or resid 1202)) } 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 4.320 Check model and map are aligned: 0.520 Set scattering table: 0.330 Process input model: 105.940 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 : 0.008 0.100 32592 Z= 0.536 Angle : 0.906 18.644 44156 Z= 0.537 Chirality : 0.055 0.421 4912 Planarity : 0.006 0.141 5652 Dihedral : 15.162 111.996 12160 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.95 % Favored : 94.90 % Rotamer: Outliers : 1.51 % Allowed : 0.95 % Favored : 97.54 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 2.55 % 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: -1.38 (0.13), residues: 4068 helix: -0.25 (0.12), residues: 1788 sheet: -0.80 (0.21), residues: 604 loop : -1.59 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1088 HIS 0.012 0.001 HIS D1072 PHE 0.021 0.002 PHE D1043 TYR 0.030 0.002 TYR A 542 ARG 0.017 0.001 ARG C 691 *********************** 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 **************************** Evaluate side-chains 456 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 409 time to evaluate : 3.249 Fit side-chains revert: symmetry clash REVERT: A 847 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.7563 (pt0) REVERT: D 847 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7986 (pt0) outliers start: 47 outliers final: 20 residues processed: 450 average time/residue: 0.4489 time to fit residues: 320.8394 Evaluate side-chains 366 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 344 time to evaluate : 3.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain D residue 847 GLU Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 926 SER Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 952 SER Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 965 LYS Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 978 LYS Chi-restraints excluded: chain D residue 1011 GLU Chi-restraints excluded: chain D residue 1037 LEU Chi-restraints excluded: chain D residue 1038 ARG Chi-restraints excluded: chain D residue 1054 ILE Chi-restraints excluded: chain D residue 1060 ILE Chi-restraints excluded: chain D residue 1065 ARG Chi-restraints excluded: chain D residue 1078 ARG Chi-restraints excluded: chain D residue 1087 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 7.9990 chunk 309 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 208 optimal weight: 20.0000 chunk 165 optimal weight: 5.9990 chunk 319 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 238 optimal weight: 20.0000 chunk 370 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS A1081 GLN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 32592 Z= 0.488 Angle : 0.696 9.676 44156 Z= 0.358 Chirality : 0.050 0.299 4912 Planarity : 0.005 0.099 5652 Dihedral : 8.187 107.204 4720 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.28 % Allowed : 6.09 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -1.34 (0.13), residues: 4068 helix: -0.31 (0.12), residues: 1804 sheet: -0.80 (0.22), residues: 604 loop : -1.46 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 40 HIS 0.008 0.001 HIS B1086 PHE 0.019 0.002 PHE C 959 TYR 0.024 0.002 TYR A 124 ARG 0.008 0.001 ARG D 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 **************************** Evaluate side-chains 417 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 378 time to evaluate : 3.611 Fit side-chains revert: symmetry clash REVERT: A 615 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7548 (mt0) REVERT: A 847 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7520 (pt0) REVERT: B 919 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8228 (p0) REVERT: D 992 ASP cc_start: 0.7532 (m-30) cc_final: 0.7284 (m-30) REVERT: D 1065 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8385 (tpp80) outliers start: 39 outliers final: 30 residues processed: 402 average time/residue: 0.4381 time to fit residues: 284.7523 Evaluate side-chains 388 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 355 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 707 THR Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 952 SER Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1011 GLU Chi-restraints excluded: chain D residue 1044 THR Chi-restraints excluded: chain D residue 1060 ILE Chi-restraints excluded: chain D residue 1065 ARG Chi-restraints excluded: chain D residue 1078 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 308 optimal weight: 50.0000 chunk 252 optimal weight: 3.9990 chunk 102 optimal weight: 40.0000 chunk 371 optimal weight: 5.9990 chunk 400 optimal weight: 0.8980 chunk 330 optimal weight: 8.9990 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 297 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS C 671 ASN ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 32592 Z= 0.382 Angle : 0.628 8.902 44156 Z= 0.323 Chirality : 0.047 0.243 4912 Planarity : 0.004 0.091 5652 Dihedral : 7.581 104.436 4686 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.25 % Allowed : 8.73 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -1.13 (0.13), residues: 4068 helix: -0.14 (0.12), residues: 1792 sheet: -0.75 (0.21), residues: 648 loop : -1.31 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 40 HIS 0.006 0.001 HIS B1086 PHE 0.016 0.002 PHE D 785 TYR 0.023 0.002 TYR A 124 ARG 0.005 0.001 ARG D 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 **************************** Evaluate side-chains 410 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 372 time to evaluate : 3.245 Fit side-chains revert: symmetry clash REVERT: A 847 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7750 (pt0) REVERT: B 919 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8276 (p0) REVERT: D 615 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7570 (mt0) REVERT: D 992 ASP cc_start: 0.7441 (m-30) cc_final: 0.7174 (m-30) outliers start: 38 outliers final: 32 residues processed: 393 average time/residue: 0.4557 time to fit residues: 291.0424 Evaluate side-chains 391 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 357 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1011 GLU Chi-restraints excluded: chain D residue 1060 ILE Chi-restraints excluded: chain D residue 1078 ARG 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: 4.9990 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 177 optimal weight: 0.1980 chunk 249 optimal weight: 7.9990 chunk 372 optimal weight: 6.9990 chunk 394 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 353 optimal weight: 6.9990 chunk 106 optimal weight: 50.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32592 Z= 0.250 Angle : 0.561 7.777 44156 Z= 0.288 Chirality : 0.044 0.225 4912 Planarity : 0.004 0.086 5652 Dihedral : 7.056 98.201 4676 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.28 % Allowed : 9.71 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.92 (0.13), residues: 4068 helix: 0.13 (0.12), residues: 1796 sheet: -0.86 (0.21), residues: 632 loop : -1.22 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 40 HIS 0.003 0.001 HIS B1086 PHE 0.014 0.001 PHE A1061 TYR 0.022 0.001 TYR B 124 ARG 0.005 0.000 ARG D 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 **************************** Evaluate side-chains 413 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 374 time to evaluate : 3.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 847 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: B 919 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8223 (p0) REVERT: D 615 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7545 (mt0) REVERT: D 963 MET cc_start: 0.8356 (mmm) cc_final: 0.8122 (mmp) REVERT: D 992 ASP cc_start: 0.7440 (m-30) cc_final: 0.7155 (m-30) outliers start: 39 outliers final: 30 residues processed: 393 average time/residue: 0.4368 time to fit residues: 278.8401 Evaluate side-chains 384 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 352 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 1011 GLU Chi-restraints excluded: chain D residue 1077 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 0.0040 chunk 223 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 293 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 336 optimal weight: 0.9980 chunk 272 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 201 optimal weight: 0.6980 chunk 353 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 HIS ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32592 Z= 0.159 Angle : 0.508 6.367 44156 Z= 0.262 Chirality : 0.043 0.222 4912 Planarity : 0.004 0.080 5652 Dihedral : 6.444 86.348 4670 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.07 % Allowed : 10.90 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.51 (0.13), residues: 4068 helix: 0.48 (0.13), residues: 1788 sheet: -0.76 (0.22), residues: 640 loop : -0.96 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 40 HIS 0.002 0.000 HIS B1086 PHE 0.014 0.001 PHE C1061 TYR 0.021 0.001 TYR D 124 ARG 0.005 0.000 ARG D 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 **************************** Evaluate side-chains 423 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 391 time to evaluate : 3.469 Fit side-chains revert: symmetry clash REVERT: A 615 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7564 (mt0) REVERT: A 847 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7549 (pt0) REVERT: D 615 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7534 (mt0) REVERT: D 992 ASP cc_start: 0.7340 (m-30) cc_final: 0.7032 (m-30) outliers start: 32 outliers final: 25 residues processed: 401 average time/residue: 0.4328 time to fit residues: 287.4777 Evaluate side-chains 388 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 362 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 1053 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 40.0000 chunk 355 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 394 optimal weight: 0.5980 chunk 327 optimal weight: 50.0000 chunk 182 optimal weight: 0.0370 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 overall best weight: 2.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 GLN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 HIS ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN C 777 GLN ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32592 Z= 0.229 Angle : 0.534 7.819 44156 Z= 0.273 Chirality : 0.044 0.227 4912 Planarity : 0.004 0.077 5652 Dihedral : 6.383 85.189 4667 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.37 % Allowed : 11.13 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.45 (0.13), residues: 4068 helix: 0.49 (0.13), residues: 1792 sheet: -0.71 (0.22), residues: 640 loop : -0.88 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 743 HIS 0.003 0.001 HIS B1086 PHE 0.020 0.001 PHE C 405 TYR 0.021 0.001 TYR A 124 ARG 0.004 0.000 ARG C 735 *********************** 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 **************************** Evaluate side-chains 410 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 368 time to evaluate : 3.448 Fit side-chains REVERT: A 615 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7583 (mt0) REVERT: A 847 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: B 919 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8214 (p0) outliers start: 42 outliers final: 35 residues processed: 388 average time/residue: 0.4272 time to fit residues: 274.1924 Evaluate side-chains 394 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 357 time to evaluate : 3.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 1077 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 288 optimal weight: 0.8980 chunk 223 optimal weight: 10.0000 chunk 332 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 393 optimal weight: 6.9990 chunk 246 optimal weight: 0.5980 chunk 239 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN A1020 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 ASN ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32592 Z= 0.186 Angle : 0.512 7.586 44156 Z= 0.261 Chirality : 0.043 0.225 4912 Planarity : 0.003 0.074 5652 Dihedral : 6.159 79.786 4667 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.31 % Allowed : 11.64 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.31 (0.13), residues: 4068 helix: 0.58 (0.13), residues: 1792 sheet: -0.62 (0.22), residues: 640 loop : -0.79 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 40 HIS 0.002 0.000 HIS A 168 PHE 0.018 0.001 PHE A 785 TYR 0.020 0.001 TYR A 124 ARG 0.005 0.000 ARG C 735 *********************** 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 **************************** Evaluate side-chains 404 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 364 time to evaluate : 3.786 Fit side-chains revert: symmetry clash REVERT: A 615 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7523 (mt0) REVERT: A 847 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7330 (pt0) REVERT: B 919 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8237 (p0) outliers start: 40 outliers final: 36 residues processed: 385 average time/residue: 0.4209 time to fit residues: 269.3126 Evaluate side-chains 392 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 354 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 1077 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 250 optimal weight: 0.5980 chunk 267 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 309 optimal weight: 0.0870 overall best weight: 2.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32592 Z= 0.260 Angle : 0.541 7.772 44156 Z= 0.276 Chirality : 0.044 0.226 4912 Planarity : 0.004 0.073 5652 Dihedral : 6.325 81.364 4667 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.31 % Allowed : 11.70 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.36 (0.13), residues: 4068 helix: 0.51 (0.12), residues: 1788 sheet: -0.62 (0.22), residues: 640 loop : -0.78 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 743 HIS 0.005 0.001 HIS A 168 PHE 0.020 0.001 PHE C 785 TYR 0.020 0.001 TYR B 124 ARG 0.005 0.000 ARG C 735 *********************** 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 **************************** Evaluate side-chains 388 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 348 time to evaluate : 3.398 Fit side-chains revert: symmetry clash REVERT: A 847 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7427 (pt0) REVERT: B 919 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8230 (p0) REVERT: C 1014 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8170 (p) REVERT: D 615 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7562 (tm-30) outliers start: 40 outliers final: 35 residues processed: 371 average time/residue: 0.4022 time to fit residues: 245.1948 Evaluate side-chains 382 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 344 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 1077 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 6.9990 chunk 376 optimal weight: 8.9990 chunk 343 optimal weight: 7.9990 chunk 366 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 287 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 331 optimal weight: 20.0000 chunk 346 optimal weight: 20.0000 chunk 365 optimal weight: 10.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 32592 Z= 0.511 Angle : 0.667 10.109 44156 Z= 0.339 Chirality : 0.050 0.234 4912 Planarity : 0.004 0.072 5652 Dihedral : 7.165 97.624 4667 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.40 % Allowed : 11.88 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.80 (0.13), residues: 4068 helix: 0.03 (0.12), residues: 1792 sheet: -0.65 (0.23), residues: 592 loop : -0.97 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 40 HIS 0.008 0.001 HIS B1086 PHE 0.021 0.002 PHE C 785 TYR 0.021 0.002 TYR B 124 ARG 0.005 0.001 ARG B 915 *********************** 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 **************************** Evaluate side-chains 409 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 366 time to evaluate : 3.720 Fit side-chains REVERT: A 494 SER cc_start: 0.8183 (m) cc_final: 0.7916 (t) REVERT: A 847 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7528 (pt0) REVERT: B 919 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8200 (p0) REVERT: D 615 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7715 (tm-30) outliers start: 43 outliers final: 41 residues processed: 393 average time/residue: 0.4694 time to fit residues: 302.5472 Evaluate side-chains 394 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 351 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 1077 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 40.0000 chunk 387 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 269 optimal weight: 20.0000 chunk 406 optimal weight: 2.9990 chunk 374 optimal weight: 7.9990 chunk 323 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 250 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 981 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32592 Z= 0.211 Angle : 0.539 8.217 44156 Z= 0.277 Chirality : 0.044 0.247 4912 Planarity : 0.004 0.073 5652 Dihedral : 6.620 90.489 4667 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.25 % Allowed : 12.50 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.52 (0.13), residues: 4068 helix: 0.29 (0.12), residues: 1800 sheet: -0.67 (0.22), residues: 640 loop : -0.78 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 743 HIS 0.004 0.001 HIS A 168 PHE 0.022 0.001 PHE C 785 TYR 0.020 0.001 TYR D 124 ARG 0.005 0.000 ARG C 735 ********************** 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 **************************** Evaluate side-chains 398 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 360 time to evaluate : 3.640 Fit side-chains REVERT: A 847 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7553 (pt0) REVERT: B 919 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8213 (p0) REVERT: B 971 MET cc_start: 0.8187 (mmm) cc_final: 0.7941 (mmt) REVERT: C 971 MET cc_start: 0.8198 (mmm) cc_final: 0.7945 (mmt) REVERT: D 615 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7616 (tm-30) outliers start: 38 outliers final: 33 residues processed: 381 average time/residue: 0.4313 time to fit residues: 270.8178 Evaluate side-chains 391 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 356 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 1077 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 10.0000 chunk 344 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 324 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 332 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.209506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.181446 restraints weight = 68528.443| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.13 r_work: 0.3767 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32592 Z= 0.187 Angle : 0.514 7.755 44156 Z= 0.264 Chirality : 0.043 0.235 4912 Planarity : 0.003 0.071 5652 Dihedral : 6.238 81.924 4667 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.37 % Allowed : 12.35 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.27 (0.13), residues: 4068 helix: 0.54 (0.12), residues: 1796 sheet: -0.56 (0.22), residues: 640 loop : -0.70 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 40 HIS 0.004 0.001 HIS A 168 PHE 0.021 0.001 PHE C 785 TYR 0.019 0.001 TYR A 124 ARG 0.007 0.000 ARG B 127 =============================================================================== Job complete usr+sys time: 7169.65 seconds wall clock time: 131 minutes 11.37 seconds (7871.37 seconds total)