Starting phenix.real_space_refine on Sat Aug 10 19:15:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b90_44364/08_2024/9b90_44364.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b90_44364/08_2024/9b90_44364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b90_44364/08_2024/9b90_44364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b90_44364/08_2024/9b90_44364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b90_44364/08_2024/9b90_44364.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b90_44364/08_2024/9b90_44364.cif" } resolution = 3.4 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 12 5.49 5 S 152 5.16 5 C 19220 2.51 5 N 5228 2.21 5 O 5100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29720 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7397 Classifications: {'peptide': 982} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 42, 'TRANS': 939} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 424 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 347 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 19, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 18, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 298 Chain: "B" Number of atoms: 7397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7397 Classifications: {'peptide': 982} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 42, 'TRANS': 939} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 424 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 347 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 19, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 18, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 298 Chain: "C" Number of atoms: 7397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7397 Classifications: {'peptide': 982} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 42, 'TRANS': 939} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 424 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 347 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 19, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 18, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 298 Chain: "D" Number of atoms: 7397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7397 Classifications: {'peptide': 982} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 42, 'TRANS': 939} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 424 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 347 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 19, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 18, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 298 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 16.50, per 1000 atoms: 0.56 Number of scatterers: 29720 At special positions: 0 Unit cell: (169.74, 169.74, 152.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 152 16.00 P 12 15.00 O 5100 8.00 N 5228 7.00 C 19220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.89 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.89 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=2.89 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=2.88 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: 12.53 Conformation dependent library (CDL) restraints added in 4.8 seconds 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7296 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 16 sheets defined 68.7% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 removed outlier: 4.168A pdb=" N LYS A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.885A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.723A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.607A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 344 through 357 removed outlier: 3.982A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 removed outlier: 3.613A pdb=" N GLY A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 403 Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 421 through 436 removed outlier: 4.143A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.648A pdb=" N VAL A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 584 through 603 Processing helix chain 'A' and resid 607 through 634 Processing helix chain 'A' and resid 634 through 645 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 767 through 778 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 834 Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.646A pdb=" N ASP A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 906 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 916 through 926 Processing helix chain 'A' and resid 926 through 953 Processing helix chain 'A' and resid 958 through 967 Processing helix chain 'A' and resid 967 through 973 Processing helix chain 'A' and resid 974 through 976 No H-bonds generated for 'chain 'A' and resid 974 through 976' Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.767A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1071 removed outlier: 4.910A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1088 removed outlier: 4.130A pdb=" N VAL A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A1082 " --> pdb=" O PRO A1078 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1142 Processing helix chain 'A' and resid 1143 through 1176 Processing helix chain 'A' and resid 1177 through 1177 No H-bonds generated for 'chain 'A' and resid 1177 through 1177' Processing helix chain 'B' and resid 7 through 8 No H-bonds generated for 'chain 'B' and resid 7 through 8' Processing helix chain 'B' and resid 9 through 15 removed outlier: 4.168A pdb=" N LYS B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.885A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 removed outlier: 3.723A pdb=" N VAL B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.606A pdb=" N GLY B 268 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.982A pdb=" N GLN B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.613A pdb=" N GLY B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 421 through 436 removed outlier: 4.142A pdb=" N ALA B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 502 through 512 removed outlier: 3.649A pdb=" N VAL B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 584 through 603 Processing helix chain 'B' and resid 607 through 634 Processing helix chain 'B' and resid 634 through 645 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 663 through 669 Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 767 through 778 Processing helix chain 'B' and resid 778 through 803 Processing helix chain 'B' and resid 811 through 834 Processing helix chain 'B' and resid 852 through 862 removed outlier: 3.645A pdb=" N ASP B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 884 Processing helix chain 'B' and resid 887 through 906 Processing helix chain 'B' and resid 907 through 912 Processing helix chain 'B' and resid 916 through 926 Processing helix chain 'B' and resid 926 through 953 Processing helix chain 'B' and resid 958 through 967 Processing helix chain 'B' and resid 967 through 973 Processing helix chain 'B' and resid 974 through 976 No H-bonds generated for 'chain 'B' and resid 974 through 976' Processing helix chain 'B' and resid 979 through 983 Processing helix chain 'B' and resid 984 through 988 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.767A pdb=" N VAL B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1071 removed outlier: 4.910A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1088 removed outlier: 4.130A pdb=" N VAL B1081 " --> pdb=" O PRO B1077 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE B1082 " --> pdb=" O PRO B1078 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1142 Processing helix chain 'B' and resid 1143 through 1176 Processing helix chain 'B' and resid 1177 through 1177 No H-bonds generated for 'chain 'B' and resid 1177 through 1177' Processing helix chain 'C' and resid 7 through 8 No H-bonds generated for 'chain 'C' and resid 7 through 8' Processing helix chain 'C' and resid 9 through 15 removed outlier: 4.167A pdb=" N LYS C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 removed outlier: 3.885A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 150 removed outlier: 3.723A pdb=" N VAL C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.607A pdb=" N GLY C 268 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 308 through 316 Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 344 through 357 removed outlier: 3.982A pdb=" N GLN C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 removed outlier: 3.613A pdb=" N GLY C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 403 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 421 through 436 removed outlier: 4.143A pdb=" N ALA C 427 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 502 through 512 removed outlier: 3.648A pdb=" N VAL C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 571 through 582 Processing helix chain 'C' and resid 584 through 603 Processing helix chain 'C' and resid 607 through 634 Processing helix chain 'C' and resid 634 through 645 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 663 through 669 Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 705 Processing helix chain 'C' and resid 767 through 778 Processing helix chain 'C' and resid 778 through 803 Processing helix chain 'C' and resid 811 through 834 Processing helix chain 'C' and resid 852 through 862 removed outlier: 3.646A pdb=" N ASP C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 906 Processing helix chain 'C' and resid 907 through 912 Processing helix chain 'C' and resid 916 through 926 Processing helix chain 'C' and resid 926 through 953 Processing helix chain 'C' and resid 958 through 967 Processing helix chain 'C' and resid 967 through 973 Processing helix chain 'C' and resid 974 through 976 No H-bonds generated for 'chain 'C' and resid 974 through 976' Processing helix chain 'C' and resid 979 through 983 Processing helix chain 'C' and resid 984 through 988 Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.767A pdb=" N VAL C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1071 removed outlier: 4.910A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1088 removed outlier: 4.130A pdb=" N VAL C1081 " --> pdb=" O PRO C1077 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE C1082 " --> pdb=" O PRO C1078 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1142 Processing helix chain 'C' and resid 1143 through 1176 Processing helix chain 'C' and resid 1177 through 1177 No H-bonds generated for 'chain 'C' and resid 1177 through 1177' Processing helix chain 'D' and resid 7 through 8 No H-bonds generated for 'chain 'D' and resid 7 through 8' Processing helix chain 'D' and resid 9 through 15 removed outlier: 4.168A pdb=" N LYS D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 109 removed outlier: 3.885A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 150 removed outlier: 3.724A pdb=" N VAL D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 246 through 259 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.607A pdb=" N GLY D 268 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 329 through 336 Processing helix chain 'D' and resid 344 through 357 removed outlier: 3.983A pdb=" N GLN D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 386 removed outlier: 3.613A pdb=" N GLY D 386 " --> pdb=" O VAL D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 421 through 436 removed outlier: 4.143A pdb=" N ALA D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 502 through 512 removed outlier: 3.648A pdb=" N VAL D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 571 through 582 Processing helix chain 'D' and resid 584 through 603 Processing helix chain 'D' and resid 607 through 634 Processing helix chain 'D' and resid 634 through 645 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 663 through 669 Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 705 Processing helix chain 'D' and resid 767 through 778 Processing helix chain 'D' and resid 778 through 803 Processing helix chain 'D' and resid 811 through 834 Processing helix chain 'D' and resid 852 through 862 removed outlier: 3.646A pdb=" N ASP D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 884 Processing helix chain 'D' and resid 887 through 906 Processing helix chain 'D' and resid 907 through 912 Processing helix chain 'D' and resid 916 through 926 Processing helix chain 'D' and resid 926 through 953 Processing helix chain 'D' and resid 958 through 967 Processing helix chain 'D' and resid 967 through 973 Processing helix chain 'D' and resid 974 through 976 No H-bonds generated for 'chain 'D' and resid 974 through 976' Processing helix chain 'D' and resid 979 through 983 Processing helix chain 'D' and resid 984 through 988 Processing helix chain 'D' and resid 1016 through 1033 removed outlier: 3.768A pdb=" N VAL D1020 " --> pdb=" O ALA D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1071 removed outlier: 4.910A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1088 removed outlier: 4.129A pdb=" N VAL D1081 " --> pdb=" O PRO D1077 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE D1082 " --> pdb=" O PRO D1078 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1142 Processing helix chain 'D' and resid 1143 through 1176 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 removed outlier: 7.998A pdb=" N TYR A 211 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP A 79 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY A 156 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 118 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU A 276 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER A 120 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 262 removed outlier: 3.955A pdb=" N ILE A 269 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 990 removed outlier: 4.174A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 Processing sheet with id=AA6, first strand: chain 'B' and resid 210 through 211 removed outlier: 7.999A pdb=" N TYR B 211 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP B 79 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP B 236 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY B 156 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 118 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU B 276 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER B 120 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU B 300 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 261 through 262 removed outlier: 3.955A pdb=" N ILE B 269 " --> pdb=" O THR B 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 989 through 990 removed outlier: 4.174A pdb=" N GLU B 989 " --> pdb=" O HIS B1002 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 19 Processing sheet with id=AB1, first strand: chain 'C' and resid 210 through 211 removed outlier: 7.999A pdb=" N TYR C 211 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP C 79 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP C 236 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY C 156 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 118 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU C 276 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER C 120 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU C 300 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 261 through 262 removed outlier: 3.956A pdb=" N ILE C 269 " --> pdb=" O THR C 262 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 989 through 990 removed outlier: 4.173A pdb=" N GLU C 989 " --> pdb=" O HIS C1002 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 19 Processing sheet with id=AB5, first strand: chain 'D' and resid 210 through 211 removed outlier: 7.999A pdb=" N TYR D 211 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP D 79 " --> pdb=" O TYR D 211 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP D 236 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLY D 156 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL D 118 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU D 276 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER D 120 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU D 300 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 261 through 262 removed outlier: 3.955A pdb=" N ILE D 269 " --> pdb=" O THR D 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 989 through 990 removed outlier: 4.174A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) 1936 hydrogen bonds defined for protein. 5616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.41 Time building geometry restraints manager: 13.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9608 1.34 - 1.46: 7133 1.46 - 1.58: 13403 1.58 - 1.69: 20 1.69 - 1.81: 228 Bond restraints: 30392 Sorted by residual: bond pdb=" CA GLU D 371 " pdb=" CB GLU D 371 " ideal model delta sigma weight residual 1.541 1.529 0.012 1.20e-02 6.94e+03 1.04e+00 bond pdb=" CA GLU B 371 " pdb=" CB GLU B 371 " ideal model delta sigma weight residual 1.541 1.530 0.011 1.20e-02 6.94e+03 9.06e-01 bond pdb=" CA GLU A 371 " pdb=" CB GLU A 371 " ideal model delta sigma weight residual 1.541 1.530 0.011 1.20e-02 6.94e+03 8.62e-01 bond pdb=" CA GLU C 371 " pdb=" CB GLU C 371 " ideal model delta sigma weight residual 1.541 1.530 0.011 1.20e-02 6.94e+03 8.38e-01 bond pdb=" CB TRP C1124 " pdb=" CG TRP C1124 " ideal model delta sigma weight residual 1.498 1.473 0.025 3.10e-02 1.04e+03 6.57e-01 ... (remaining 30387 not shown) Histogram of bond angle deviations from ideal: 99.86 - 107.87: 1321 107.87 - 115.89: 18594 115.89 - 123.90: 20553 123.90 - 131.92: 808 131.92 - 139.93: 108 Bond angle restraints: 41384 Sorted by residual: angle pdb=" N GLU A 371 " pdb=" CA GLU A 371 " pdb=" CB GLU A 371 " ideal model delta sigma weight residual 114.17 110.48 3.69 1.14e+00 7.69e-01 1.05e+01 angle pdb=" N GLU C 371 " pdb=" CA GLU C 371 " pdb=" CB GLU C 371 " ideal model delta sigma weight residual 114.17 110.49 3.68 1.14e+00 7.69e-01 1.04e+01 angle pdb=" N GLU B 371 " pdb=" CA GLU B 371 " pdb=" CB GLU B 371 " ideal model delta sigma weight residual 114.17 110.51 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N GLU D 371 " pdb=" CA GLU D 371 " pdb=" CB GLU D 371 " ideal model delta sigma weight residual 114.17 110.51 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" C3' ATP D2003 " pdb=" C4' ATP D2003 " pdb=" C5' ATP D2003 " ideal model delta sigma weight residual 115.19 111.00 4.19 1.76e+00 3.23e-01 5.66e+00 ... (remaining 41379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 17023 16.76 - 33.51: 665 33.51 - 50.27: 152 50.27 - 67.03: 40 67.03 - 83.79: 20 Dihedral angle restraints: 17900 sinusoidal: 6628 harmonic: 11272 Sorted by residual: dihedral pdb=" CA PHE B 207 " pdb=" C PHE B 207 " pdb=" N PRO B 208 " pdb=" CA PRO B 208 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N PRO A 208 " pdb=" CA PRO A 208 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PHE C 207 " pdb=" C PHE C 207 " pdb=" N PRO C 208 " pdb=" CA PRO C 208 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 17897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4395 0.059 - 0.118: 361 0.118 - 0.177: 20 0.177 - 0.236: 0 0.236 - 0.294: 12 Chirality restraints: 4788 Sorted by residual: chirality pdb=" C2' ATP B2003 " pdb=" C1' ATP B2003 " pdb=" C3' ATP B2003 " pdb=" O2' ATP B2003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C2' ATP A2003 " pdb=" C1' ATP A2003 " pdb=" C3' ATP A2003 " pdb=" O2' ATP A2003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' ATP D2003 " pdb=" C1' ATP D2003 " pdb=" C3' ATP D2003 " pdb=" O2' ATP D2003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 4785 not shown) Planarity restraints: 5196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 437 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO C 438 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 438 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 438 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 437 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO B 438 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 438 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 438 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 437 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO A 438 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 438 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 438 " 0.018 5.00e-02 4.00e+02 ... (remaining 5193 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 851 2.70 - 3.25: 34325 3.25 - 3.80: 50589 3.80 - 4.35: 58847 4.35 - 4.90: 99939 Nonbonded interactions: 244551 Sorted by model distance: nonbonded pdb=" OE2 GLU D 828 " pdb="CA CA D2001 " model vdw 2.154 2.510 nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.154 2.510 nonbonded pdb=" OE2 GLU C 828 " pdb="CA CA C2001 " model vdw 2.154 2.510 nonbonded pdb=" OE2 GLU B 828 " pdb="CA CA B2001 " model vdw 2.154 2.510 nonbonded pdb=" OE1 GLN C 831 " pdb="CA CA C2001 " model vdw 2.184 2.510 ... (remaining 244546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.120 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 79.180 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.140 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 30392 Z= 0.247 Angle : 0.468 6.434 41384 Z= 0.255 Chirality : 0.035 0.294 4788 Planarity : 0.003 0.031 5196 Dihedral : 10.679 83.785 10592 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.42 % Allowed : 5.61 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.44 (0.14), residues: 3848 helix: 1.66 (0.10), residues: 2440 sheet: -1.03 (0.35), residues: 244 loop : 0.01 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 776 HIS 0.002 0.001 HIS D1070 PHE 0.006 0.001 PHE B1069 TYR 0.005 0.001 TYR B 968 ARG 0.003 0.000 ARG D 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 274 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1034 LEU cc_start: 0.9170 (mp) cc_final: 0.8893 (tp) REVERT: B 1034 LEU cc_start: 0.9136 (mp) cc_final: 0.8831 (tp) REVERT: C 1034 LEU cc_start: 0.9099 (mp) cc_final: 0.8819 (tp) REVERT: D 1034 LEU cc_start: 0.9151 (mp) cc_final: 0.8863 (tp) outliers start: 12 outliers final: 8 residues processed: 286 average time/residue: 0.4098 time to fit residues: 189.3655 Evaluate side-chains 205 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 197 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain D residue 373 PHE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 1032 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 10.0000 chunk 297 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 101 optimal weight: 0.0050 chunk 200 optimal weight: 0.0370 chunk 158 optimal weight: 8.9990 chunk 307 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 chunk 228 optimal weight: 9.9990 chunk 355 optimal weight: 9.9990 overall best weight: 3.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 410 GLN A 505 HIS A 973 GLN B 165 HIS B 410 GLN B 505 HIS B 973 GLN C 165 HIS C 410 GLN C 505 HIS C 973 GLN D 165 HIS D 410 GLN D 505 HIS D 973 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30392 Z= 0.302 Angle : 0.603 10.470 41384 Z= 0.306 Chirality : 0.038 0.161 4788 Planarity : 0.004 0.042 5196 Dihedral : 7.563 86.262 4368 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.67 % Allowed : 8.11 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.14), residues: 3848 helix: 2.56 (0.10), residues: 2476 sheet: -1.03 (0.37), residues: 244 loop : 0.20 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1058 HIS 0.008 0.001 HIS C 505 PHE 0.019 0.001 PHE B 373 TYR 0.007 0.001 TYR D 227 ARG 0.006 0.001 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 246 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9015 (tpp) cc_final: 0.8626 (mmm) REVERT: A 669 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8173 (tm-30) REVERT: A 1034 LEU cc_start: 0.9157 (mp) cc_final: 0.8928 (tp) REVERT: A 1037 ASN cc_start: 0.9327 (m-40) cc_final: 0.9102 (m110) REVERT: B 576 MET cc_start: 0.8815 (mmm) cc_final: 0.8403 (mmm) REVERT: B 669 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8078 (tm-30) REVERT: B 784 MET cc_start: 0.8510 (tpp) cc_final: 0.8297 (tpt) REVERT: B 951 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9241 (mp) REVERT: B 1034 LEU cc_start: 0.9103 (mp) cc_final: 0.8891 (tp) REVERT: B 1146 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8319 (mp0) REVERT: C 576 MET cc_start: 0.8847 (mmm) cc_final: 0.8443 (mmm) REVERT: C 660 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.8793 (mt0) REVERT: C 669 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8106 (tm-30) REVERT: C 951 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9245 (mp) REVERT: C 1051 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8207 (tm-30) REVERT: C 1146 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8316 (mp0) REVERT: D 576 MET cc_start: 0.8905 (mmm) cc_final: 0.8259 (mmm) REVERT: D 669 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8170 (tm-30) REVERT: D 951 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9267 (mp) REVERT: D 1034 LEU cc_start: 0.9137 (mp) cc_final: 0.8888 (tp) REVERT: D 1037 ASN cc_start: 0.9296 (m-40) cc_final: 0.9066 (m110) REVERT: D 1146 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8321 (mp0) outliers start: 48 outliers final: 14 residues processed: 281 average time/residue: 0.3895 time to fit residues: 179.2838 Evaluate side-chains 219 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 373 PHE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1032 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 296 optimal weight: 0.4980 chunk 242 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 356 optimal weight: 0.8980 chunk 385 optimal weight: 2.9990 chunk 317 optimal weight: 8.9990 chunk 353 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 286 optimal weight: 0.9980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 410 GLN B 165 HIS B 410 GLN C 165 HIS C 410 GLN D 165 HIS D 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30392 Z= 0.221 Angle : 0.541 8.908 41384 Z= 0.276 Chirality : 0.037 0.159 4788 Planarity : 0.004 0.045 5196 Dihedral : 7.141 86.229 4364 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.74 % Allowed : 9.40 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.14), residues: 3848 helix: 2.54 (0.10), residues: 2480 sheet: -1.02 (0.37), residues: 244 loop : 0.17 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.004 0.001 HIS B1128 PHE 0.012 0.001 PHE B 373 TYR 0.008 0.001 TYR D 227 ARG 0.007 0.000 ARG B1138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 251 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.9324 (tpp) cc_final: 0.8862 (mmm) REVERT: A 576 MET cc_start: 0.9048 (tpp) cc_final: 0.8652 (mmm) REVERT: A 599 MET cc_start: 0.9040 (ttm) cc_final: 0.8732 (ttm) REVERT: A 622 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8095 (ttm) REVERT: A 951 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9201 (mp) REVERT: A 1034 LEU cc_start: 0.9152 (mp) cc_final: 0.8929 (tp) REVERT: A 1037 ASN cc_start: 0.9308 (m-40) cc_final: 0.9102 (m110) REVERT: B 430 MET cc_start: 0.9352 (tpp) cc_final: 0.8763 (mmm) REVERT: B 576 MET cc_start: 0.8892 (mmm) cc_final: 0.8291 (mmm) REVERT: B 580 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8331 (mt-10) REVERT: B 599 MET cc_start: 0.8941 (ttm) cc_final: 0.8641 (ttm) REVERT: B 669 GLN cc_start: 0.8331 (tm-30) cc_final: 0.8058 (tm-30) REVERT: B 1034 LEU cc_start: 0.9023 (mp) cc_final: 0.8811 (tp) REVERT: B 1146 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8457 (mp0) REVERT: C 175 MET cc_start: 0.9536 (OUTLIER) cc_final: 0.9310 (mtp) REVERT: C 576 MET cc_start: 0.9042 (mmm) cc_final: 0.8515 (mmm) REVERT: C 580 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8174 (mt-10) REVERT: C 599 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8527 (ttm) REVERT: C 660 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.8764 (mt0) REVERT: C 669 GLN cc_start: 0.8307 (tm-30) cc_final: 0.8062 (tm-30) REVERT: C 951 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9257 (mp) REVERT: C 1146 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8424 (mp0) REVERT: D 430 MET cc_start: 0.9347 (tpp) cc_final: 0.8892 (mmm) REVERT: D 576 MET cc_start: 0.9068 (mmm) cc_final: 0.8694 (mmm) REVERT: D 580 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8226 (mt-10) REVERT: D 951 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9271 (mp) REVERT: D 1034 LEU cc_start: 0.9126 (mp) cc_final: 0.8870 (tp) REVERT: D 1037 ASN cc_start: 0.9290 (m-40) cc_final: 0.9075 (m110) REVERT: D 1146 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8446 (mp0) outliers start: 50 outliers final: 21 residues processed: 283 average time/residue: 0.3776 time to fit residues: 180.7825 Evaluate side-chains 248 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 220 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 373 PHE Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1157 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 8.9990 chunk 268 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 chunk 357 optimal weight: 6.9990 chunk 378 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 339 optimal weight: 9.9990 chunk 102 optimal weight: 50.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30392 Z= 0.356 Angle : 0.580 9.600 41384 Z= 0.293 Chirality : 0.037 0.159 4788 Planarity : 0.004 0.052 5196 Dihedral : 6.969 88.245 4362 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.16 % Allowed : 10.58 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.14), residues: 3848 helix: 2.51 (0.10), residues: 2488 sheet: -1.01 (0.36), residues: 244 loop : 0.15 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 680 HIS 0.008 0.001 HIS D 505 PHE 0.026 0.001 PHE C 373 TYR 0.008 0.001 TYR D1063 ARG 0.005 0.000 ARG B 612 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 219 time to evaluate : 3.050 Fit side-chains REVERT: A 576 MET cc_start: 0.8991 (tpp) cc_final: 0.8613 (mmm) REVERT: A 599 MET cc_start: 0.9043 (ttm) cc_final: 0.8688 (ttm) REVERT: A 622 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8043 (ttm) REVERT: A 669 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 1034 LEU cc_start: 0.9172 (mp) cc_final: 0.8915 (tp) REVERT: A 1037 ASN cc_start: 0.9359 (m-40) cc_final: 0.9131 (m110) REVERT: B 599 MET cc_start: 0.8987 (ttm) cc_final: 0.8745 (ttm) REVERT: B 669 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7948 (tm-30) REVERT: B 1034 LEU cc_start: 0.9098 (mp) cc_final: 0.8845 (tp) REVERT: B 1146 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8501 (mp0) REVERT: C 576 MET cc_start: 0.8885 (mmm) cc_final: 0.8410 (mmm) REVERT: C 580 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8190 (mt-10) REVERT: C 599 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8398 (ttp) REVERT: C 660 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.8787 (mt0) REVERT: C 669 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8036 (tm-30) REVERT: C 951 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9261 (mp) REVERT: C 1146 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8517 (mp0) REVERT: D 430 MET cc_start: 0.9343 (tpp) cc_final: 0.8955 (mmm) REVERT: D 576 MET cc_start: 0.8892 (mmm) cc_final: 0.8335 (mmm) REVERT: D 580 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8146 (mt-10) REVERT: D 877 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9408 (mp) REVERT: D 951 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9297 (mp) REVERT: D 1034 LEU cc_start: 0.9169 (mp) cc_final: 0.8873 (tp) REVERT: D 1037 ASN cc_start: 0.9366 (m-40) cc_final: 0.9132 (m110) REVERT: D 1146 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8496 (mp0) outliers start: 62 outliers final: 29 residues processed: 262 average time/residue: 0.3551 time to fit residues: 156.9121 Evaluate side-chains 237 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1085 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 50.0000 chunk 215 optimal weight: 8.9990 chunk 5 optimal weight: 30.0000 chunk 282 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 323 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 340 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30392 Z= 0.199 Angle : 0.535 10.670 41384 Z= 0.268 Chirality : 0.036 0.157 4788 Planarity : 0.004 0.051 5196 Dihedral : 6.862 89.380 4360 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.54 % Allowed : 11.07 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.14), residues: 3848 helix: 2.58 (0.10), residues: 2488 sheet: -1.06 (0.36), residues: 244 loop : 0.16 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1058 HIS 0.007 0.001 HIS C 505 PHE 0.017 0.001 PHE C 373 TYR 0.008 0.001 TYR D1063 ARG 0.010 0.000 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 243 time to evaluate : 3.542 Fit side-chains REVERT: A 136 ASP cc_start: 0.9580 (t0) cc_final: 0.9184 (m-30) REVERT: A 430 MET cc_start: 0.9121 (mmt) cc_final: 0.8750 (mmm) REVERT: A 576 MET cc_start: 0.8980 (tpp) cc_final: 0.8545 (mmm) REVERT: A 599 MET cc_start: 0.9042 (ttm) cc_final: 0.8700 (ttm) REVERT: A 622 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7993 (ttm) REVERT: A 927 MET cc_start: 0.8719 (mmp) cc_final: 0.8475 (mmp) REVERT: A 951 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9205 (mp) REVERT: A 1034 LEU cc_start: 0.9152 (mp) cc_final: 0.8915 (tp) REVERT: A 1037 ASN cc_start: 0.9321 (m-40) cc_final: 0.9107 (m110) REVERT: B 136 ASP cc_start: 0.9583 (t0) cc_final: 0.9206 (m-30) REVERT: B 576 MET cc_start: 0.9214 (mmm) cc_final: 0.8478 (mmm) REVERT: B 602 LEU cc_start: 0.9754 (OUTLIER) cc_final: 0.9547 (tt) REVERT: B 951 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9191 (mp) REVERT: B 1034 LEU cc_start: 0.9046 (mp) cc_final: 0.8826 (tp) REVERT: B 1146 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8504 (mp0) REVERT: C 136 ASP cc_start: 0.9569 (t0) cc_final: 0.9202 (m-30) REVERT: C 576 MET cc_start: 0.8880 (mmm) cc_final: 0.8415 (mmm) REVERT: C 580 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8176 (mt-10) REVERT: C 599 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8704 (ttm) REVERT: C 660 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8812 (mt0) REVERT: C 951 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9230 (mp) REVERT: C 1146 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8537 (mp0) REVERT: D 136 ASP cc_start: 0.9575 (t0) cc_final: 0.9213 (m-30) REVERT: D 430 MET cc_start: 0.9349 (tpp) cc_final: 0.8998 (mmm) REVERT: D 576 MET cc_start: 0.8867 (mmm) cc_final: 0.8403 (mmm) REVERT: D 580 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8248 (mt-10) REVERT: D 599 MET cc_start: 0.9045 (ttm) cc_final: 0.8525 (ttp) REVERT: D 951 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9238 (mp) REVERT: D 1034 LEU cc_start: 0.9136 (mp) cc_final: 0.8843 (tp) REVERT: D 1146 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8537 (mp0) outliers start: 73 outliers final: 31 residues processed: 304 average time/residue: 0.3512 time to fit residues: 182.5024 Evaluate side-chains 266 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 227 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 5.9990 chunk 341 optimal weight: 0.0970 chunk 74 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 379 optimal weight: 0.7980 chunk 314 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 30.0000 chunk 199 optimal weight: 50.0000 overall best weight: 3.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 30392 Z= 0.300 Angle : 0.580 11.529 41384 Z= 0.288 Chirality : 0.037 0.163 4788 Planarity : 0.004 0.052 5196 Dihedral : 6.768 89.918 4360 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.12 % Allowed : 11.80 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.14), residues: 3848 helix: 2.55 (0.10), residues: 2492 sheet: -1.10 (0.36), residues: 244 loop : 0.20 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 680 HIS 0.006 0.001 HIS C 505 PHE 0.014 0.001 PHE A 627 TYR 0.009 0.001 TYR C1063 ARG 0.007 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 229 time to evaluate : 3.512 Fit side-chains REVERT: A 576 MET cc_start: 0.8979 (tpp) cc_final: 0.8655 (mmm) REVERT: A 951 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9231 (mp) REVERT: A 1034 LEU cc_start: 0.9166 (mp) cc_final: 0.8904 (tp) REVERT: A 1037 ASN cc_start: 0.9324 (m-40) cc_final: 0.9078 (m110) REVERT: B 430 MET cc_start: 0.9077 (mmt) cc_final: 0.8754 (mmm) REVERT: B 602 LEU cc_start: 0.9738 (OUTLIER) cc_final: 0.9524 (tt) REVERT: B 951 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9196 (mp) REVERT: B 1034 LEU cc_start: 0.9088 (mp) cc_final: 0.8821 (tp) REVERT: B 1146 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8578 (mp0) REVERT: C 576 MET cc_start: 0.9054 (mmm) cc_final: 0.8548 (mmm) REVERT: C 580 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8191 (mt-10) REVERT: C 599 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8467 (ttp) REVERT: C 660 GLN cc_start: 0.9325 (OUTLIER) cc_final: 0.8856 (mt0) REVERT: C 951 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9235 (mp) REVERT: C 1138 ARG cc_start: 0.9149 (ttp80) cc_final: 0.8588 (ttp80) REVERT: C 1146 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8577 (mp0) REVERT: D 430 MET cc_start: 0.9350 (tpp) cc_final: 0.8845 (mmm) REVERT: D 576 MET cc_start: 0.8891 (mmm) cc_final: 0.8419 (mmm) REVERT: D 580 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8302 (mt-10) REVERT: D 951 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9276 (mp) REVERT: D 1034 LEU cc_start: 0.9137 (mp) cc_final: 0.8855 (tp) REVERT: D 1146 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8613 (mp0) outliers start: 61 outliers final: 39 residues processed: 274 average time/residue: 0.3452 time to fit residues: 161.5019 Evaluate side-chains 263 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 217 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1157 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 7.9990 chunk 42 optimal weight: 0.0170 chunk 216 optimal weight: 9.9990 chunk 276 optimal weight: 0.9980 chunk 214 optimal weight: 0.4980 chunk 319 optimal weight: 7.9990 chunk 211 optimal weight: 20.0000 chunk 377 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1037 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 30392 Z= 0.155 Angle : 0.547 11.701 41384 Z= 0.268 Chirality : 0.037 0.279 4788 Planarity : 0.004 0.053 5196 Dihedral : 6.703 89.956 4360 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.88 % Allowed : 12.36 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.14), residues: 3848 helix: 2.48 (0.10), residues: 2512 sheet: -1.18 (0.34), residues: 252 loop : 0.14 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 772 HIS 0.005 0.001 HIS D 505 PHE 0.013 0.001 PHE C 373 TYR 0.008 0.001 TYR B1063 ARG 0.015 0.000 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 283 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.8988 (tpp) cc_final: 0.8643 (mmm) REVERT: A 599 MET cc_start: 0.9005 (ttm) cc_final: 0.8730 (ttm) REVERT: A 951 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9199 (mp) REVERT: A 1034 LEU cc_start: 0.9131 (mp) cc_final: 0.8896 (tp) REVERT: B 175 MET cc_start: 0.9523 (OUTLIER) cc_final: 0.9317 (mtp) REVERT: B 922 ILE cc_start: 0.9395 (mt) cc_final: 0.9177 (mm) REVERT: B 951 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9178 (mp) REVERT: B 1034 LEU cc_start: 0.8942 (mp) cc_final: 0.8741 (tp) REVERT: B 1138 ARG cc_start: 0.9110 (ttp80) cc_final: 0.8534 (ttp80) REVERT: C 136 ASP cc_start: 0.9559 (t0) cc_final: 0.9210 (m-30) REVERT: C 599 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8543 (ttm) REVERT: C 660 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.8856 (mt0) REVERT: D 136 ASP cc_start: 0.9567 (t0) cc_final: 0.9230 (m-30) REVERT: D 430 MET cc_start: 0.9362 (tpp) cc_final: 0.9002 (mmm) REVERT: D 877 LEU cc_start: 0.9619 (mp) cc_final: 0.9375 (mp) REVERT: D 1034 LEU cc_start: 0.9086 (mp) cc_final: 0.8821 (tp) outliers start: 54 outliers final: 24 residues processed: 328 average time/residue: 0.3462 time to fit residues: 192.7481 Evaluate side-chains 276 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 247 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 1032 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 113 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 240 optimal weight: 20.0000 chunk 257 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 35 optimal weight: 0.0570 chunk 296 optimal weight: 20.0000 overall best weight: 1.8504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30392 Z= 0.199 Angle : 0.570 14.250 41384 Z= 0.277 Chirality : 0.037 0.183 4788 Planarity : 0.004 0.050 5196 Dihedral : 6.600 89.604 4360 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.50 % Allowed : 13.54 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.14), residues: 3848 helix: 2.42 (0.10), residues: 2516 sheet: -1.18 (0.34), residues: 252 loop : 0.18 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1124 HIS 0.004 0.001 HIS D 505 PHE 0.011 0.001 PHE C 373 TYR 0.008 0.001 TYR B1063 ARG 0.010 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 261 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.9566 (t0) cc_final: 0.9222 (m-30) REVERT: A 576 MET cc_start: 0.8919 (tpp) cc_final: 0.8484 (mmm) REVERT: A 580 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8462 (mt-10) REVERT: A 599 MET cc_start: 0.8999 (ttm) cc_final: 0.8707 (ttm) REVERT: A 951 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9220 (mp) REVERT: A 1034 LEU cc_start: 0.9128 (mp) cc_final: 0.8897 (tp) REVERT: B 136 ASP cc_start: 0.9564 (t0) cc_final: 0.9203 (m-30) REVERT: B 951 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9206 (mp) REVERT: B 1034 LEU cc_start: 0.9025 (mp) cc_final: 0.8782 (tp) REVERT: B 1146 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8592 (mp0) REVERT: C 136 ASP cc_start: 0.9573 (t0) cc_final: 0.9227 (m-30) REVERT: C 580 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8230 (mp0) REVERT: C 599 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8624 (ttm) REVERT: C 1138 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8558 (ttp80) REVERT: D 136 ASP cc_start: 0.9577 (t0) cc_final: 0.9223 (m-30) REVERT: D 430 MET cc_start: 0.9356 (tpp) cc_final: 0.9004 (mmm) REVERT: D 580 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8273 (mp0) REVERT: D 1034 LEU cc_start: 0.9097 (mp) cc_final: 0.8818 (tp) outliers start: 43 outliers final: 28 residues processed: 294 average time/residue: 0.3701 time to fit residues: 186.5420 Evaluate side-chains 282 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 251 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 3.9990 chunk 361 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 chunk 352 optimal weight: 0.9980 chunk 211 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 276 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 318 optimal weight: 2.9990 chunk 332 optimal weight: 5.9990 chunk 350 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1037 ASN ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30392 Z= 0.220 Angle : 0.581 13.474 41384 Z= 0.282 Chirality : 0.037 0.194 4788 Planarity : 0.004 0.050 5196 Dihedral : 6.514 89.369 4360 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.53 % Allowed : 13.72 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.14), residues: 3848 helix: 2.43 (0.10), residues: 2516 sheet: -1.18 (0.34), residues: 252 loop : 0.17 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1124 HIS 0.008 0.001 HIS A 505 PHE 0.011 0.001 PHE C 373 TYR 0.008 0.001 TYR A1063 ARG 0.007 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 252 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.9564 (t0) cc_final: 0.9215 (m-30) REVERT: A 576 MET cc_start: 0.8918 (tpp) cc_final: 0.8643 (mmm) REVERT: A 599 MET cc_start: 0.9024 (ttm) cc_final: 0.8725 (ttm) REVERT: A 951 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9218 (mp) REVERT: A 1034 LEU cc_start: 0.9132 (mp) cc_final: 0.8851 (tp) REVERT: B 136 ASP cc_start: 0.9569 (t0) cc_final: 0.9206 (m-30) REVERT: B 951 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9207 (mp) REVERT: B 1034 LEU cc_start: 0.9036 (mp) cc_final: 0.8766 (tp) REVERT: B 1146 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8643 (mp0) REVERT: C 136 ASP cc_start: 0.9575 (t0) cc_final: 0.9206 (m-30) REVERT: C 580 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8266 (mp0) REVERT: C 599 MET cc_start: 0.8910 (ttm) cc_final: 0.8645 (ttm) REVERT: D 136 ASP cc_start: 0.9581 (t0) cc_final: 0.9230 (m-30) REVERT: D 430 MET cc_start: 0.9347 (tpp) cc_final: 0.8994 (mmm) REVERT: D 1034 LEU cc_start: 0.9113 (mp) cc_final: 0.8824 (tp) outliers start: 44 outliers final: 37 residues processed: 287 average time/residue: 0.3462 time to fit residues: 169.8469 Evaluate side-chains 289 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 250 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 781 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 10.0000 chunk 372 optimal weight: 0.7980 chunk 227 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 258 optimal weight: 0.8980 chunk 390 optimal weight: 10.0000 chunk 359 optimal weight: 0.0030 chunk 310 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 190 optimal weight: 3.9990 overall best weight: 3.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30392 Z= 0.262 Angle : 0.598 13.008 41384 Z= 0.291 Chirality : 0.038 0.189 4788 Planarity : 0.004 0.051 5196 Dihedral : 6.452 89.331 4360 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.46 % Allowed : 14.03 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.14), residues: 3848 helix: 2.45 (0.10), residues: 2512 sheet: -1.19 (0.34), residues: 252 loop : 0.06 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1124 HIS 0.013 0.001 HIS A 505 PHE 0.011 0.001 PHE C 373 TYR 0.009 0.001 TYR C1063 ARG 0.007 0.000 ARG D1138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 249 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.9152 (ttt) cc_final: 0.8591 (mtp) REVERT: A 509 MET cc_start: 0.8790 (mtm) cc_final: 0.8324 (mmt) REVERT: A 576 MET cc_start: 0.8936 (tpp) cc_final: 0.8706 (mmm) REVERT: A 581 MET cc_start: 0.8764 (mmm) cc_final: 0.8516 (mmm) REVERT: A 951 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9233 (mp) REVERT: A 1034 LEU cc_start: 0.9139 (mp) cc_final: 0.8847 (tp) REVERT: B 951 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9214 (mp) REVERT: B 1034 LEU cc_start: 0.9047 (mp) cc_final: 0.8763 (tp) REVERT: B 1146 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8665 (mp0) REVERT: C 576 MET cc_start: 0.9242 (mmm) cc_final: 0.8776 (mmm) REVERT: C 580 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8331 (mp0) REVERT: C 599 MET cc_start: 0.8926 (ttm) cc_final: 0.8585 (ttm) REVERT: C 1146 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8655 (mp0) REVERT: D 430 MET cc_start: 0.9352 (tpp) cc_final: 0.8993 (mmm) REVERT: D 1034 LEU cc_start: 0.9135 (mp) cc_final: 0.8839 (tp) REVERT: D 1146 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8606 (mp0) outliers start: 42 outliers final: 39 residues processed: 285 average time/residue: 0.3665 time to fit residues: 178.9564 Evaluate side-chains 282 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 241 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 781 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 9.9990 chunk 331 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 86 optimal weight: 0.0870 chunk 311 optimal weight: 40.0000 chunk 130 optimal weight: 30.0000 chunk 319 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1037 ASN ** 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 = 0.3541 r_free = 0.3541 target = 0.075088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.055877 restraints weight = 138630.658| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.92 r_work: 0.2714 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30392 Z= 0.254 Angle : 0.602 13.766 41384 Z= 0.292 Chirality : 0.038 0.216 4788 Planarity : 0.004 0.054 5196 Dihedral : 6.399 89.730 4360 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.67 % Allowed : 13.96 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.14), residues: 3848 helix: 2.48 (0.10), residues: 2492 sheet: -1.19 (0.34), residues: 252 loop : 0.05 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1124 HIS 0.007 0.001 HIS C 505 PHE 0.012 0.001 PHE D 627 TYR 0.008 0.001 TYR B 704 ARG 0.014 0.000 ARG C 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5266.57 seconds wall clock time: 95 minutes 42.77 seconds (5742.77 seconds total)