Starting phenix.real_space_refine on Sat Nov 16 18:01:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghk_40046/11_2024/8ghk_40046.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghk_40046/11_2024/8ghk_40046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghk_40046/11_2024/8ghk_40046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghk_40046/11_2024/8ghk_40046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghk_40046/11_2024/8ghk_40046.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghk_40046/11_2024/8ghk_40046.cif" } resolution = 3.47 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= -0.000 sd= 0.011 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 7396 2.51 5 N 1986 2.21 5 O 2244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11671 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2722 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 137 Chain: "B" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2690 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 2 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 136 Chain: "C" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2738 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain breaks: 1 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 120 Chain: "H" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 897 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "L" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 762 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "M" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 874 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "N" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 756 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.54, per 1000 atoms: 0.90 Number of scatterers: 11671 At special positions: 0 Unit cell: (94.5, 135, 141.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 2244 8.00 N 1986 7.00 C 7396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 84 " distance=2.04 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 319 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 84 " distance=2.03 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 295 " - pdb=" SG CYS C 319 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 117 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 107 " distance=2.03 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 117 " distance=2.04 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 601 " - " ASN A 142 " " NAG A 602 " - " ASN A 71 " " NAG A 603 " - " ASN A 176 " " NAG B 601 " - " ASN B 142 " " NAG B 602 " - " ASN B 71 " " NAG B 603 " - " ASN B 176 " " NAG C 601 " - " ASN C 142 " " NAG C 602 " - " ASN C 71 " " NAG C 603 " - " ASN C 176 " " NAG D 1 " - " ASN A 104 " " NAG E 1 " - " ASN B 104 " " NAG F 1 " - " ASN C 104 " Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.7 seconds 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2886 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 36 sheets defined 18.8% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.787A pdb=" N LEU A 87 " --> pdb=" O CYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 removed outlier: 3.735A pdb=" N GLU A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 Processing helix chain 'A' and resid 396 through 403 removed outlier: 4.263A pdb=" N GLU A 400 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 445 removed outlier: 3.532A pdb=" N ASN A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 466 Processing helix chain 'B' and resid 73 through 79 Processing helix chain 'B' and resid 84 through 88 removed outlier: 4.118A pdb=" N LEU B 87 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE B 88 " --> pdb=" O GLU B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 88' Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.586A pdb=" N LEU B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 206 removed outlier: 4.019A pdb=" N GLN B 204 " --> pdb=" O ASN B 200 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 404 removed outlier: 3.583A pdb=" N ILE B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 464 removed outlier: 3.855A pdb=" N THR B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP B 452 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 79 removed outlier: 4.039A pdb=" N LEU C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.601A pdb=" N LEU C 87 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 88 " --> pdb=" O GLU C 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 84 through 88' Processing helix chain 'C' and resid 114 through 123 removed outlier: 3.763A pdb=" N GLU C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 removed outlier: 4.597A pdb=" N TRP C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 206 removed outlier: 3.559A pdb=" N GLN C 204 " --> pdb=" O ASN C 200 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 404 removed outlier: 3.577A pdb=" N VAL C 398 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 466 removed outlier: 3.732A pdb=" N VAL C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 450 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 452 " --> pdb=" O GLU C 448 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 466 " --> pdb=" O TYR C 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 76 removed outlier: 3.526A pdb=" N ASN H 75 " --> pdb=" O THR H 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 51 removed outlier: 3.685A pdb=" N THR M 50 " --> pdb=" O THR M 47 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE M 51 " --> pdb=" O PHE M 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 47 through 51' Processing helix chain 'M' and resid 72 through 76 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 48 removed outlier: 3.592A pdb=" N MET A 330 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 removed outlier: 7.437A pdb=" N LEU A 67 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 96 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 154 removed outlier: 4.770A pdb=" N CYS A 152 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 159 " --> pdb=" O CYS A 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 166 removed outlier: 8.513A pdb=" N LEU A 192 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 242 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 166 removed outlier: 8.513A pdb=" N LEU A 192 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 177 through 182 removed outlier: 3.736A pdb=" N ALA A 260 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AA8, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA9, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.634A pdb=" N VAL B 47 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET B 330 " --> pdb=" O VAL B 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 58 through 61 removed outlier: 9.426A pdb=" N LEU B 58 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ALA B 293 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU B 60 " --> pdb=" O ALA B 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 67 through 68 removed outlier: 7.234A pdb=" N LEU B 67 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 96 " --> pdb=" O ILE B 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 130 through 132 removed outlier: 3.523A pdb=" N PHE B 131 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR B 269 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU B 192 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU B 192 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 130 through 132 removed outlier: 3.523A pdb=" N PHE B 131 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR B 269 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU B 192 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP B 193 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 149 through 154 removed outlier: 4.591A pdb=" N CYS B 152 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 177 through 182 removed outlier: 3.684A pdb=" N VAL B 217 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 300 through 302 removed outlier: 3.963A pdb=" N ILE B 302 " --> pdb=" O CYS B 295 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N CYS B 295 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AB9, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.639A pdb=" N VAL C 47 " --> pdb=" O MET C 330 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 58 through 61 removed outlier: 9.058A pdb=" N LEU C 58 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ALA C 293 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C 60 " --> pdb=" O ALA C 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.725A pdb=" N LEU C 67 " --> pdb=" O VAL C 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 110 through 112 removed outlier: 6.898A pdb=" N TYR C 111 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N TRP C 247 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 131 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AC5, first strand: chain 'C' and resid 149 through 154 removed outlier: 4.647A pdb=" N CYS C 152 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 159 " --> pdb=" O CYS C 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 164 through 166 Processing sheet with id=AC7, first strand: chain 'C' and resid 177 through 182 removed outlier: 3.542A pdb=" N ALA C 260 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 300 through 302 removed outlier: 3.590A pdb=" N ILE C 302 " --> pdb=" O CYS C 295 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS C 295 " --> pdb=" O ILE C 302 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AD1, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.509A pdb=" N SER H 92 " --> pdb=" O TYR H 101 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 79 through 81 removed outlier: 5.079A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET H 53 " --> pdb=" O ILE H 70 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 63 through 67 removed outlier: 6.634A pdb=" N TRP L 54 " --> pdb=" O LEU L 66 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 81 through 84 removed outlier: 3.607A pdb=" N SER L 82 " --> pdb=" O THR L 93 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER L 84 " --> pdb=" O SER L 91 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 22 through 26 removed outlier: 3.532A pdb=" N GLN M 22 " --> pdb=" O SER M 44 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER M 44 " --> pdb=" O GLN M 22 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP M 94 " --> pdb=" O MET M 99 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR M 101 " --> pdb=" O SER M 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 53 through 58 removed outlier: 4.084A pdb=" N VAL M 118 " --> pdb=" O HIS M 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL M 56 " --> pdb=" O TYR M 116 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU M 138 " --> pdb=" O ALA M 113 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 68 through 70 Processing sheet with id=AD8, first strand: chain 'N' and resid 39 through 42 removed outlier: 3.956A pdb=" N TYR N 90 " --> pdb=" O CYS N 42 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER N 91 " --> pdb=" O SER N 84 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 63 through 65 346 hydrogen bonds defined for protein. 933 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: 3.85 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3748 1.34 - 1.46: 2535 1.46 - 1.58: 5612 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 11953 Sorted by residual: bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" C GLU B 318 " pdb=" N CYS B 319 " ideal model delta sigma weight residual 1.329 1.357 -0.028 1.16e-02 7.43e+03 5.83e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.68e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C1 NAG B 603 " pdb=" O5 NAG B 603 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.05e+00 ... (remaining 11948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 15956 1.76 - 3.53: 326 3.53 - 5.29: 41 5.29 - 7.05: 9 7.05 - 8.81: 3 Bond angle restraints: 16335 Sorted by residual: angle pdb=" C GLU B 318 " pdb=" N CYS B 319 " pdb=" CA CYS B 319 " ideal model delta sigma weight residual 122.26 114.81 7.45 1.60e+00 3.91e-01 2.17e+01 angle pdb=" N ASN A 104 " pdb=" CA ASN A 104 " pdb=" CB ASN A 104 " ideal model delta sigma weight residual 110.49 104.26 6.23 1.69e+00 3.50e-01 1.36e+01 angle pdb=" C ASN A 104 " pdb=" CA ASN A 104 " pdb=" CB ASN A 104 " ideal model delta sigma weight residual 110.42 117.15 -6.73 1.99e+00 2.53e-01 1.15e+01 angle pdb=" N ARG A 268 " pdb=" CA ARG A 268 " pdb=" C ARG A 268 " ideal model delta sigma weight residual 114.56 110.46 4.10 1.27e+00 6.20e-01 1.04e+01 angle pdb=" N CYS B 319 " pdb=" CA CYS B 319 " pdb=" C CYS B 319 " ideal model delta sigma weight residual 108.22 110.96 -2.74 9.00e-01 1.23e+00 9.24e+00 ... (remaining 16330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.26: 6493 22.26 - 44.53: 582 44.53 - 66.79: 88 66.79 - 89.06: 26 89.06 - 111.32: 8 Dihedral angle restraints: 7197 sinusoidal: 2685 harmonic: 4512 Sorted by residual: dihedral pdb=" CA GLU A 103 " pdb=" C GLU A 103 " pdb=" N ASN A 104 " pdb=" CA ASN A 104 " ideal model delta harmonic sigma weight residual 180.00 -145.16 -34.84 0 5.00e+00 4.00e-02 4.86e+01 dihedral pdb=" CB CYS C 295 " pdb=" SG CYS C 295 " pdb=" SG CYS C 319 " pdb=" CB CYS C 319 " ideal model delta sinusoidal sigma weight residual 93.00 33.76 59.24 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CB CYS B 295 " pdb=" SG CYS B 295 " pdb=" SG CYS B 319 " pdb=" CB CYS B 319 " ideal model delta sinusoidal sigma weight residual 93.00 49.97 43.03 1 1.00e+01 1.00e-02 2.58e+01 ... (remaining 7194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1828 0.107 - 0.214: 65 0.214 - 0.322: 4 0.322 - 0.429: 0 0.429 - 0.536: 3 Chirality restraints: 1900 Sorted by residual: chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 142 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.19e+00 chirality pdb=" C1 NAG B 602 " pdb=" ND2 ASN B 71 " pdb=" C2 NAG B 602 " pdb=" O5 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 104 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 1897 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 104 " -0.002 2.00e-02 2.50e+03 5.64e-02 3.98e+01 pdb=" CG ASN A 104 " 0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN A 104 " -0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN A 104 " 0.069 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 71 " -0.034 2.00e-02 2.50e+03 3.14e-02 1.23e+01 pdb=" CG ASN B 71 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 71 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 71 " 0.036 2.00e-02 2.50e+03 pdb=" C1 NAG B 602 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 104 " 0.001 2.00e-02 2.50e+03 3.01e-02 1.13e+01 pdb=" CG ASN C 104 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 104 " -0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN C 104 " 0.041 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.033 2.00e-02 2.50e+03 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 183 2.64 - 3.21: 10079 3.21 - 3.77: 16022 3.77 - 4.34: 21399 4.34 - 4.90: 37373 Nonbonded interactions: 85056 Sorted by model distance: nonbonded pdb=" O TYR M 128 " pdb=" OH TYR N 55 " model vdw 2.080 3.040 nonbonded pdb=" O TYR H 128 " pdb=" OH TYR L 55 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR A 297 " pdb=" O GLY A 300 " model vdw 2.120 3.040 nonbonded pdb=" OG1 THR B 297 " pdb=" O GLY B 300 " model vdw 2.181 3.040 nonbonded pdb=" OD1 ASN N 50 " pdb=" OG1 THR N 70 " model vdw 2.183 3.040 ... (remaining 85051 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' and (resid 40 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 47 or (resid 48 through 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 51 or (res \ id 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ gh 63 or (resid 64 through 65 and (name N or name CA or name C or name O or name \ CB )) or resid 66 through 84 or (resid 85 and (name N or name CA or name C or n \ ame O or name CB )) or resid 86 through 89 or (resid 90 through 91 and (name N o \ r name CA or name C or name O or name CB )) or resid 92 through 97 or (resid 98 \ and (name N or name CA or name C or name O or name CB )) or resid 99 through 250 \ or (resid 251 and (name N or name CA or name C or name O or name CB )) or resid \ 252 through 253 or (resid 254 and (name N or name CA or name C or name O or nam \ e CB )) or resid 255 through 397 or (resid 398 through 404 and (name N or name C \ A or name C or name O or name CB )) or resid 407 through 408 or (resid 409 and ( \ name N or name CA or name C or name O or name CB )) or resid 410 through 443 or \ (resid 444 through 446 and (name N or name CA or name C or name O or name CB )) \ or resid 447 through 449 or (resid 450 and (name N or name CA or name C or name \ O or name CB )) or resid 451 through 452 or (resid 453 and (name N or name CA or \ name C or name O or name CB )) or resid 454 through 456 or (resid 457 through 4 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 601 through \ 603)) selection = (chain 'B' and (resid 40 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 56 or (resid 57 and (name N or nam \ e CA or name C or name O or name CB )) or resid 58 through 102 or (resid 103 and \ (name N or name CA or name C or name O or name CB )) or resid 104 through 113 o \ r (resid 114 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 15 through 131 or (resid 132 and (name N or name CA or name C or name O or name \ CB )) or resid 133 through 135 or (resid 136 through 137 and (name N or name CA \ or name C or name O or name CB )) or resid 138 through 202 or (resid 203 and (na \ me N or name CA or name C or name O or name CB )) or resid 204 through 211 or (r \ esid 212 through 213 and (name N or name CA or name C or name O or name CB )) or \ resid 214 through 228 or (resid 229 and (name N or name CA or name C or name O \ or name CB )) or resid 230 through 239 or (resid 240 and (name N or name CA or n \ ame C or name O or name CB )) or resid 241 through 287 or (resid 288 through 290 \ and (name N or name CA or name C or name O or name CB )) or resid 291 through 3 \ 02 or (resid 303 and (name N or name CA or name C or name O or name CB )) or res \ id 304 through 320 or (resid 321 and (name N or name CA or name C or name O or n \ ame CB )) or resid 322 through 332 or resid 393 through 424 or (resid 425 and (n \ ame N or name CA or name C or name O or name CB )) or resid 426 through 427 or ( \ resid 428 through 429 and (name N or name CA or name C or name O or name CB )) o \ r resid 430 through 441 or (resid 442 and (name N or name CA or name C or name O \ or name CB )) or resid 443 through 457 or (resid 458 through 464 and (name N or \ name CA or name C or name O or name CB )) or resid 601 through 603)) selection = (chain 'C' and (resid 40 through 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and (na \ me N or name CA or name C or name O or name CB )) or resid 53 through 63 or (res \ id 64 through 65 and (name N or name CA or name C or name O or name CB )) or res \ id 66 through 84 or (resid 85 and (name N or name CA or name C or name O or name \ CB )) or resid 86 through 89 or (resid 90 through 91 and (name N or name CA or \ name C or name O or name CB )) or resid 92 through 97 or (resid 98 and (name N o \ r name CA or name C or name O or name CB )) or resid 99 through 102 or (resid 10 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 104 through \ 113 or (resid 114 and (name N or name CA or name C or name O or name CB )) or re \ sid 115 through 131 or (resid 132 and (name N or name CA or name C or name O or \ name CB )) or resid 133 through 135 or (resid 136 through 137 and (name N or nam \ e CA or name C or name O or name CB )) or resid 138 through 156 or (resid 157 an \ d (name N or name CA or name C or name O or name CB )) or resid 158 through 210 \ or (resid 211 through 213 and (name N or name CA or name C or name O or name CB \ )) or resid 214 through 228 or (resid 229 and (name N or name CA or name C or na \ me O or name CB )) or resid 230 through 239 or (resid 240 and (name N or name CA \ or name C or name O or name CB )) or resid 241 through 253 or (resid 254 and (n \ ame N or name CA or name C or name O or name CB )) or resid 255 through 287 or ( \ resid 288 through 290 and (name N or name CA or name C or name O or name CB )) o \ r resid 291 through 302 or (resid 303 and (name N or name CA or name C or name O \ or name CB )) or resid 304 through 332 or resid 393 through 397 or (resid 398 t \ hrough 404 and (name N or name CA or name C or name O or name CB )) or resid 407 \ through 408 or (resid 409 and (name N or name CA or name C or name O or name CB \ )) or resid 410 through 424 or (resid 425 and (name N or name CA or name C or n \ ame O or name CB )) or resid 426 through 428 or (resid 429 and (name N or name C \ A or name C or name O or name CB )) or resid 430 through 441 or (resid 442 and ( \ name N or name CA or name C or name O or name CB )) or resid 443 or (resid 444 t \ hrough 446 and (name N or name CA or name C or name O or name CB )) or resid 447 \ through 449 or (resid 450 and (name N or name CA or name C or name O or name CB \ )) or resid 451 through 464 or resid 601 through 603)) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'H' and (resid 20 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 through 24 or (resid 25 and (name N or nam \ e CA or name C or name O or name CB )) or resid 26 through 37 or (resid 38 and ( \ name N or name CA or name C or name O or name CB )) or resid 39 through 64 or (r \ esid 65 and (name N or name CA or name C or name O or name CB )) or resid 66 thr \ ough 102 or (resid 103 through 105 and (name N or name CA or name C or name O or \ name CB )) or resid 106 through 140)) selection = (chain 'M' and (resid 20 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 113 or (resid 114 and (name N or n \ ame CA or name C or name O or name CB )) or resid 115 through 140)) } ncs_group { reference = (chain 'L' and (resid 21 through 25 or (resid 26 through 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 through 121 or (resid 122 throu \ gh 123 and (name N or name CA or name C or name O or name CB )))) selection = chain 'N' } 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: 11.190 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: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 32.130 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 0.049 11953 Z= 0.291 Angle : 0.617 8.815 16335 Z= 0.323 Chirality : 0.050 0.536 1900 Planarity : 0.004 0.056 2078 Dihedral : 17.269 111.320 4272 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.45 % Allowed : 31.48 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.08 (0.21), residues: 1534 helix: -0.06 (0.33), residues: 250 sheet: -1.25 (0.25), residues: 432 loop : -1.88 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 66 HIS 0.005 0.001 HIS A 143 PHE 0.013 0.001 PHE C 128 TYR 0.016 0.001 TYR N 49 ARG 0.003 0.000 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 1.328 Fit side-chains REVERT: H 69 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8209 (ttt-90) outliers start: 5 outliers final: 3 residues processed: 131 average time/residue: 0.1903 time to fit residues: 39.4953 Evaluate side-chains 128 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain L residue 38 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 0.0030 chunk 64 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 244 ASN B 143 HIS B 212 ASN C 68 GLN L 109 GLN N 109 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11953 Z= 0.245 Angle : 0.593 7.672 16335 Z= 0.312 Chirality : 0.048 0.397 1900 Planarity : 0.004 0.048 2078 Dihedral : 8.537 71.683 2039 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.65 % Allowed : 26.39 % Favored : 68.96 % 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: -1.84 (0.21), residues: 1534 helix: 0.42 (0.32), residues: 262 sheet: -0.94 (0.25), residues: 443 loop : -1.97 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.003 0.001 HIS B 197 PHE 0.013 0.001 PHE N 106 TYR 0.016 0.001 TYR N 49 ARG 0.003 0.000 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 1.335 Fit side-chains REVERT: C 137 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7939 (mm-30) REVERT: C 407 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7817 (t) REVERT: C 420 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7417 (mmt) REVERT: H 57 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.5932 (ttp80) outliers start: 52 outliers final: 31 residues processed: 170 average time/residue: 0.1936 time to fit residues: 51.1610 Evaluate side-chains 158 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 109 GLN Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 56 GLN Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 102 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 ASN L 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11953 Z= 0.342 Angle : 0.621 8.306 16335 Z= 0.323 Chirality : 0.049 0.367 1900 Planarity : 0.004 0.051 2078 Dihedral : 7.095 55.339 2032 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.64 % Allowed : 26.03 % Favored : 68.34 % 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: -1.85 (0.21), residues: 1534 helix: 0.62 (0.32), residues: 262 sheet: -0.99 (0.25), residues: 440 loop : -2.03 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 93 HIS 0.003 0.001 HIS B 197 PHE 0.015 0.002 PHE C 128 TYR 0.013 0.002 TYR N 51 ARG 0.002 0.000 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 125 time to evaluate : 1.274 Fit side-chains REVERT: C 137 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7979 (mm-30) REVERT: C 407 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7817 (t) REVERT: C 420 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7718 (mmt) REVERT: H 57 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.6755 (ttp80) outliers start: 63 outliers final: 41 residues processed: 173 average time/residue: 0.1773 time to fit residues: 48.9257 Evaluate side-chains 165 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 56 GLN Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 102 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 147 optimal weight: 0.0970 chunk 132 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11953 Z= 0.159 Angle : 0.520 8.794 16335 Z= 0.270 Chirality : 0.046 0.381 1900 Planarity : 0.004 0.050 2078 Dihedral : 5.757 58.669 2032 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.49 % Allowed : 27.82 % Favored : 68.69 % 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: -1.51 (0.21), residues: 1534 helix: 1.07 (0.32), residues: 262 sheet: -0.77 (0.25), residues: 446 loop : -1.87 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 66 HIS 0.001 0.000 HIS C 196 PHE 0.019 0.001 PHE A 453 TYR 0.011 0.001 TYR N 51 ARG 0.002 0.000 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 1.302 Fit side-chains REVERT: C 407 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7751 (t) REVERT: C 420 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7459 (mmt) REVERT: C 456 SER cc_start: 0.8460 (t) cc_final: 0.8058 (p) REVERT: H 57 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.5931 (ttp80) REVERT: N 82 SER cc_start: 0.8347 (p) cc_final: 0.8074 (p) outliers start: 39 outliers final: 25 residues processed: 169 average time/residue: 0.1849 time to fit residues: 49.9845 Evaluate side-chains 161 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 109 GLN Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 102 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 37 optimal weight: 0.0670 chunk 49 optimal weight: 4.9990 overall best weight: 2.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 11953 Z= 0.390 Angle : 0.630 8.015 16335 Z= 0.328 Chirality : 0.049 0.382 1900 Planarity : 0.004 0.054 2078 Dihedral : 6.026 54.037 2032 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 5.90 % Allowed : 25.76 % Favored : 68.34 % 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: -1.69 (0.21), residues: 1534 helix: 0.97 (0.33), residues: 262 sheet: -0.93 (0.25), residues: 434 loop : -1.97 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 77 HIS 0.004 0.001 HIS B 197 PHE 0.027 0.002 PHE A 453 TYR 0.014 0.002 TYR H 128 ARG 0.002 0.000 ARG H 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 126 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: C 407 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7753 (t) REVERT: C 420 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7815 (mmt) REVERT: C 456 SER cc_start: 0.8512 (t) cc_final: 0.8108 (p) REVERT: N 82 SER cc_start: 0.8374 (p) cc_final: 0.8097 (p) outliers start: 66 outliers final: 51 residues processed: 178 average time/residue: 0.1766 time to fit residues: 50.7709 Evaluate side-chains 175 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 122 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 102 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 0.4980 chunk 36 optimal weight: 20.0000 chunk 148 optimal weight: 0.2980 chunk 122 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 142 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11953 Z= 0.207 Angle : 0.544 9.266 16335 Z= 0.281 Chirality : 0.047 0.382 1900 Planarity : 0.004 0.053 2078 Dihedral : 5.621 56.868 2032 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.65 % Allowed : 26.92 % Favored : 68.43 % 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: -1.50 (0.21), residues: 1534 helix: 1.24 (0.33), residues: 262 sheet: -0.82 (0.25), residues: 436 loop : -1.88 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 66 HIS 0.002 0.001 HIS C 196 PHE 0.028 0.001 PHE A 453 TYR 0.011 0.001 TYR N 51 ARG 0.002 0.000 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 1.370 Fit side-chains REVERT: C 137 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7933 (mm-30) REVERT: C 420 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7831 (mmt) REVERT: C 456 SER cc_start: 0.8498 (t) cc_final: 0.8109 (p) REVERT: H 57 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.6017 (ttp80) REVERT: M 43 THR cc_start: 0.8590 (p) cc_final: 0.8290 (p) REVERT: N 82 SER cc_start: 0.8346 (p) cc_final: 0.8111 (p) outliers start: 52 outliers final: 39 residues processed: 174 average time/residue: 0.1938 time to fit residues: 53.8552 Evaluate side-chains 171 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 109 GLN Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 102 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 147 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11953 Z= 0.173 Angle : 0.523 7.290 16335 Z= 0.269 Chirality : 0.046 0.393 1900 Planarity : 0.004 0.053 2078 Dihedral : 5.344 56.787 2032 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.11 % Allowed : 27.73 % Favored : 68.16 % 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: -1.30 (0.21), residues: 1534 helix: 1.55 (0.33), residues: 262 sheet: -0.72 (0.25), residues: 436 loop : -1.80 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 66 HIS 0.002 0.000 HIS C 196 PHE 0.026 0.001 PHE A 453 TYR 0.010 0.001 TYR N 51 ARG 0.004 0.000 ARG M 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 1.309 Fit side-chains REVERT: C 137 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7916 (mm-30) REVERT: C 456 SER cc_start: 0.8484 (t) cc_final: 0.8107 (p) REVERT: H 57 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.5982 (ttp80) REVERT: M 43 THR cc_start: 0.8600 (p) cc_final: 0.8325 (p) outliers start: 46 outliers final: 36 residues processed: 172 average time/residue: 0.1783 time to fit residues: 49.0736 Evaluate side-chains 170 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 109 GLN Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 102 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 11953 Z= 0.407 Angle : 0.657 8.136 16335 Z= 0.341 Chirality : 0.050 0.379 1900 Planarity : 0.005 0.055 2078 Dihedral : 5.951 53.273 2032 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.65 % Allowed : 27.55 % Favored : 67.80 % 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: -1.61 (0.21), residues: 1534 helix: 1.16 (0.33), residues: 261 sheet: -0.82 (0.26), residues: 423 loop : -1.99 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 77 HIS 0.004 0.001 HIS H 54 PHE 0.027 0.002 PHE A 453 TYR 0.016 0.002 TYR H 128 ARG 0.003 0.000 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 128 time to evaluate : 1.380 Fit side-chains revert: symmetry clash REVERT: C 137 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7970 (mm-30) REVERT: C 456 SER cc_start: 0.8567 (t) cc_final: 0.8177 (p) outliers start: 52 outliers final: 43 residues processed: 168 average time/residue: 0.1802 time to fit residues: 48.3455 Evaluate side-chains 166 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 102 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11953 Z= 0.180 Angle : 0.539 7.472 16335 Z= 0.278 Chirality : 0.046 0.394 1900 Planarity : 0.004 0.056 2078 Dihedral : 5.431 57.003 2032 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.85 % Allowed : 28.35 % Favored : 67.80 % 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: -1.33 (0.21), residues: 1534 helix: 1.48 (0.33), residues: 262 sheet: -0.74 (0.25), residues: 434 loop : -1.79 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 66 HIS 0.002 0.000 HIS B 197 PHE 0.026 0.001 PHE A 453 TYR 0.009 0.001 TYR N 51 ARG 0.003 0.000 ARG C 419 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 1.250 Fit side-chains REVERT: A 420 MET cc_start: 0.7146 (mmt) cc_final: 0.6736 (mmt) REVERT: C 83 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: C 456 SER cc_start: 0.8507 (t) cc_final: 0.8149 (p) outliers start: 43 outliers final: 36 residues processed: 168 average time/residue: 0.1982 time to fit residues: 53.5641 Evaluate side-chains 170 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 109 GLN Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11953 Z= 0.318 Angle : 0.598 7.840 16335 Z= 0.310 Chirality : 0.048 0.396 1900 Planarity : 0.004 0.056 2078 Dihedral : 5.684 54.455 2032 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.85 % Allowed : 28.62 % Favored : 67.53 % 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: -1.45 (0.21), residues: 1534 helix: 1.34 (0.33), residues: 262 sheet: -0.74 (0.26), residues: 421 loop : -1.89 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 132 HIS 0.003 0.001 HIS A 312 PHE 0.025 0.002 PHE A 453 TYR 0.012 0.002 TYR L 111 ARG 0.002 0.000 ARG C 419 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 1.429 Fit side-chains REVERT: C 83 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8224 (mt-10) outliers start: 43 outliers final: 40 residues processed: 166 average time/residue: 0.1808 time to fit residues: 47.6934 Evaluate side-chains 170 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 109 GLN Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.131459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106865 restraints weight = 20642.202| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.76 r_work: 0.3170 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11953 Z= 0.299 Angle : 0.596 9.343 16335 Z= 0.308 Chirality : 0.048 0.392 1900 Planarity : 0.004 0.057 2078 Dihedral : 5.733 55.078 2032 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.29 % Allowed : 27.91 % Favored : 67.80 % 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: -1.50 (0.21), residues: 1534 helix: 1.30 (0.33), residues: 262 sheet: -0.81 (0.25), residues: 429 loop : -1.90 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 93 HIS 0.003 0.001 HIS H 54 PHE 0.025 0.002 PHE A 453 TYR 0.011 0.001 TYR L 111 ARG 0.003 0.000 ARG H 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2750.16 seconds wall clock time: 52 minutes 41.07 seconds (3161.07 seconds total)