Starting phenix.real_space_refine on Thu Dec 14 12:49:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uc2_20725/12_2023/6uc2_20725_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uc2_20725/12_2023/6uc2_20725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uc2_20725/12_2023/6uc2_20725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uc2_20725/12_2023/6uc2_20725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uc2_20725/12_2023/6uc2_20725_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uc2_20725/12_2023/6uc2_20725_updated.pdb" } resolution = 4.48 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= 0.148 sd= 3.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 144 5.16 5 C 17688 2.51 5 N 4880 2.21 5 O 5624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E ARG 231": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 136": "NH1" <-> "NH2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 231": "NH1" <-> "NH2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "F ARG 412": "NH1" <-> "NH2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ARG 231": "NH1" <-> "NH2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "G ARG 412": "NH1" <-> "NH2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 128": "NH1" <-> "NH2" Residue "H PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H ARG 149": "NH1" <-> "NH2" Residue "H ARG 153": "NH1" <-> "NH2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "H ARG 412": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 28408 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "C" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "D" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "E" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "F" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "G" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "H" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3456 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 435} Chain breaks: 2 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 14.52, per 1000 atoms: 0.51 Number of scatterers: 28408 At special positions: 0 Unit cell: (152.25, 152.25, 116.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 72 15.00 O 5624 8.00 N 4880 7.00 C 17688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.61 Conformation dependent library (CDL) restraints added in 5.0 seconds 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 40 sheets defined 35.3% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.70 Creating SS restraints... Processing helix chain 'A' and resid 21 through 24 No H-bonds generated for 'chain 'A' and resid 21 through 24' Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.538A pdb=" N ALA A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 removed outlier: 3.951A pdb=" N GLU A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.851A pdb=" N PHE A 131 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 135 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.847A pdb=" N LYS A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 258 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 261 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.660A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 334 through 337 No H-bonds generated for 'chain 'A' and resid 334 through 337' Processing helix chain 'A' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 removed outlier: 3.782A pdb=" N ALA A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 477 through 485 Processing helix chain 'A' and resid 495 through 499 removed outlier: 4.189A pdb=" N VAL A 499 " --> pdb=" O SER A 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 24 No H-bonds generated for 'chain 'B' and resid 21 through 24' Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.538A pdb=" N ALA B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 108 removed outlier: 3.951A pdb=" N GLU B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.852A pdb=" N PHE B 131 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 135 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.848A pdb=" N LYS B 257 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 258 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 261 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.660A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 334 through 337 No H-bonds generated for 'chain 'B' and resid 334 through 337' Processing helix chain 'B' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 removed outlier: 3.782A pdb=" N ALA B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'B' and resid 495 through 499 removed outlier: 4.189A pdb=" N VAL B 499 " --> pdb=" O SER B 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 76 through 84 removed outlier: 3.538A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 108 removed outlier: 3.952A pdb=" N GLU C 103 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 137 removed outlier: 3.852A pdb=" N PHE C 131 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA C 135 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.847A pdb=" N LYS C 257 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 258 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP C 261 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 removed outlier: 3.659A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 334 through 337 No H-bonds generated for 'chain 'C' and resid 334 through 337' Processing helix chain 'C' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 removed outlier: 3.782A pdb=" N ALA C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 453 through 455 No H-bonds generated for 'chain 'C' and resid 453 through 455' Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 477 through 485 Processing helix chain 'C' and resid 495 through 499 removed outlier: 4.189A pdb=" N VAL C 499 " --> pdb=" O SER C 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 24 No H-bonds generated for 'chain 'D' and resid 21 through 24' Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 76 through 84 removed outlier: 3.538A pdb=" N ALA D 81 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 108 removed outlier: 3.952A pdb=" N GLU D 103 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 137 removed outlier: 3.852A pdb=" N PHE D 131 " --> pdb=" O ARG D 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA D 135 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.847A pdb=" N LYS D 257 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 258 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 261 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 removed outlier: 3.660A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 334 through 337 No H-bonds generated for 'chain 'D' and resid 334 through 337' Processing helix chain 'D' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 removed outlier: 3.782A pdb=" N ALA D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 457 through 471 Processing helix chain 'D' and resid 477 through 485 Processing helix chain 'D' and resid 495 through 499 removed outlier: 4.188A pdb=" N VAL D 499 " --> pdb=" O SER D 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 24 No H-bonds generated for 'chain 'E' and resid 21 through 24' Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.539A pdb=" N ALA E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 108 removed outlier: 3.952A pdb=" N GLU E 103 " --> pdb=" O PHE E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 137 removed outlier: 3.852A pdb=" N PHE E 131 " --> pdb=" O ARG E 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA E 135 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 182 through 184 No H-bonds generated for 'chain 'E' and resid 182 through 184' Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 225 through 232 Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.848A pdb=" N LYS E 257 " --> pdb=" O GLU E 254 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR E 258 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP E 261 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 removed outlier: 3.659A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 316 Processing helix chain 'E' and resid 334 through 337 No H-bonds generated for 'chain 'E' and resid 334 through 337' Processing helix chain 'E' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER E 351 " --> pdb=" O VAL E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 removed outlier: 3.783A pdb=" N ALA E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 453 through 455 No H-bonds generated for 'chain 'E' and resid 453 through 455' Processing helix chain 'E' and resid 457 through 471 Processing helix chain 'E' and resid 477 through 485 Processing helix chain 'E' and resid 495 through 499 removed outlier: 4.190A pdb=" N VAL E 499 " --> pdb=" O SER E 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 24 No H-bonds generated for 'chain 'F' and resid 21 through 24' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 76 through 84 removed outlier: 3.538A pdb=" N ALA F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 108 removed outlier: 3.952A pdb=" N GLU F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.851A pdb=" N PHE F 131 " --> pdb=" O ARG F 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA F 135 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 225 through 232 Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.848A pdb=" N LYS F 257 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR F 258 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP F 261 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 removed outlier: 3.659A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 316 Processing helix chain 'F' and resid 334 through 337 No H-bonds generated for 'chain 'F' and resid 334 through 337' Processing helix chain 'F' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 removed outlier: 3.782A pdb=" N ALA F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 390 No H-bonds generated for 'chain 'F' and resid 388 through 390' Processing helix chain 'F' and resid 453 through 455 No H-bonds generated for 'chain 'F' and resid 453 through 455' Processing helix chain 'F' and resid 457 through 471 Processing helix chain 'F' and resid 477 through 485 Processing helix chain 'F' and resid 495 through 499 removed outlier: 4.189A pdb=" N VAL F 499 " --> pdb=" O SER F 496 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 24 No H-bonds generated for 'chain 'G' and resid 21 through 24' Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 76 through 84 removed outlier: 3.538A pdb=" N ALA G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 108 removed outlier: 3.951A pdb=" N GLU G 103 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 137 removed outlier: 3.852A pdb=" N PHE G 131 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA G 135 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 182 through 184 No H-bonds generated for 'chain 'G' and resid 182 through 184' Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 225 through 232 Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.848A pdb=" N LYS G 257 " --> pdb=" O GLU G 254 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR G 258 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP G 261 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 removed outlier: 3.659A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 316 Processing helix chain 'G' and resid 334 through 337 No H-bonds generated for 'chain 'G' and resid 334 through 337' Processing helix chain 'G' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 removed outlier: 3.783A pdb=" N ALA G 374 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 390 No H-bonds generated for 'chain 'G' and resid 388 through 390' Processing helix chain 'G' and resid 453 through 455 No H-bonds generated for 'chain 'G' and resid 453 through 455' Processing helix chain 'G' and resid 457 through 471 Processing helix chain 'G' and resid 477 through 485 Processing helix chain 'G' and resid 495 through 499 removed outlier: 4.189A pdb=" N VAL G 499 " --> pdb=" O SER G 496 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 24 No H-bonds generated for 'chain 'H' and resid 21 through 24' Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 76 through 84 removed outlier: 3.538A pdb=" N ALA H 81 " --> pdb=" O GLY H 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 108 removed outlier: 3.951A pdb=" N GLU H 103 " --> pdb=" O PHE H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 137 removed outlier: 3.852A pdb=" N PHE H 131 " --> pdb=" O ARG H 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA H 135 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 225 through 232 Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.848A pdb=" N LYS H 257 " --> pdb=" O GLU H 254 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 258 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP H 261 " --> pdb=" O TYR H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 removed outlier: 3.660A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 316 Processing helix chain 'H' and resid 334 through 337 No H-bonds generated for 'chain 'H' and resid 334 through 337' Processing helix chain 'H' and resid 343 through 354 removed outlier: 3.649A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 removed outlier: 3.783A pdb=" N ALA H 374 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 390 No H-bonds generated for 'chain 'H' and resid 388 through 390' Processing helix chain 'H' and resid 453 through 455 No H-bonds generated for 'chain 'H' and resid 453 through 455' Processing helix chain 'H' and resid 457 through 471 Processing helix chain 'H' and resid 477 through 485 Processing helix chain 'H' and resid 495 through 499 removed outlier: 4.189A pdb=" N VAL H 499 " --> pdb=" O SER H 496 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU A 36 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU A 491 " --> pdb=" O LEU A 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.023A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 270 through 273 removed outlier: 6.672A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 321 through 323 Processing sheet with id= E, first strand: chain 'A' and resid 142 through 145 Processing sheet with id= F, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU B 36 " --> pdb=" O GLU B 491 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B 491 " --> pdb=" O LEU B 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 187 through 189 removed outlier: 4.023A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 270 through 273 removed outlier: 6.671A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 321 through 323 Processing sheet with id= J, first strand: chain 'B' and resid 142 through 145 Processing sheet with id= K, first strand: chain 'C' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU C 36 " --> pdb=" O GLU C 491 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU C 491 " --> pdb=" O LEU C 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 187 through 189 removed outlier: 4.023A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 270 through 273 removed outlier: 6.672A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 321 through 323 Processing sheet with id= O, first strand: chain 'C' and resid 142 through 145 Processing sheet with id= P, first strand: chain 'D' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU D 36 " --> pdb=" O GLU D 491 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU D 491 " --> pdb=" O LEU D 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 187 through 189 removed outlier: 4.023A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 270 through 273 removed outlier: 6.672A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 321 through 323 Processing sheet with id= T, first strand: chain 'D' and resid 142 through 145 Processing sheet with id= U, first strand: chain 'E' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU E 36 " --> pdb=" O GLU E 491 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU E 491 " --> pdb=" O LEU E 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 187 through 189 removed outlier: 4.024A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 270 through 273 removed outlier: 6.671A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 321 through 323 Processing sheet with id= Y, first strand: chain 'E' and resid 142 through 145 Processing sheet with id= Z, first strand: chain 'F' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU F 36 " --> pdb=" O GLU F 491 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU F 491 " --> pdb=" O LEU F 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 187 through 189 removed outlier: 4.023A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 270 through 273 removed outlier: 6.672A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'F' and resid 321 through 323 Processing sheet with id= AD, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= AE, first strand: chain 'G' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU G 36 " --> pdb=" O GLU G 491 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU G 491 " --> pdb=" O LEU G 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'G' and resid 187 through 189 removed outlier: 4.023A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 270 through 273 removed outlier: 6.672A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'G' and resid 321 through 323 Processing sheet with id= AI, first strand: chain 'G' and resid 142 through 145 Processing sheet with id= AJ, first strand: chain 'H' and resid 35 through 37 removed outlier: 3.633A pdb=" N LEU H 36 " --> pdb=" O GLU H 491 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU H 491 " --> pdb=" O LEU H 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'H' and resid 187 through 189 removed outlier: 4.022A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 270 through 273 removed outlier: 6.672A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'H' and resid 321 through 323 Processing sheet with id= AN, first strand: chain 'H' and resid 142 through 145 672 hydrogen bonds defined for protein. 1632 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: 8.90 Time building geometry restraints manager: 12.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4872 1.31 - 1.44: 6832 1.44 - 1.56: 16697 1.56 - 1.69: 231 1.69 - 1.81: 232 Bond restraints: 28864 Sorted by residual: bond pdb=" C2' ATP D 603 " pdb=" C3' ATP D 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.34e+02 bond pdb=" C2' ATP E 603 " pdb=" C3' ATP E 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.32e+02 bond pdb=" C2' ATP B 603 " pdb=" C3' ATP B 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.32e+02 bond pdb=" C2' ATP A 603 " pdb=" C3' ATP A 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.31e+02 bond pdb=" C2' ATP C 603 " pdb=" C3' ATP C 603 " ideal model delta sigma weight residual 1.531 1.254 0.277 1.20e-02 6.94e+03 5.31e+02 ... (remaining 28859 not shown) Histogram of bond angle deviations from ideal: 91.41 - 101.32: 104 101.32 - 111.24: 11098 111.24 - 121.15: 19983 121.15 - 131.07: 7805 131.07 - 140.99: 146 Bond angle restraints: 39136 Sorted by residual: angle pdb=" PB ATP D 603 " pdb=" O3B ATP D 603 " pdb=" PG ATP D 603 " ideal model delta sigma weight residual 139.87 120.89 18.98 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 120.89 18.98 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP C 603 " pdb=" O3B ATP C 603 " pdb=" PG ATP C 603 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP H 603 " pdb=" O3B ATP H 603 " pdb=" PG ATP H 603 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 120.93 18.94 1.00e+00 1.00e+00 3.59e+02 ... (remaining 39131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 16637 33.77 - 67.55: 875 67.55 - 101.32: 45 101.32 - 135.10: 19 135.10 - 168.87: 24 Dihedral angle restraints: 17600 sinusoidal: 7264 harmonic: 10336 Sorted by residual: dihedral pdb=" CA GLU B 111 " pdb=" C GLU B 111 " pdb=" N GLN B 112 " pdb=" CA GLN B 112 " ideal model delta harmonic sigma weight residual -180.00 -131.80 -48.20 0 5.00e+00 4.00e-02 9.29e+01 dihedral pdb=" CA GLU C 111 " pdb=" C GLU C 111 " pdb=" N GLN C 112 " pdb=" CA GLN C 112 " ideal model delta harmonic sigma weight residual -180.00 -131.81 -48.19 0 5.00e+00 4.00e-02 9.29e+01 dihedral pdb=" CA GLU D 111 " pdb=" C GLU D 111 " pdb=" N GLN D 112 " pdb=" CA GLN D 112 " ideal model delta harmonic sigma weight residual 180.00 -131.83 -48.17 0 5.00e+00 4.00e-02 9.28e+01 ... (remaining 17597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3536 0.087 - 0.174: 807 0.174 - 0.261: 89 0.261 - 0.348: 24 0.348 - 0.436: 16 Chirality restraints: 4472 Sorted by residual: chirality pdb=" CB VAL A 479 " pdb=" CA VAL A 479 " pdb=" CG1 VAL A 479 " pdb=" CG2 VAL A 479 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CB VAL H 479 " pdb=" CA VAL H 479 " pdb=" CG1 VAL H 479 " pdb=" CG2 VAL H 479 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB VAL B 479 " pdb=" CA VAL B 479 " pdb=" CG1 VAL B 479 " pdb=" CG2 VAL B 479 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 4469 not shown) Planarity restraints: 4928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 72 " 0.019 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C THR C 72 " -0.063 2.00e-02 2.50e+03 pdb=" O THR C 72 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL C 73 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 72 " -0.019 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C THR D 72 " 0.063 2.00e-02 2.50e+03 pdb=" O THR D 72 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL D 73 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 72 " -0.019 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C THR G 72 " 0.063 2.00e-02 2.50e+03 pdb=" O THR G 72 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL G 73 " -0.020 2.00e-02 2.50e+03 ... (remaining 4925 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4162 2.75 - 3.29: 28651 3.29 - 3.82: 51766 3.82 - 4.36: 58394 4.36 - 4.90: 89307 Nonbonded interactions: 232280 Sorted by model distance: nonbonded pdb=" O PRO B 64 " pdb=" OG1 THR B 383 " model vdw 2.208 2.440 nonbonded pdb=" O PRO A 64 " pdb=" OG1 THR A 383 " model vdw 2.208 2.440 nonbonded pdb=" O PRO C 64 " pdb=" OG1 THR C 383 " model vdw 2.209 2.440 nonbonded pdb=" O PRO G 64 " pdb=" OG1 THR G 383 " model vdw 2.209 2.440 nonbonded pdb=" O PRO H 64 " pdb=" OG1 THR H 383 " model vdw 2.209 2.440 ... (remaining 232275 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.150 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 72.610 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 : 0.016 0.289 28864 Z= 1.076 Angle : 1.928 24.685 39136 Z= 1.081 Chirality : 0.078 0.436 4472 Planarity : 0.008 0.059 4928 Dihedral : 20.466 168.874 10976 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 14.82 % Allowed : 15.90 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.92 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.11), residues: 3576 helix: -3.27 (0.10), residues: 1192 sheet: -3.01 (0.27), residues: 272 loop : -2.79 (0.11), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS B 454 PHE 0.024 0.004 PHE B 456 TYR 0.027 0.004 TYR E 411 ARG 0.036 0.003 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1883 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 440 poor density : 1443 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 440 outliers final: 183 residues processed: 1615 average time/residue: 0.4103 time to fit residues: 1020.9570 Evaluate side-chains 1235 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1052 time to evaluate : 3.207 Switching outliers to nearest non-outliers outliers start: 183 outliers final: 0 residues processed: 183 average time/residue: 0.3317 time to fit residues: 107.1357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.7980 chunk 272 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 282 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 326 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 298 GLN A 466 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 283 GLN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS C 230 ASN C 298 GLN C 343 GLN C 466 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 283 GLN ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN D 466 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN E 298 GLN E 466 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN F 283 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN F 466 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN G 298 GLN G 466 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN H 466 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 28864 Z= 0.260 Angle : 0.890 9.985 39136 Z= 0.440 Chirality : 0.049 0.179 4472 Planarity : 0.005 0.045 4928 Dihedral : 19.255 170.072 4368 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.40 % Allowed : 7.11 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.12), residues: 3576 helix: -2.22 (0.13), residues: 1176 sheet: -2.77 (0.21), residues: 480 loop : -1.99 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 372 PHE 0.020 0.002 PHE A 114 TYR 0.024 0.003 TYR C 400 ARG 0.004 0.001 ARG F 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1331 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 1333 average time/residue: 0.3947 time to fit residues: 838.0096 Evaluate side-chains 1022 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1019 time to evaluate : 3.287 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2501 time to fit residues: 5.8514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 272 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 327 optimal weight: 0.9990 chunk 353 optimal weight: 10.0000 chunk 291 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 262 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 230 ASN E 465 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN F 298 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28864 Z= 0.310 Angle : 0.863 9.944 39136 Z= 0.433 Chirality : 0.049 0.184 4472 Planarity : 0.005 0.050 4928 Dihedral : 18.890 166.572 4368 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 30.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.24 % Allowed : 5.15 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.13), residues: 3576 helix: -1.88 (0.13), residues: 1128 sheet: -3.30 (0.20), residues: 424 loop : -1.81 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 372 PHE 0.018 0.002 PHE H 456 TYR 0.037 0.003 TYR C 484 ARG 0.003 0.001 ARG G 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1304 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1297 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 1298 average time/residue: 0.3975 time to fit residues: 820.2064 Evaluate side-chains 975 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 972 time to evaluate : 3.032 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2685 time to fit residues: 5.8106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 328 optimal weight: 9.9990 chunk 347 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 311 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 265 GLN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN C 448 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN G 448 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 GLN H 283 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28864 Z= 0.275 Angle : 0.834 11.716 39136 Z= 0.414 Chirality : 0.050 0.221 4472 Planarity : 0.004 0.053 4928 Dihedral : 18.591 166.009 4368 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 29.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.10 % Allowed : 3.67 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.13), residues: 3576 helix: -1.77 (0.13), residues: 1176 sheet: -3.47 (0.18), residues: 504 loop : -1.78 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 466 PHE 0.018 0.002 PHE B 139 TYR 0.030 0.002 TYR B 484 ARG 0.009 0.001 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1382 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1379 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 1379 average time/residue: 0.3802 time to fit residues: 842.2115 Evaluate side-chains 996 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 994 time to evaluate : 3.312 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6592 time to fit residues: 6.3248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 259 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 177 optimal weight: 0.0870 chunk 312 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS A 283 GLN A 448 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 448 GLN C 230 ASN ** C 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 283 GLN D 448 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN E 448 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN F 265 GLN F 283 GLN F 448 GLN F 465 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 GLN ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 28864 Z= 0.321 Angle : 0.837 10.585 39136 Z= 0.420 Chirality : 0.049 0.194 4472 Planarity : 0.004 0.072 4928 Dihedral : 18.463 166.275 4368 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 32.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.03 % Allowed : 4.92 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.13), residues: 3576 helix: -1.61 (0.14), residues: 1160 sheet: -3.42 (0.18), residues: 504 loop : -1.80 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 137 PHE 0.025 0.002 PHE G 139 TYR 0.039 0.002 TYR G 233 ARG 0.004 0.001 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1277 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1277 average time/residue: 0.3868 time to fit residues: 790.8413 Evaluate side-chains 1001 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1001 time to evaluate : 3.280 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 2.9990 chunk 313 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 204 optimal weight: 9.9990 chunk 85 optimal weight: 0.0470 chunk 348 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 overall best weight: 2.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 283 GLN B 448 GLN ** C 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 448 GLN D 465 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS F 265 GLN F 283 GLN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 448 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 GLN ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 28864 Z= 0.300 Angle : 0.844 11.760 39136 Z= 0.419 Chirality : 0.050 0.236 4472 Planarity : 0.004 0.056 4928 Dihedral : 18.388 167.664 4368 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 32.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.78 (0.13), residues: 3576 helix: -1.49 (0.14), residues: 1152 sheet: -2.82 (0.20), residues: 512 loop : -1.73 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 466 PHE 0.019 0.002 PHE E 139 TYR 0.033 0.003 TYR A 233 ARG 0.005 0.000 ARG E 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1324 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1324 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1324 average time/residue: 0.4016 time to fit residues: 858.7590 Evaluate side-chains 1009 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1009 time to evaluate : 3.385 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 346 optimal weight: 0.0060 chunk 217 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 160 optimal weight: 0.5980 overall best weight: 2.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 448 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 283 GLN B 448 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN F 283 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN G 283 GLN ** G 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28864 Z= 0.265 Angle : 0.852 12.177 39136 Z= 0.417 Chirality : 0.050 0.258 4472 Planarity : 0.004 0.072 4928 Dihedral : 18.397 168.151 4368 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 29.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.68 (0.13), residues: 3576 helix: -1.45 (0.15), residues: 1152 sheet: -2.96 (0.23), residues: 376 loop : -1.73 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 372 PHE 0.032 0.002 PHE C 456 TYR 0.040 0.002 TYR C 484 ARG 0.004 0.001 ARG E 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1317 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1317 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1317 average time/residue: 0.3816 time to fit residues: 803.6938 Evaluate side-chains 1022 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1022 time to evaluate : 3.354 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 10.0000 chunk 138 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 272 optimal weight: 0.3980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 448 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 448 GLN C 171 HIS C 198 ASN C 283 GLN ** C 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN G 465 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28864 Z= 0.243 Angle : 0.850 12.968 39136 Z= 0.413 Chirality : 0.049 0.247 4472 Planarity : 0.004 0.072 4928 Dihedral : 18.263 166.710 4368 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 28.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.76 (0.13), residues: 3576 helix: -1.48 (0.14), residues: 1168 sheet: -2.97 (0.22), residues: 416 loop : -1.76 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 372 PHE 0.032 0.002 PHE C 456 TYR 0.032 0.002 TYR B 484 ARG 0.004 0.001 ARG G 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1314 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1314 average time/residue: 0.3851 time to fit residues: 804.1016 Evaluate side-chains 1023 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1023 time to evaluate : 3.152 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 2.9990 chunk 332 optimal weight: 0.3980 chunk 303 optimal weight: 2.9990 chunk 323 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 140 optimal weight: 0.9990 chunk 253 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 292 optimal weight: 0.8980 chunk 305 optimal weight: 4.9990 chunk 322 optimal weight: 0.0970 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 368 GLN A 448 GLN A 465 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN C 465 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN H 465 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28864 Z= 0.227 Angle : 0.856 13.278 39136 Z= 0.413 Chirality : 0.050 0.265 4472 Planarity : 0.004 0.068 4928 Dihedral : 18.158 166.665 4368 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 26.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.72 (0.13), residues: 3576 helix: -1.53 (0.14), residues: 1192 sheet: -2.65 (0.26), residues: 296 loop : -1.86 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 454 PHE 0.021 0.002 PHE E 456 TYR 0.045 0.002 TYR C 484 ARG 0.009 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1350 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1350 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1350 average time/residue: 0.3833 time to fit residues: 830.5276 Evaluate side-chains 1042 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1042 time to evaluate : 2.991 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 0.8980 chunk 341 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 358 optimal weight: 1.9990 chunk 330 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 448 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN C 448 GLN C 465 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN G 283 GLN ** G 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28864 Z= 0.231 Angle : 0.875 13.234 39136 Z= 0.422 Chirality : 0.050 0.234 4472 Planarity : 0.005 0.053 4928 Dihedral : 18.108 167.858 4368 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.03 % Allowed : 0.51 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.83 (0.13), residues: 3576 helix: -1.62 (0.14), residues: 1192 sheet: -2.72 (0.21), residues: 456 loop : -1.79 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 372 PHE 0.021 0.002 PHE G 456 TYR 0.037 0.002 TYR C 484 ARG 0.011 0.001 ARG G 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1342 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1343 average time/residue: 0.3751 time to fit residues: 810.8748 Evaluate side-chains 1025 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1024 time to evaluate : 2.906 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2666 time to fit residues: 4.3983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 10.0000 chunk 304 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 286 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 293 optimal weight: 8.9990 chunk 36 optimal weight: 0.0170 chunk 52 optimal weight: 0.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN C 448 GLN C 465 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.126818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.090132 restraints weight = 56301.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.093994 restraints weight = 36326.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096872 restraints weight = 26171.766| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28864 Z= 0.249 Angle : 0.857 14.000 39136 Z= 0.421 Chirality : 0.049 0.260 4472 Planarity : 0.005 0.077 4928 Dihedral : 18.061 168.873 4368 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 28.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.88 (0.13), residues: 3576 helix: -1.65 (0.14), residues: 1208 sheet: -2.52 (0.24), residues: 392 loop : -1.95 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 454 PHE 0.025 0.002 PHE G 99 TYR 0.040 0.002 TYR E 233 ARG 0.006 0.001 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11225.26 seconds wall clock time: 201 minutes 46.97 seconds (12106.97 seconds total)