Starting phenix.real_space_refine on Sat Jul 4 09:00:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u02_20594/07_2026/6u02_20594.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u02_20594/07_2026/6u02_20594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u02_20594/07_2026/6u02_20594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u02_20594/07_2026/6u02_20594.map" model { file = "/net/cci-nas-00/data/ceres_data/6u02_20594/07_2026/6u02_20594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u02_20594/07_2026/6u02_20594.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6u02_20594/07_2026/6u02_20594.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u02_20594/07_2026/6u02_20594.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.160 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 12284 2.51 5 N 3336 2.21 5 O 3932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19672 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "M" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, E, J, C, F, I, D, G, K, N, O, P Time building chain proxies: 3.51, per 1000 atoms: 0.18 Number of scatterers: 19672 At special positions: 0 Unit cell: (198.79, 198.79, 84.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3932 8.00 N 3336 7.00 C 12284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.04 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.04 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.02 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.02 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.02 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.09 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 417 " distance=2.04 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.04 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.04 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.04 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.04 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=2.03 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.02 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.02 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.02 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 237 " distance=2.02 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.02 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 291 " distance=2.02 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.02 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.02 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.02 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.02 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.02 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.02 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.04 Simple disulfide: pdb=" SG CYS E 421 " - pdb=" SG CYS E 447 " distance=2.04 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.09 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.09 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.09 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN M 5 " - " MAN M 6 " " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN P 4 " - " MAN P 5 " " MAN P 5 " - " MAN P 6 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " MAN M 7 " - " MAN M 8 " " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA O 3 " - " MAN O 4 " " MAN O 7 " - " MAN O 8 " " BMA P 3 " - " MAN P 4 " " MAN P 7 " - " MAN P 8 " ALPHA1-6 " BMA M 3 " - " MAN M 7 " " MAN M 7 " - " MAN M 9 " " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 9 " " BMA O 3 " - " MAN O 7 " " MAN O 7 " - " MAN O 9 " " BMA P 3 " - " MAN P 7 " " MAN P 7 " - " MAN P 9 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A 510 " - " ASN A 86 " " NAG A 511 " - " ASN A 146 " " NAG B 510 " - " ASN B 86 " " NAG B 511 " - " ASN B 146 " " NAG E 510 " - " ASN E 86 " " NAG E 511 " - " ASN E 146 " " NAG J 510 " - " ASN J 86 " " NAG J 511 " - " ASN J 146 " " NAG M 1 " - " ASN A 200 " " NAG N 1 " - " ASN B 200 " " NAG O 1 " - " ASN E 200 " " NAG P 1 " - " ASN J 200 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 834.8 milliseconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 48 sheets defined 7.0% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 356 through 359 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.131A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 356 through 359 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.131A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 356 through 359 Processing helix chain 'E' and resid 463 through 468 Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.131A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 104 through 109 Processing helix chain 'J' and resid 142 through 146 Processing helix chain 'J' and resid 356 through 359 Processing helix chain 'J' and resid 463 through 468 Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.131A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.725A pdb=" N SER A 445 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA A 420 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 125 removed outlier: 4.716A pdb=" N LEU A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR A 138 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 158 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.633A pdb=" N ALA A 203 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU A 214 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 205 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 236 through 244 removed outlier: 7.433A pdb=" N THR A 252 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER A 267 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A 254 " --> pdb=" O TRP A 265 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TRP A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR A 256 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 283 removed outlier: 4.626A pdb=" N CYS A 278 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS A 280 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY A 282 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.870A pdb=" N SER A 372 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.643A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.251A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.251A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.606A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AB4, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.726A pdb=" N SER B 445 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA B 420 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 115 through 125 removed outlier: 4.715A pdb=" N LEU B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR B 138 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU B 158 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.633A pdb=" N ALA B 203 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU B 214 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 205 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 236 through 244 removed outlier: 7.434A pdb=" N THR B 252 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER B 267 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE B 254 " --> pdb=" O TRP B 265 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR B 256 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 276 through 283 removed outlier: 4.627A pdb=" N CYS B 278 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N THR B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS B 280 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY B 282 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.870A pdb=" N SER B 372 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU B 399 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 393 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.644A pdb=" N SER C 67 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.607A pdb=" N MET D 34 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA D 40 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AC7, first strand: chain 'E' and resid 96 through 102 removed outlier: 6.726A pdb=" N SER E 445 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA E 420 " --> pdb=" O SER E 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 115 through 125 removed outlier: 4.715A pdb=" N LEU E 115 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR E 138 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU E 158 " --> pdb=" O GLU E 174 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 179 through 184 removed outlier: 6.634A pdb=" N ALA E 203 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU E 214 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL E 205 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 236 through 244 removed outlier: 7.434A pdb=" N THR E 252 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER E 267 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE E 254 " --> pdb=" O TRP E 265 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TRP E 265 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR E 256 " --> pdb=" O LEU E 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 276 through 283 removed outlier: 4.626A pdb=" N CYS E 278 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR E 290 " --> pdb=" O CYS E 278 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS E 280 " --> pdb=" O THR E 288 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR E 288 " --> pdb=" O CYS E 280 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY E 282 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 353 through 354 removed outlier: 6.870A pdb=" N SER E 372 " --> pdb=" O LEU E 399 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU E 399 " --> pdb=" O SER E 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR E 374 " --> pdb=" O ILE E 397 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 393 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.644A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.607A pdb=" N MET G 34 " --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA G 40 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLY G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 11 Processing sheet with id=AE1, first strand: chain 'J' and resid 96 through 102 removed outlier: 6.726A pdb=" N SER J 445 " --> pdb=" O TYR J 100 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA J 420 " --> pdb=" O SER J 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 115 through 125 removed outlier: 4.716A pdb=" N LEU J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR J 138 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU J 158 " --> pdb=" O GLU J 174 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 179 through 184 removed outlier: 6.633A pdb=" N ALA J 203 " --> pdb=" O GLU J 214 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU J 214 " --> pdb=" O ALA J 203 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL J 205 " --> pdb=" O VAL J 212 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 236 through 244 removed outlier: 7.434A pdb=" N THR J 252 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER J 267 " --> pdb=" O THR J 252 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE J 254 " --> pdb=" O TRP J 265 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TRP J 265 " --> pdb=" O ILE J 254 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR J 256 " --> pdb=" O LEU J 263 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 276 through 283 removed outlier: 4.626A pdb=" N CYS J 278 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR J 290 " --> pdb=" O CYS J 278 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS J 280 " --> pdb=" O THR J 288 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR J 288 " --> pdb=" O CYS J 280 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY J 282 " --> pdb=" O GLY J 286 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY J 286 " --> pdb=" O GLY J 282 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 353 through 354 removed outlier: 6.870A pdb=" N SER J 372 " --> pdb=" O LEU J 399 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU J 399 " --> pdb=" O SER J 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR J 374 " --> pdb=" O ILE J 397 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN J 393 " --> pdb=" O LYS J 378 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.644A pdb=" N SER I 67 " --> pdb=" O ASP I 70 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.251A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.251A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.606A pdb=" N MET K 34 " --> pdb=" O ASN K 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA K 40 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 11 684 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3633 1.31 - 1.45: 6238 1.45 - 1.58: 10129 1.58 - 1.71: 16 1.71 - 1.85: 144 Bond restraints: 20160 Sorted by residual: bond pdb=" C1 NAG A 510 " pdb=" O5 NAG A 510 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C1 NAG J 510 " pdb=" O5 NAG J 510 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C1 NAG B 510 " pdb=" O5 NAG B 510 " ideal model delta sigma weight residual 1.406 1.543 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C1 NAG E 510 " pdb=" O5 NAG E 510 " ideal model delta sigma weight residual 1.406 1.543 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.542 -0.136 2.00e-02 2.50e+03 4.63e+01 ... (remaining 20155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 22390 2.19 - 4.37: 4178 4.37 - 6.56: 714 6.56 - 8.74: 106 8.74 - 10.93: 24 Bond angle restraints: 27412 Sorted by residual: angle pdb=" C TYR A 341 " pdb=" N PRO A 342 " pdb=" CA PRO A 342 " ideal model delta sigma weight residual 120.03 129.26 -9.23 9.90e-01 1.02e+00 8.68e+01 angle pdb=" C TYR J 341 " pdb=" N PRO J 342 " pdb=" CA PRO J 342 " ideal model delta sigma weight residual 120.03 129.25 -9.22 9.90e-01 1.02e+00 8.67e+01 angle pdb=" C TYR B 341 " pdb=" N PRO B 342 " pdb=" CA PRO B 342 " ideal model delta sigma weight residual 120.03 129.24 -9.21 9.90e-01 1.02e+00 8.66e+01 angle pdb=" C TYR E 341 " pdb=" N PRO E 342 " pdb=" CA PRO E 342 " ideal model delta sigma weight residual 120.03 129.22 -9.19 9.90e-01 1.02e+00 8.62e+01 angle pdb=" C ASP A 330 " pdb=" N PRO A 331 " pdb=" CA PRO A 331 " ideal model delta sigma weight residual 120.98 130.76 -9.78 1.07e+00 8.73e-01 8.35e+01 ... (remaining 27407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11204 17.93 - 35.86: 330 35.86 - 53.78: 66 53.78 - 71.71: 40 71.71 - 89.64: 12 Dihedral angle restraints: 11652 sinusoidal: 4596 harmonic: 7056 Sorted by residual: dihedral pdb=" CB CYS J 318 " pdb=" SG CYS J 318 " pdb=" SG CYS J 337 " pdb=" CB CYS J 337 " ideal model delta sinusoidal sigma weight residual 93.00 130.69 -37.69 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CB CYS B 318 " pdb=" SG CYS B 318 " pdb=" SG CYS B 337 " pdb=" CB CYS B 337 " ideal model delta sinusoidal sigma weight residual 93.00 130.68 -37.68 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 130.65 -37.65 1 1.00e+01 1.00e-02 2.00e+01 ... (remaining 11649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2212 0.102 - 0.204: 716 0.204 - 0.306: 111 0.306 - 0.408: 21 0.408 - 0.510: 4 Chirality restraints: 3064 Sorted by residual: chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.32e+01 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.30e+01 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.19e+01 ... (remaining 3061 not shown) Planarity restraints: 3476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 155 " -0.056 2.00e-02 2.50e+03 2.85e-02 1.63e+01 pdb=" CG TYR B 155 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 155 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 155 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 155 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 155 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 155 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 155 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 155 " -0.056 2.00e-02 2.50e+03 2.84e-02 1.61e+01 pdb=" CG TYR E 155 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR E 155 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR E 155 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR E 155 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 155 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR E 155 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 155 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 155 " 0.056 2.00e-02 2.50e+03 2.83e-02 1.60e+01 pdb=" CG TYR J 155 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR J 155 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR J 155 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR J 155 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR J 155 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR J 155 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR J 155 " 0.033 2.00e-02 2.50e+03 ... (remaining 3473 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 9692 2.94 - 3.43: 16837 3.43 - 3.92: 34456 3.92 - 4.41: 41521 4.41 - 4.90: 67558 Nonbonded interactions: 170064 Sorted by model distance: nonbonded pdb=" N ASP B 434 " pdb=" OD1 ASP B 434 " model vdw 2.449 3.120 nonbonded pdb=" N ASP J 416 " pdb=" OD1 ASP J 416 " model vdw 2.450 3.120 nonbonded pdb=" N ASP J 434 " pdb=" OD1 ASP J 434 " model vdw 2.450 3.120 nonbonded pdb=" N ASP E 416 " pdb=" OD1 ASP E 416 " model vdw 2.450 3.120 nonbonded pdb=" N ASP A 434 " pdb=" OD1 ASP A 434 " model vdw 2.451 3.120 ... (remaining 170059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'D' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.470 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 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 : 0.022 0.138 20248 Z= 1.169 Angle : 1.806 10.926 27632 Z= 1.185 Chirality : 0.101 0.510 3064 Planarity : 0.009 0.044 3464 Dihedral : 10.460 89.641 7032 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.49 % Allowed : 2.31 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.17), residues: 2428 helix: -2.15 (0.51), residues: 48 sheet: 1.08 (0.17), residues: 892 loop : 0.31 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 292 TYR 0.056 0.008 TYR B 155 PHE 0.032 0.008 PHE B 241 TRP 0.045 0.008 TRP A 456 HIS 0.006 0.002 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.02240 / 1.17 (20160) covalent geometry : angle 1.79095 / 1.18 (27412) SS BOND : bond 0.01923 / 1.47 ( 44) SS BOND : angle 3.40782 / 2.43 ( 88) hydrogen bonds : bond 0.16992 / 11.59 ( 652) hydrogen bonds : angle 8.80511 / 6.19 ( 1536) link_ALPHA1-2 : bond 0.03500 / 1.89 ( 8) link_ALPHA1-2 : angle 3.43187 / 2.18 ( 24) link_ALPHA1-3 : bond 0.03201 / 1.73 ( 8) link_ALPHA1-3 : angle 2.32301 / 1.49 ( 24) link_ALPHA1-6 : bond 0.02368 / 1.28 ( 8) link_ALPHA1-6 : angle 2.92899 / 1.92 ( 24) link_BETA1-4 : bond 0.03579 / 1.93 ( 8) link_BETA1-4 : angle 3.25865 / 1.92 ( 24) link_NAG-ASN : bond 0.02841 / 1.86 ( 12) link_NAG-ASN : angle 2.80047 / 1.94 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 614 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 SER cc_start: 0.7720 (p) cc_final: 0.7407 (m) REVERT: L 54 LEU cc_start: 0.7564 (mt) cc_final: 0.7143 (mt) REVERT: B 372 SER cc_start: 0.6967 (p) cc_final: 0.6711 (m) REVERT: E 372 SER cc_start: 0.7259 (p) cc_final: 0.6968 (m) REVERT: J 372 SER cc_start: 0.7742 (p) cc_final: 0.7410 (m) REVERT: I 54 LEU cc_start: 0.7628 (mt) cc_final: 0.7229 (mt) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.1382 time to fit residues: 131.7579 Evaluate side-chains 366 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN A 329 ASN L 37 GLN H 72 HIS B 325 ASN B 329 ASN D 50 ASN D 72 HIS D 81 GLN E 329 ASN F 37 GLN G 50 ASN G 72 HIS J 325 ASN I 37 GLN K 72 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.092877 restraints weight = 24856.401| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.35 r_work: 0.2972 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20248 Z= 0.189 Angle : 0.722 8.584 27632 Z= 0.380 Chirality : 0.047 0.206 3064 Planarity : 0.005 0.054 3464 Dihedral : 5.341 21.734 2700 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.47 % Favored : 97.36 % Rotamer: Outliers : 2.70 % Allowed : 9.54 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2428 helix: -2.02 (0.66), residues: 48 sheet: 0.51 (0.16), residues: 980 loop : 0.13 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 430 TYR 0.017 0.002 TYR G 79 PHE 0.033 0.002 PHE H 67 TRP 0.031 0.003 TRP J 206 HIS 0.006 0.002 HIS G 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (20160) covalent geometry : angle 0.70729 / 0.38 (27412) SS BOND : bond 0.00635 / 0.45 ( 44) SS BOND : angle 1.49873 / 1.00 ( 88) hydrogen bonds : bond 0.04453 / 2.97 ( 652) hydrogen bonds : angle 6.80013 / 4.73 ( 1536) link_ALPHA1-2 : bond 0.01558 / 0.88 ( 8) link_ALPHA1-2 : angle 1.38805 / 0.99 ( 24) link_ALPHA1-3 : bond 0.00717 / 0.39 ( 8) link_ALPHA1-3 : angle 1.49131 / 1.10 ( 24) link_ALPHA1-6 : bond 0.01132 / 0.62 ( 8) link_ALPHA1-6 : angle 1.77424 / 1.23 ( 24) link_BETA1-4 : bond 0.01041 / 0.56 ( 8) link_BETA1-4 : angle 2.68667 / 1.86 ( 24) link_NAG-ASN : bond 0.00294 / 0.18 ( 12) link_NAG-ASN : angle 2.00070 / 1.26 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 428 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 372 SER cc_start: 0.8207 (p) cc_final: 0.7697 (m) REVERT: L 11 LEU cc_start: 0.7506 (mt) cc_final: 0.7260 (mp) REVERT: L 24 ARG cc_start: 0.7446 (ttm110) cc_final: 0.7109 (tpp80) REVERT: L 54 LEU cc_start: 0.8367 (mt) cc_final: 0.8130 (mm) REVERT: L 82 ASP cc_start: 0.6619 (OUTLIER) cc_final: 0.6255 (t0) REVERT: H 34 MET cc_start: 0.6718 (mmp) cc_final: 0.6464 (mmt) REVERT: B 372 SER cc_start: 0.7685 (p) cc_final: 0.7292 (m) REVERT: B 413 TYR cc_start: 0.7986 (m-80) cc_final: 0.7779 (m-80) REVERT: B 433 GLU cc_start: 0.8195 (mp0) cc_final: 0.7827 (mp0) REVERT: C 24 ARG cc_start: 0.7462 (tpp80) cc_final: 0.6981 (tpp80) REVERT: C 54 LEU cc_start: 0.8129 (mt) cc_final: 0.7929 (mm) REVERT: D 55 SER cc_start: 0.6746 (t) cc_final: 0.6529 (m) REVERT: E 118 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.6636 (ttp-170) REVERT: E 372 SER cc_start: 0.7832 (p) cc_final: 0.7381 (m) REVERT: E 413 TYR cc_start: 0.8054 (m-80) cc_final: 0.7844 (m-80) REVERT: E 433 GLU cc_start: 0.8288 (mp0) cc_final: 0.7942 (mp0) REVERT: F 24 ARG cc_start: 0.7536 (tpp80) cc_final: 0.6881 (tpp80) REVERT: J 372 SER cc_start: 0.8179 (p) cc_final: 0.7675 (m) REVERT: I 24 ARG cc_start: 0.8050 (ttm170) cc_final: 0.7544 (ttm110) REVERT: I 54 LEU cc_start: 0.8452 (mt) cc_final: 0.8156 (mm) REVERT: K 34 MET cc_start: 0.6687 (mmp) cc_final: 0.6413 (mmt) REVERT: K 89 VAL cc_start: 0.7614 (t) cc_final: 0.7225 (p) outliers start: 57 outliers final: 31 residues processed: 461 average time/residue: 0.1340 time to fit residues: 95.4861 Evaluate side-chains 386 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 353 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.6359 > 50: distance: 91 - 126: 36.620 distance: 94 - 123: 17.446 distance: 119 - 123: 19.496 distance: 123 - 124: 31.221 distance: 124 - 125: 31.411 distance: 124 - 127: 21.805 distance: 125 - 126: 37.041 distance: 125 - 137: 20.118 distance: 127 - 128: 15.297 distance: 128 - 129: 6.441 distance: 128 - 130: 3.326 distance: 129 - 131: 4.812 distance: 130 - 132: 3.824 distance: 131 - 132: 5.711 distance: 132 - 134: 4.460 distance: 133 - 135: 3.625 distance: 134 - 136: 5.282 distance: 135 - 136: 5.006 distance: 137 - 138: 19.142 distance: 137 - 143: 4.744 distance: 138 - 139: 11.171 distance: 138 - 141: 12.518 distance: 139 - 140: 16.862 distance: 139 - 144: 8.343 distance: 141 - 142: 10.035 distance: 142 - 143: 16.150 distance: 144 - 145: 17.968 distance: 145 - 146: 11.932 distance: 145 - 148: 17.594 distance: 146 - 147: 20.064 distance: 146 - 152: 29.529 distance: 148 - 149: 13.628 distance: 149 - 150: 9.089 distance: 149 - 151: 6.894 distance: 152 - 153: 14.024 distance: 153 - 154: 23.531 distance: 153 - 156: 31.280 distance: 154 - 155: 25.863 distance: 154 - 158: 8.155 distance: 156 - 157: 25.224 distance: 158 - 159: 4.428 distance: 159 - 160: 12.085 distance: 159 - 162: 15.978 distance: 160 - 161: 12.368 distance: 160 - 164: 16.477 distance: 162 - 163: 7.888 distance: 164 - 165: 14.838 distance: 164 - 170: 15.176 distance: 165 - 166: 21.707 distance: 165 - 168: 27.525 distance: 166 - 167: 16.552 distance: 166 - 171: 16.135 distance: 168 - 169: 9.116 distance: 169 - 170: 22.368 distance: 171 - 172: 11.364 distance: 171 - 177: 27.320 distance: 172 - 173: 32.477 distance: 172 - 175: 28.254 distance: 173 - 174: 44.793 distance: 173 - 178: 39.379 distance: 175 - 176: 24.541 distance: 176 - 177: 31.448 distance: 178 - 179: 24.058 distance: 179 - 180: 22.872 distance: 179 - 182: 13.703 distance: 180 - 181: 15.615 distance: 180 - 185: 21.054 distance: 182 - 183: 34.844 distance: 182 - 184: 15.292 distance: 185 - 186: 7.623 distance: 186 - 187: 8.508 distance: 186 - 189: 6.859 distance: 187 - 188: 3.857 distance: 187 - 192: 5.591 distance: 189 - 190: 20.340 distance: 189 - 191: 16.044 distance: 192 - 193: 12.689 distance: 193 - 194: 5.391 distance: 193 - 196: 15.713 distance: 194 - 195: 7.532 distance: 194 - 204: 7.713 distance: 196 - 197: 11.110 distance: 197 - 198: 7.859 distance: 197 - 199: 7.997 distance: 198 - 200: 11.298 distance: 199 - 201: 5.649 distance: 200 - 202: 9.387 distance: 201 - 202: 11.012 distance: 202 - 203: 6.711