Starting phenix.real_space_refine on Wed May 28 03:29:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zk2_60165/05_2025/8zk2_60165.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zk2_60165/05_2025/8zk2_60165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zk2_60165/05_2025/8zk2_60165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zk2_60165/05_2025/8zk2_60165.map" model { file = "/net/cci-nas-00/data/ceres_data/8zk2_60165/05_2025/8zk2_60165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zk2_60165/05_2025/8zk2_60165.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4470 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 7 5.49 5 Mg 55 5.21 5 S 133 5.16 5 C 18777 2.51 5 N 3834 2.21 5 O 4137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26948 Number of models: 1 Model: "" Number of chains: 72 Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2618 Classifications: {'peptide': 342} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 314} Chain: "L" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2163 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "M" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2269 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 269} Chain: "H" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1906 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "A" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "F" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "I" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "J" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "K" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "N" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "O" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "P" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "Q" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "R" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "S" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "T" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "U" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "V" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "W" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "X" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "Y" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "Z" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 369 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "a" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "b" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "c" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "d" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "e" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "f" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "g" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "h" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "i" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "j" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {' MG': 3, '8K6': 1, 'HEC': 4, 'PGV': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "L" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 338 Unusual residues: {'8K6': 5, 'BCL': 2, 'BPH': 1, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 401 Unusual residues: {' FE': 1, '8K6': 1, 'BCL': 2, 'BPH': 1, 'CRT': 1, 'MQ8': 1, 'PGV': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 171 Unusual residues: {' MG': 1, '8K6': 4, 'PGV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 163 Unusual residues: {'8K6': 2, 'BCL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'8K6': 1, 'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'8K6': 1, 'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 227 Unusual residues: {'BCL': 2, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 168 Unusual residues: {'8K6': 2, 'BCL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "W" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'8K6': 1, 'BCL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "a" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'8K6': 1, 'BCL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'8K6': 1, 'BCL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 212 Unusual residues: {'8K6': 2, 'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 16.39, per 1000 atoms: 0.61 Number of scatterers: 26948 At special positions: 0 Unit cell: (139.36, 126.88, 133.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 133 16.00 P 7 15.00 Mg 55 11.99 O 4137 8.00 N 3834 7.00 C 18777 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 - 3.00 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=63, symmetry=0 Number of additional bonds: simple=63, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.82 Conformation dependent library (CDL) restraints added in 2.9 seconds 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5122 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 9 sheets defined 62.1% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'C' and resid 26 through 45 Processing helix chain 'C' and resid 66 through 75 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 94 through 99 removed outlier: 3.538A pdb=" N VAL C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 124 Processing helix chain 'C' and resid 128 through 133 removed outlier: 3.888A pdb=" N ASN C 131 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS C 133 " --> pdb=" O CYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 164 removed outlier: 3.823A pdb=" N ILE C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 174 through 179 removed outlier: 4.301A pdb=" N CYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 273 through 277 Processing helix chain 'C' and resid 291 through 310 removed outlier: 3.581A pdb=" N THR C 295 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 333 through 339 removed outlier: 4.113A pdb=" N CYS C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.542A pdb=" N GLU C 348 " --> pdb=" O MET C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.997A pdb=" N ALA C 359 " --> pdb=" O SER C 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 33 through 56 Processing helix chain 'L' and resid 72 through 76 Processing helix chain 'L' and resid 85 through 114 Processing helix chain 'L' and resid 117 through 135 removed outlier: 3.617A pdb=" N PHE L 125 " --> pdb=" O PHE L 121 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA L 126 " --> pdb=" O ALA L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 142 Processing helix chain 'L' and resid 143 through 147 Processing helix chain 'L' and resid 153 through 165 removed outlier: 3.506A pdb=" N ASP L 157 " --> pdb=" O MET L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 167 No H-bonds generated for 'chain 'L' and resid 166 through 167' Processing helix chain 'L' and resid 168 through 171 Processing helix chain 'L' and resid 172 through 201 Processing helix chain 'L' and resid 210 through 222 removed outlier: 3.657A pdb=" N PHE L 218 " --> pdb=" O GLU L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 252 removed outlier: 3.509A pdb=" N ILE L 231 " --> pdb=" O GLY L 227 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N HIS L 232 " --> pdb=" O THR L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 264 Processing helix chain 'L' and resid 265 through 270 Processing helix chain 'M' and resid 39 through 44 removed outlier: 3.832A pdb=" N ILE M 43 " --> pdb=" O TRP M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 82 through 90 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 109 through 112 Processing helix chain 'M' and resid 113 through 141 Processing helix chain 'M' and resid 145 through 163 removed outlier: 3.640A pdb=" N TRP M 149 " --> pdb=" O THR M 145 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER M 153 " --> pdb=" O TRP M 149 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA M 154 " --> pdb=" O ALA M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 170 Processing helix chain 'M' and resid 171 through 175 Processing helix chain 'M' and resid 180 through 194 removed outlier: 3.806A pdb=" N LEU M 184 " --> pdb=" O ILE M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 199 Processing helix chain 'M' and resid 200 through 227 Processing helix chain 'M' and resid 228 through 231 Processing helix chain 'M' and resid 234 through 241 Processing helix chain 'M' and resid 243 through 258 removed outlier: 3.614A pdb=" N TRP M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 287 removed outlier: 3.937A pdb=" N THR M 278 " --> pdb=" O ALA M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 302 Processing helix chain 'H' and resid 10 through 34 Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'H' and resid 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'H' and resid 217 through 222 removed outlier: 3.552A pdb=" N ALA H 222 " --> pdb=" O ALA H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 252 removed outlier: 3.809A pdb=" N THR H 249 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 47 removed outlier: 3.663A pdb=" N VAL B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.959A pdb=" N TRP A 9 " --> pdb=" O HIS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 38 Processing helix chain 'D' and resid 14 through 47 Processing helix chain 'E' and resid 5 through 11 removed outlier: 3.875A pdb=" N TRP E 9 " --> pdb=" O HIS E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 38 Processing helix chain 'F' and resid 14 through 47 removed outlier: 3.569A pdb=" N LYS F 19 " --> pdb=" O GLU F 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 11 removed outlier: 3.750A pdb=" N TRP G 9 " --> pdb=" O HIS G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 38 Processing helix chain 'I' and resid 14 through 47 Processing helix chain 'J' and resid 5 through 11 removed outlier: 3.752A pdb=" N TRP J 9 " --> pdb=" O HIS J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 38 Processing helix chain 'K' and resid 14 through 47 Processing helix chain 'N' and resid 5 through 11 removed outlier: 3.766A pdb=" N VAL N 8 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP N 9 " --> pdb=" O HIS N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 38 Processing helix chain 'O' and resid 16 through 47 removed outlier: 3.562A pdb=" N VAL O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 11 removed outlier: 3.786A pdb=" N TRP P 9 " --> pdb=" O HIS P 6 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU P 10 " --> pdb=" O LYS P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 38 Processing helix chain 'Q' and resid 14 through 47 Processing helix chain 'R' and resid 5 through 11 removed outlier: 3.777A pdb=" N VAL R 8 " --> pdb=" O THR R 5 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TRP R 9 " --> pdb=" O HIS R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 38 Processing helix chain 'S' and resid 14 through 47 Processing helix chain 'T' and resid 5 through 11 removed outlier: 3.583A pdb=" N VAL T 8 " --> pdb=" O THR T 5 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP T 9 " --> pdb=" O HIS T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 38 Processing helix chain 'U' and resid 14 through 47 Processing helix chain 'V' and resid 5 through 11 removed outlier: 3.830A pdb=" N VAL V 8 " --> pdb=" O THR V 5 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP V 9 " --> pdb=" O HIS V 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 38 Processing helix chain 'W' and resid 14 through 47 Processing helix chain 'X' and resid 5 through 11 removed outlier: 3.536A pdb=" N VAL X 8 " --> pdb=" O THR X 5 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP X 9 " --> pdb=" O HIS X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 38 Processing helix chain 'Y' and resid 14 through 47 Processing helix chain 'Z' and resid 6 through 11 removed outlier: 4.406A pdb=" N TRP Z 9 " --> pdb=" O HIS Z 6 " (cutoff:3.500A) Processing helix chain 'Z' and resid 13 through 38 Processing helix chain 'a' and resid 14 through 47 Processing helix chain 'b' and resid 5 through 11 removed outlier: 3.662A pdb=" N VAL b 8 " --> pdb=" O THR b 5 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP b 9 " --> pdb=" O HIS b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 38 Processing helix chain 'c' and resid 14 through 47 Processing helix chain 'd' and resid 5 through 11 removed outlier: 3.564A pdb=" N VAL d 8 " --> pdb=" O THR d 5 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP d 9 " --> pdb=" O HIS d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 38 removed outlier: 4.882A pdb=" N VAL d 19 " --> pdb=" O ARG d 15 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ALA d 20 " --> pdb=" O SER d 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 16 through 47 Processing helix chain 'f' and resid 5 through 11 removed outlier: 3.997A pdb=" N VAL f 8 " --> pdb=" O THR f 5 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP f 9 " --> pdb=" O HIS f 6 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 38 removed outlier: 3.565A pdb=" N LEU f 18 " --> pdb=" O PRO f 14 " (cutoff:3.500A) Processing helix chain 'g' and resid 14 through 47 removed outlier: 3.654A pdb=" N VAL g 24 " --> pdb=" O GLU g 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 11 removed outlier: 3.655A pdb=" N VAL h 8 " --> pdb=" O THR h 5 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP h 9 " --> pdb=" O HIS h 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 39 Processing helix chain 'i' and resid 14 through 47 Processing helix chain 'j' and resid 5 through 11 removed outlier: 3.550A pdb=" N VAL j 8 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP j 9 " --> pdb=" O HIS j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 13 through 38 Processing sheet with id=AA1, first strand: chain 'C' and resid 50 through 53 Processing sheet with id=AA2, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AA3, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.643A pdb=" N PHE L 25 " --> pdb=" O VAL L 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 35 through 36 removed outlier: 3.687A pdb=" N THR M 35 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 94 through 95 Processing sheet with id=AA6, first strand: chain 'H' and resid 61 through 64 Processing sheet with id=AA7, first strand: chain 'H' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'H' and resid 129 through 131 removed outlier: 6.386A pdb=" N GLY H 161 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU H 182 " --> pdb=" O GLY H 161 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL H 163 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL H 180 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP H 165 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU H 178 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP H 167 " --> pdb=" O ARG H 176 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE H 174 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 129 through 131 removed outlier: 6.638A pdb=" N THR H 159 " --> pdb=" O ALA H 154 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA H 154 " --> pdb=" O THR H 159 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY H 161 " --> pdb=" O VAL H 152 " (cutoff:3.500A) 1319 hydrogen bonds defined for protein. 3735 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: 7.99 Time building geometry restraints manager: 9.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.38: 8759 1.38 - 1.58: 18873 1.58 - 1.79: 88 1.79 - 2.00: 176 2.00 - 2.20: 191 Bond restraints: 28087 Sorted by residual: bond pdb=" NA BCL M 403 " pdb="MG BCL M 403 " ideal model delta sigma weight residual 2.170 1.977 0.193 2.40e-02 1.74e+03 6.45e+01 bond pdb=" NA BCL G 101 " pdb="MG BCL G 101 " ideal model delta sigma weight residual 2.170 1.983 0.187 2.40e-02 1.74e+03 6.09e+01 bond pdb=" NA BCL P 101 " pdb="MG BCL P 101 " ideal model delta sigma weight residual 2.170 1.983 0.187 2.40e-02 1.74e+03 6.05e+01 bond pdb=" NA BCL M 402 " pdb="MG BCL M 402 " ideal model delta sigma weight residual 2.170 1.984 0.186 2.40e-02 1.74e+03 6.02e+01 bond pdb=" NA BCL f 101 " pdb="MG BCL f 101 " ideal model delta sigma weight residual 2.170 1.985 0.185 2.40e-02 1.74e+03 5.96e+01 ... (remaining 28082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.73: 38046 6.73 - 13.46: 722 13.46 - 20.19: 52 20.19 - 26.92: 2 26.92 - 33.65: 2 Bond angle restraints: 38824 Sorted by residual: angle pdb=" ND BCL M 403 " pdb="MG BCL M 403 " pdb=" NA BCL M 403 " ideal model delta sigma weight residual 88.02 97.69 -9.66 1.29e+00 6.02e-01 5.62e+01 angle pdb=" C1D BCL d 102 " pdb=" C2D BCL d 102 " pdb=" CMD BCL d 102 " ideal model delta sigma weight residual 125.57 139.08 -13.50 1.83e+00 2.99e-01 5.46e+01 angle pdb=" ND BCL J 101 " pdb="MG BCL J 101 " pdb=" NA BCL J 101 " ideal model delta sigma weight residual 88.02 97.51 -9.48 1.29e+00 6.02e-01 5.41e+01 angle pdb=" ND BCL f 101 " pdb="MG BCL f 101 " pdb=" NA BCL f 101 " ideal model delta sigma weight residual 88.02 97.37 -9.35 1.29e+00 6.02e-01 5.26e+01 angle pdb=" ND BCL h 101 " pdb="MG BCL h 101 " pdb=" NA BCL h 101 " ideal model delta sigma weight residual 88.02 97.30 -9.27 1.29e+00 6.02e-01 5.18e+01 ... (remaining 38819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 14210 35.82 - 71.63: 639 71.63 - 107.45: 62 107.45 - 143.26: 15 143.26 - 179.08: 10 Dihedral angle restraints: 14936 sinusoidal: 7021 harmonic: 7915 Sorted by residual: dihedral pdb=" C1 BCL h 102 " pdb=" CGA BCL h 102 " pdb=" O2A BCL h 102 " pdb=" CBA BCL h 102 " ideal model delta sinusoidal sigma weight residual -180.00 -0.92 -179.08 1 6.00e+00 2.78e-02 5.33e+02 dihedral pdb=" C1 BCL X 102 " pdb=" CGA BCL X 102 " pdb=" O2A BCL X 102 " pdb=" CBA BCL X 102 " ideal model delta sinusoidal sigma weight residual -180.00 -1.96 -178.04 1 6.00e+00 2.78e-02 5.33e+02 dihedral pdb=" C1 BCL V 102 " pdb=" CGA BCL V 102 " pdb=" O2A BCL V 102 " pdb=" CBA BCL V 102 " ideal model delta sinusoidal sigma weight residual 180.00 2.41 177.59 1 6.00e+00 2.78e-02 5.33e+02 ... (remaining 14933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3215 0.066 - 0.132: 431 0.132 - 0.198: 104 0.198 - 0.263: 19 0.263 - 0.329: 11 Chirality restraints: 3780 Sorted by residual: chirality pdb=" CBD BCL I 101 " pdb=" CAD BCL I 101 " pdb=" CGD BCL I 101 " pdb=" CHA BCL I 101 " both_signs ideal model delta sigma weight residual False 2.62 2.29 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CBD BCL B 101 " pdb=" CAD BCL B 101 " pdb=" CGD BCL B 101 " pdb=" CHA BCL B 101 " both_signs ideal model delta sigma weight residual False 2.62 2.30 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA VAL W 57 " pdb=" N VAL W 57 " pdb=" C VAL W 57 " pdb=" CB VAL W 57 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 3777 not shown) Planarity restraints: 4704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL G 102 " -0.350 3.00e-02 1.11e+03 2.87e-01 4.58e+02 pdb=" CBA BCL G 102 " -0.176 3.00e-02 1.11e+03 pdb=" CGA BCL G 102 " 0.081 3.00e-02 1.11e+03 pdb=" O1A BCL G 102 " -0.054 3.00e-02 1.11e+03 pdb=" O2A BCL G 102 " 0.499 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL J 102 " -0.352 3.00e-02 1.11e+03 2.86e-01 4.55e+02 pdb=" CBA BCL J 102 " -0.190 3.00e-02 1.11e+03 pdb=" CGA BCL J 102 " 0.086 3.00e-02 1.11e+03 pdb=" O1A BCL J 102 " -0.034 3.00e-02 1.11e+03 pdb=" O2A BCL J 102 " 0.491 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL M 402 " -0.327 3.00e-02 1.11e+03 2.71e-01 4.07e+02 pdb=" CBA BCL M 402 " -0.152 3.00e-02 1.11e+03 pdb=" CGA BCL M 402 " 0.064 3.00e-02 1.11e+03 pdb=" O1A BCL M 402 " -0.063 3.00e-02 1.11e+03 pdb=" O2A BCL M 402 " 0.478 3.00e-02 1.11e+03 ... (remaining 4701 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 259 2.62 - 3.19: 20984 3.19 - 3.76: 45735 3.76 - 4.33: 69564 4.33 - 4.90: 110746 Nonbonded interactions: 247288 Sorted by model distance: nonbonded pdb=" NE2 HIS C 338 " pdb="FE HEC C 504 " model vdw 2.047 3.080 nonbonded pdb=" OD2 ASP C 214 " pdb="MG MG C 506 " model vdw 2.070 2.170 nonbonded pdb=" OD1 ASP C 194 " pdb="MG MG C 506 " model vdw 2.073 2.170 nonbonded pdb=" NE2 HIS L 192 " pdb="FE FE M 401 " model vdw 2.144 2.340 nonbonded pdb=" NE2 HIS M 220 " pdb="FE FE M 401 " model vdw 2.147 2.340 ... (remaining 247283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 51) selection = (chain 'E' and resid 6 through 51) selection = (chain 'G' and resid 6 through 51) selection = (chain 'J' and resid 6 through 51) selection = (chain 'N' and resid 6 through 51) selection = (chain 'P' and resid 6 through 51) selection = (chain 'R' and resid 6 through 51) selection = (chain 'T' and resid 6 through 51) selection = (chain 'V' and resid 6 through 51) selection = (chain 'X' and resid 6 through 51) selection = (chain 'Z' and resid 6 through 51) selection = (chain 'b' and resid 6 through 51) selection = (chain 'd' and resid 6 through 51) selection = (chain 'f' and resid 6 through 51) selection = (chain 'h' and resid 6 through 51) selection = (chain 'j' and resid 6 through 51) } ncs_group { reference = (chain 'B' and (resid 9 through 57 or resid 101)) selection = chain 'D' selection = chain 'F' selection = (chain 'I' and (resid 9 through 57 or resid 101)) selection = (chain 'K' and (resid 9 through 57 or resid 101)) selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = (chain 'U' and (resid 9 through 57 or resid 101)) selection = (chain 'W' and (resid 9 through 57 or resid 101)) selection = (chain 'Y' and (resid 9 through 57 or resid 101)) selection = (chain 'a' and (resid 9 through 57 or resid 101)) selection = chain 'c' selection = (chain 'e' and (resid 9 through 57 or resid 101)) selection = chain 'g' selection = (chain 'i' and (resid 9 through 57 or resid 101)) } 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 58.510 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 0.348 28150 Z= 1.025 Angle : 2.009 33.654 38824 Z= 0.905 Chirality : 0.055 0.329 3780 Planarity : 0.021 0.287 4704 Dihedral : 19.507 179.077 9814 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.16), residues: 2698 helix: 2.14 (0.13), residues: 1492 sheet: 0.58 (0.98), residues: 26 loop : -0.05 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 50 HIS 0.016 0.001 HIS M 183 PHE 0.058 0.002 PHE L 218 TYR 0.021 0.002 TYR M 194 ARG 0.007 0.000 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.12040 ( 1317) hydrogen bonds : angle 4.73226 ( 3735) covalent geometry : bond 0.02085 (28087) covalent geometry : angle 2.00870 (38824) Misc. bond : bond 0.11981 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 2.288 Fit side-chains REVERT: H 1 MET cc_start: 0.7285 (mmt) cc_final: 0.6864 (mpt) REVERT: E 1 MET cc_start: 0.7695 (ttm) cc_final: 0.7183 (mtp) REVERT: F 27 GLN cc_start: 0.8063 (mt0) cc_final: 0.7854 (mt0) REVERT: U 27 GLN cc_start: 0.7945 (mt0) cc_final: 0.7634 (mt0) REVERT: V 46 GLU cc_start: 0.8138 (tp30) cc_final: 0.7934 (mm-30) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 1.5799 time to fit residues: 565.6304 Evaluate side-chains 273 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 232 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 146 HIS L 168 HIS ** L 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 ASN ** H 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 ASN P 6 HIS T 39 HIS W 27 GLN i 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.096418 restraints weight = 31368.324| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.12 r_work: 0.2945 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.390 28150 Z= 0.177 Angle : 0.849 13.372 38824 Z= 0.312 Chirality : 0.039 0.189 3780 Planarity : 0.005 0.067 4704 Dihedral : 19.385 179.851 5265 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.87 % Allowed : 6.47 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.16), residues: 2698 helix: 2.20 (0.12), residues: 1495 sheet: 0.60 (1.03), residues: 26 loop : -0.03 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 265 HIS 0.009 0.001 HIS M 183 PHE 0.031 0.002 PHE L 218 TYR 0.025 0.002 TYR M 194 ARG 0.006 0.000 ARG j 15 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 1317) hydrogen bonds : angle 4.02669 ( 3735) covalent geometry : bond 0.00433 (28087) covalent geometry : angle 0.84863 (38824) Misc. bond : bond 0.13158 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 295 time to evaluate : 2.847 Fit side-chains revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7437 (ptm160) REVERT: C 214 ASP cc_start: 0.8663 (m-30) cc_final: 0.8285 (m-30) REVERT: D 19 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7915 (tttt) REVERT: E 1 MET cc_start: 0.7315 (ttm) cc_final: 0.6849 (mtp) REVERT: F 27 GLN cc_start: 0.8500 (mt0) cc_final: 0.8279 (mt0) REVERT: F 54 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7628 (pp20) REVERT: U 27 GLN cc_start: 0.8235 (mt0) cc_final: 0.7940 (mt0) REVERT: f 11 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8088 (ttm) REVERT: i 19 LYS cc_start: 0.8042 (tttt) cc_final: 0.7768 (tttp) outliers start: 19 outliers final: 6 residues processed: 305 average time/residue: 1.5199 time to fit residues: 533.4978 Evaluate side-chains 279 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 270 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain f residue 11 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 182 optimal weight: 0.6980 chunk 254 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 168 HIS H 90 ASN W 27 GLN i 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.093894 restraints weight = 31355.609| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.17 r_work: 0.2914 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.397 28150 Z= 0.197 Angle : 0.805 15.634 38824 Z= 0.312 Chirality : 0.039 0.147 3780 Planarity : 0.005 0.062 4704 Dihedral : 19.194 179.511 5265 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.50 % Allowed : 8.07 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.15), residues: 2698 helix: 2.16 (0.12), residues: 1495 sheet: 0.42 (1.04), residues: 26 loop : -0.04 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 265 HIS 0.009 0.001 HIS M 183 PHE 0.028 0.002 PHE L 218 TYR 0.026 0.002 TYR M 194 ARG 0.004 0.000 ARG L 13 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 1317) hydrogen bonds : angle 3.98421 ( 3735) covalent geometry : bond 0.00482 (28087) covalent geometry : angle 0.80536 (38824) Misc. bond : bond 0.12209 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 283 time to evaluate : 2.291 Fit side-chains revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7410 (ptm-80) REVERT: L 79 PHE cc_start: 0.8394 (m-80) cc_final: 0.8010 (m-80) REVERT: L 191 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8384 (mmm) REVERT: Q 15 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: V 15 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7131 (ttp-110) REVERT: b 7 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8398 (mtpm) REVERT: f 11 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8078 (ttm) REVERT: i 19 LYS cc_start: 0.8090 (tttt) cc_final: 0.7837 (tttm) outliers start: 33 outliers final: 15 residues processed: 297 average time/residue: 1.4616 time to fit residues: 498.8448 Evaluate side-chains 294 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 273 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain L residue 191 MET Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain f residue 11 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.0084 > 50: distance: 16 - 34: 8.675 distance: 20 - 42: 16.370 distance: 24 - 29: 4.325 distance: 25 - 47: 16.633 distance: 29 - 30: 10.211 distance: 30 - 31: 8.839 distance: 30 - 33: 14.353 distance: 31 - 32: 5.685 distance: 31 - 34: 4.070 distance: 32 - 52: 10.759 distance: 34 - 35: 3.275 distance: 35 - 36: 7.464 distance: 35 - 38: 8.797 distance: 36 - 37: 6.034 distance: 36 - 42: 9.191 distance: 37 - 63: 18.641 distance: 38 - 39: 5.131 distance: 39 - 40: 13.096 distance: 39 - 41: 7.240 distance: 42 - 43: 9.224 distance: 43 - 44: 7.401 distance: 43 - 46: 5.861 distance: 44 - 45: 6.595 distance: 44 - 47: 4.590 distance: 45 - 71: 41.411 distance: 47 - 48: 11.849 distance: 48 - 49: 7.793 distance: 48 - 51: 12.336 distance: 49 - 50: 7.578 distance: 49 - 52: 7.437 distance: 50 - 78: 34.390 distance: 52 - 53: 6.919 distance: 53 - 54: 8.191 distance: 53 - 56: 13.183 distance: 54 - 55: 9.328 distance: 55 - 85: 13.725 distance: 56 - 57: 7.475 distance: 57 - 58: 18.873 distance: 57 - 59: 18.015 distance: 58 - 60: 8.549 distance: 59 - 61: 3.626 distance: 60 - 62: 19.790 distance: 61 - 62: 16.301 distance: 63 - 64: 5.889 distance: 64 - 65: 12.930 distance: 64 - 67: 5.555 distance: 65 - 66: 20.005 distance: 65 - 71: 27.802 distance: 66 - 93: 20.303 distance: 67 - 68: 13.038 distance: 68 - 69: 5.588 distance: 68 - 70: 8.652 distance: 71 - 72: 38.644 distance: 72 - 73: 11.773 distance: 72 - 75: 18.973 distance: 73 - 74: 11.285 distance: 73 - 78: 14.370 distance: 74 - 98: 14.419 distance: 75 - 76: 7.316 distance: 75 - 77: 23.470 distance: 78 - 79: 11.211 distance: 79 - 80: 7.108 distance: 79 - 82: 11.293 distance: 80 - 85: 5.139 distance: 82 - 83: 19.828 distance: 82 - 84: 30.514 distance: 85 - 86: 6.380 distance: 86 - 87: 8.287 distance: 86 - 89: 6.970 distance: 87 - 88: 5.371 distance: 87 - 93: 3.051 distance: 88 - 113: 13.161 distance: 89 - 90: 10.797 distance: 90 - 91: 8.283 distance: 90 - 92: 5.824 distance: 93 - 94: 5.761 distance: 94 - 95: 8.569 distance: 94 - 97: 5.507 distance: 95 - 96: 7.737 distance: 95 - 98: 6.039 distance: 96 - 119: 12.756