Starting phenix.real_space_refine on Wed Jan 22 09:39:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnv_33327/01_2025/7xnv_33327.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnv_33327/01_2025/7xnv_33327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xnv_33327/01_2025/7xnv_33327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnv_33327/01_2025/7xnv_33327.map" model { file = "/net/cci-nas-00/data/ceres_data/7xnv_33327/01_2025/7xnv_33327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnv_33327/01_2025/7xnv_33327.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 156 5.16 5 C 12618 2.51 5 N 2712 2.21 5 O 2892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 18378 Number of models: 1 Model: "" Number of chains: 24 Chain: "G" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "H" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "I" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "J" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "K" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "L" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "A" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "B" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "C" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "D" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "E" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "F" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "G" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "I" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "J" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "K" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "L" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 8} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 8} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 8} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 8} Unresolved non-hydrogen planarities: 48 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 8} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 8} Unresolved non-hydrogen planarities: 48 Time building chain proxies: 13.26, per 1000 atoms: 0.72 Number of scatterers: 18378 At special positions: 0 Unit cell: (104.622, 115.15, 144.76, 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 156 16.00 O 2892 8.00 N 2712 7.00 C 12618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.98 Conformation dependent library (CDL) restraints added in 2.8 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 74.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'G' and resid 3 through 15 removed outlier: 4.227A pdb=" N LEU G 7 " --> pdb=" O GLU G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 34 Processing helix chain 'G' and resid 34 through 39 Processing helix chain 'G' and resid 41 through 46 removed outlier: 4.011A pdb=" N VAL G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 41 through 46' Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 87 through 100 removed outlier: 4.211A pdb=" N PHE G 93 " --> pdb=" O PRO G 89 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ILE G 94 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL G 98 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN G 100 " --> pdb=" O TYR G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 221 Processing helix chain 'G' and resid 246 through 276 removed outlier: 3.596A pdb=" N LYS G 250 " --> pdb=" O ARG G 246 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 15 removed outlier: 4.256A pdb=" N LEU H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 34 Processing helix chain 'H' and resid 34 through 39 Processing helix chain 'H' and resid 41 through 46 removed outlier: 4.019A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 41 through 46' Processing helix chain 'H' and resid 61 through 71 Processing helix chain 'H' and resid 74 through 87 Processing helix chain 'H' and resid 87 through 100 removed outlier: 4.242A pdb=" N PHE H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE H 94 " --> pdb=" O SER H 90 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL H 98 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 221 Processing helix chain 'H' and resid 246 through 276 removed outlier: 3.599A pdb=" N LYS H 250 " --> pdb=" O ARG H 246 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR H 251 " --> pdb=" O PRO H 247 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 15 removed outlier: 4.218A pdb=" N LEU I 7 " --> pdb=" O GLU I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 34 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 46 removed outlier: 4.020A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 41 through 46' Processing helix chain 'I' and resid 61 through 71 Processing helix chain 'I' and resid 74 through 87 Processing helix chain 'I' and resid 87 through 100 removed outlier: 4.237A pdb=" N PHE I 93 " --> pdb=" O PRO I 89 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE I 94 " --> pdb=" O SER I 90 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL I 98 " --> pdb=" O ILE I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 221 Processing helix chain 'I' and resid 246 through 276 removed outlier: 3.601A pdb=" N LYS I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR I 251 " --> pdb=" O PRO I 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE I 253 " --> pdb=" O GLU I 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 15 removed outlier: 4.228A pdb=" N LEU J 7 " --> pdb=" O GLU J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 34 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 41 through 46 removed outlier: 4.014A pdb=" N VAL J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 41 through 46' Processing helix chain 'J' and resid 61 through 71 Processing helix chain 'J' and resid 74 through 87 Processing helix chain 'J' and resid 87 through 100 removed outlier: 4.208A pdb=" N PHE J 93 " --> pdb=" O PRO J 89 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL J 98 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN J 100 " --> pdb=" O TYR J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 221 Processing helix chain 'J' and resid 246 through 276 removed outlier: 3.605A pdb=" N LYS J 250 " --> pdb=" O ARG J 246 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR J 251 " --> pdb=" O PRO J 247 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE J 253 " --> pdb=" O GLU J 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 15 removed outlier: 4.255A pdb=" N LEU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 34 Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 41 through 46 removed outlier: 4.020A pdb=" N VAL K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 41 through 46' Processing helix chain 'K' and resid 61 through 71 Processing helix chain 'K' and resid 74 through 87 Processing helix chain 'K' and resid 87 through 100 removed outlier: 4.207A pdb=" N PHE K 93 " --> pdb=" O PRO K 89 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE K 94 " --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR K 95 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL K 98 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 221 Processing helix chain 'K' and resid 246 through 276 removed outlier: 3.602A pdb=" N LYS K 250 " --> pdb=" O ARG K 246 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR K 251 " --> pdb=" O PRO K 247 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE K 253 " --> pdb=" O GLU K 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 15 removed outlier: 4.215A pdb=" N LEU L 7 " --> pdb=" O GLU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 34 Processing helix chain 'L' and resid 34 through 39 Processing helix chain 'L' and resid 41 through 46 removed outlier: 4.019A pdb=" N VAL L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 41 through 46' Processing helix chain 'L' and resid 61 through 71 Processing helix chain 'L' and resid 74 through 87 Processing helix chain 'L' and resid 87 through 100 removed outlier: 4.192A pdb=" N PHE L 93 " --> pdb=" O PRO L 89 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE L 94 " --> pdb=" O SER L 90 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR L 95 " --> pdb=" O LEU L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 221 Processing helix chain 'L' and resid 246 through 276 removed outlier: 3.603A pdb=" N LYS L 250 " --> pdb=" O ARG L 246 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR L 251 " --> pdb=" O PRO L 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE L 253 " --> pdb=" O GLU L 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 41 removed outlier: 4.105A pdb=" N ARG A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 removed outlier: 3.728A pdb=" N VAL A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 46' Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 87 through 100 removed outlier: 3.635A pdb=" N LEU A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 246 through 276 Processing helix chain 'B' and resid 20 through 41 removed outlier: 4.059A pdb=" N ARG B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.770A pdb=" N VAL B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 87 through 100 removed outlier: 3.577A pdb=" N LEU B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 222 Processing helix chain 'B' and resid 246 through 276 Processing helix chain 'C' and resid 20 through 41 removed outlier: 4.214A pdb=" N ARG C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.769A pdb=" N VAL C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 46' Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 87 through 100 removed outlier: 3.616A pdb=" N LEU C 91 " --> pdb=" O CYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 222 Processing helix chain 'C' and resid 246 through 276 Processing helix chain 'D' and resid 20 through 41 removed outlier: 4.114A pdb=" N ARG D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.765A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 74 through 86 Processing helix chain 'D' and resid 87 through 100 removed outlier: 3.633A pdb=" N LEU D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 222 Processing helix chain 'D' and resid 246 through 276 Processing helix chain 'E' and resid 20 through 41 removed outlier: 4.108A pdb=" N ARG E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.773A pdb=" N VAL E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 41 through 46' Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 87 through 100 removed outlier: 3.574A pdb=" N LEU E 91 " --> pdb=" O CYS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 222 Processing helix chain 'E' and resid 246 through 276 Processing helix chain 'F' and resid 20 through 41 removed outlier: 4.300A pdb=" N ARG F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.740A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 61 through 71 Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 87 through 100 removed outlier: 3.621A pdb=" N LEU F 91 " --> pdb=" O CYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 222 Processing helix chain 'F' and resid 246 through 276 Processing sheet with id=AA1, first strand: chain 'G' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'H' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'I' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'J' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'K' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA9, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AB2, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AB3, first strand: chain 'F' and resid 54 through 55 1153 hydrogen bonds defined for protein. 3387 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: 5.36 Time building geometry restraints manager: 5.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5181 1.34 - 1.46: 4404 1.46 - 1.58: 8889 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 18678 Sorted by residual: bond pdb=" CB LEU F 26 " pdb=" CG LEU F 26 " ideal model delta sigma weight residual 1.530 1.560 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C11 MC3 D 407 " pdb=" C12 MC3 D 407 " ideal model delta sigma weight residual 1.502 1.529 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C11 MC3 E 407 " pdb=" C12 MC3 E 407 " ideal model delta sigma weight residual 1.502 1.529 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C11 MC3 F 407 " pdb=" C12 MC3 F 407 " ideal model delta sigma weight residual 1.502 1.528 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C11 MC3 B 404 " pdb=" C12 MC3 B 404 " ideal model delta sigma weight residual 1.502 1.528 -0.026 2.00e-02 2.50e+03 1.74e+00 ... (remaining 18673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 22837 1.57 - 3.14: 841 3.14 - 4.71: 900 4.71 - 6.28: 187 6.28 - 7.84: 15 Bond angle restraints: 24780 Sorted by residual: angle pdb=" C CYS C 236 " pdb=" N ILE C 237 " pdb=" CA ILE C 237 " ideal model delta sigma weight residual 121.80 125.72 -3.92 1.40e+00 5.10e-01 7.86e+00 angle pdb=" C CYS A 236 " pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta sigma weight residual 121.80 125.59 -3.79 1.40e+00 5.10e-01 7.33e+00 angle pdb=" N ILE L 237 " pdb=" CA ILE L 237 " pdb=" C ILE L 237 " ideal model delta sigma weight residual 109.80 106.31 3.49 1.33e+00 5.65e-01 6.87e+00 angle pdb=" C LEU F 58 " pdb=" N GLN F 59 " pdb=" CA GLN F 59 " ideal model delta sigma weight residual 121.61 125.14 -3.53 1.39e+00 5.18e-01 6.43e+00 angle pdb=" C LEU E 58 " pdb=" N GLN E 59 " pdb=" CA GLN E 59 " ideal model delta sigma weight residual 121.61 125.13 -3.52 1.39e+00 5.18e-01 6.40e+00 ... (remaining 24775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 9657 16.81 - 33.63: 1147 33.63 - 50.44: 363 50.44 - 67.25: 119 67.25 - 84.07: 24 Dihedral angle restraints: 11310 sinusoidal: 5190 harmonic: 6120 Sorted by residual: dihedral pdb=" CB GLU B 241 " pdb=" CG GLU B 241 " pdb=" CD GLU B 241 " pdb=" OE1 GLU B 241 " ideal model delta sinusoidal sigma weight residual 0.00 84.07 -84.07 1 3.00e+01 1.11e-03 9.56e+00 dihedral pdb=" CB GLU C 241 " pdb=" CG GLU C 241 " pdb=" CD GLU C 241 " pdb=" OE1 GLU C 241 " ideal model delta sinusoidal sigma weight residual 0.00 83.98 -83.98 1 3.00e+01 1.11e-03 9.55e+00 dihedral pdb=" CB GLU F 241 " pdb=" CG GLU F 241 " pdb=" CD GLU F 241 " pdb=" OE1 GLU F 241 " ideal model delta sinusoidal sigma weight residual 0.00 83.91 -83.91 1 3.00e+01 1.11e-03 9.54e+00 ... (remaining 11307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1614 0.035 - 0.069: 752 0.069 - 0.104: 283 0.104 - 0.139: 71 0.139 - 0.174: 10 Chirality restraints: 2730 Sorted by residual: chirality pdb=" CA VAL A 240 " pdb=" N VAL A 240 " pdb=" C VAL A 240 " pdb=" CB VAL A 240 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA VAL E 240 " pdb=" N VAL E 240 " pdb=" C VAL E 240 " pdb=" CB VAL E 240 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CA VAL C 240 " pdb=" N VAL C 240 " pdb=" C VAL C 240 " pdb=" CB VAL C 240 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 2727 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 77 " 0.093 9.50e-02 1.11e+02 4.32e-02 2.77e+00 pdb=" NE ARG F 77 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG F 77 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG F 77 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG F 77 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 77 " -0.091 9.50e-02 1.11e+02 4.23e-02 2.75e+00 pdb=" NE ARG C 77 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ARG C 77 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG C 77 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 77 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 77 " 0.090 9.50e-02 1.11e+02 4.18e-02 2.62e+00 pdb=" NE ARG B 77 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG B 77 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B 77 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 77 " 0.011 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2299 2.75 - 3.29: 16225 3.29 - 3.83: 29467 3.83 - 4.36: 33943 4.36 - 4.90: 61975 Nonbonded interactions: 143909 Sorted by model distance: nonbonded pdb=" OE1 GLU H 230 " pdb=" NZ LYS E 238 " model vdw 2.213 3.120 nonbonded pdb=" OE1 GLU G 230 " pdb=" NZ LYS D 238 " model vdw 2.213 3.120 nonbonded pdb=" OE1 GLU K 230 " pdb=" NZ LYS B 238 " model vdw 2.218 3.120 nonbonded pdb=" OE1 GLU I 230 " pdb=" NZ LYS F 238 " model vdw 2.227 3.120 nonbonded pdb=" OE1 GLU L 230 " pdb=" NZ LYS C 238 " model vdw 2.237 3.120 ... (remaining 143904 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)) or resid 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'B' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C \ 36 or name C37 or name C38 or name C39 or name C40)) or (resid 403 and (name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20)) or (resid 404 and (name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or na \ me C22 or name C23 or name C24)) or resid 405 through 407 or (resid 408 and (nam \ e C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C40)))) selection = (chain 'C' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)) or resid 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'D' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)) or resid 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'E' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)) or resid 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'F' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)) or resid 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'G' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'H' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'I' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'J' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'K' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'L' and (resid 19 through 100 or resid 196 through 276 or resid 403 or (r \ esid 404 through 405 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or resid 406 th \ rough 410)) } 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: 0.010 Normalize map: mean=0, sd=1: 7.560 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 44.420 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 : 0.005 0.043 18678 Z= 0.320 Angle : 1.072 7.844 24780 Z= 0.462 Chirality : 0.046 0.174 2730 Planarity : 0.005 0.043 2904 Dihedral : 16.869 84.065 7266 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.59 % Allowed : 1.03 % Favored : 98.38 % Rotamer: Outliers : 0.90 % Allowed : 11.25 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.24 (0.17), residues: 2040 helix: 0.92 (0.13), residues: 1380 sheet: -0.28 (0.36), residues: 204 loop : -1.81 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 79 HIS 0.004 0.001 HIS I 75 PHE 0.019 0.001 PHE C 198 TYR 0.018 0.002 TYR H 96 ARG 0.023 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 390 time to evaluate : 1.949 Fit side-chains REVERT: I 69 ARG cc_start: 0.7919 (tpt170) cc_final: 0.7702 (tpt90) REVERT: I 204 VAL cc_start: 0.9039 (t) cc_final: 0.8819 (m) REVERT: I 207 ASN cc_start: 0.8432 (m-40) cc_final: 0.8109 (m110) REVERT: L 204 VAL cc_start: 0.9029 (t) cc_final: 0.8816 (m) REVERT: A 69 ARG cc_start: 0.7874 (tpt170) cc_final: 0.7651 (ttm-80) REVERT: B 69 ARG cc_start: 0.7889 (tpt170) cc_final: 0.7649 (ttm-80) REVERT: B 77 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8141 (mpt180) REVERT: B 232 ASN cc_start: 0.9042 (p0) cc_final: 0.8831 (p0) REVERT: B 275 LEU cc_start: 0.6905 (mp) cc_final: 0.6692 (mp) REVERT: C 69 ARG cc_start: 0.7838 (tpt170) cc_final: 0.7635 (ttm-80) REVERT: C 275 LEU cc_start: 0.6725 (mp) cc_final: 0.6502 (mp) REVERT: D 77 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8209 (mpt180) REVERT: E 69 ARG cc_start: 0.7861 (tpt170) cc_final: 0.7631 (ttm-80) REVERT: E 232 ASN cc_start: 0.9045 (p0) cc_final: 0.8839 (p0) REVERT: E 239 GLU cc_start: 0.8360 (tt0) cc_final: 0.8120 (tt0) REVERT: E 275 LEU cc_start: 0.6905 (mp) cc_final: 0.6689 (mp) REVERT: F 275 LEU cc_start: 0.6756 (mp) cc_final: 0.6503 (mp) outliers start: 17 outliers final: 13 residues processed: 399 average time/residue: 0.3265 time to fit residues: 193.8109 Evaluate side-chains 344 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 329 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain H residue 253 PHE Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain J residue 253 PHE Chi-restraints excluded: chain K residue 253 PHE Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 77 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 20.0000 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 50 GLN H 50 GLN I 50 GLN J 50 GLN K 50 GLN L 50 GLN ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN A 82 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 82 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 82 GLN C 99 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 82 GLN D 99 HIS ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN E 82 GLN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 82 GLN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.143995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.111694 restraints weight = 20117.869| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.19 r_work: 0.2747 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18678 Z= 0.205 Angle : 0.520 5.553 24780 Z= 0.278 Chirality : 0.042 0.137 2730 Planarity : 0.003 0.025 2904 Dihedral : 13.796 59.996 3525 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.29 % Allowed : 0.98 % Favored : 98.73 % Rotamer: Outliers : 3.56 % Allowed : 13.22 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.18), residues: 2040 helix: 2.08 (0.13), residues: 1404 sheet: 0.41 (0.38), residues: 174 loop : -1.19 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 277 HIS 0.003 0.001 HIS B 99 PHE 0.011 0.001 PHE A 53 TYR 0.011 0.001 TYR H 96 ARG 0.003 0.000 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 352 time to evaluate : 1.886 Fit side-chains REVERT: G 52 MET cc_start: 0.9301 (mmt) cc_final: 0.8831 (mmt) REVERT: H 52 MET cc_start: 0.9319 (mmt) cc_final: 0.8894 (mmt) REVERT: I 69 ARG cc_start: 0.8894 (tpt170) cc_final: 0.8535 (tpt90) REVERT: I 230 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8162 (mm-30) REVERT: K 52 MET cc_start: 0.9328 (mmt) cc_final: 0.8906 (mmt) REVERT: L 34 ARG cc_start: 0.8463 (mtt180) cc_final: 0.8237 (mtt180) REVERT: L 230 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8165 (mm-30) REVERT: L 237 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8350 (mm) REVERT: A 69 ARG cc_start: 0.9022 (tpt170) cc_final: 0.8668 (ttm-80) REVERT: A 238 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8332 (mtmt) REVERT: B 69 ARG cc_start: 0.8986 (tpt170) cc_final: 0.8633 (ttm-80) REVERT: B 275 LEU cc_start: 0.7353 (mp) cc_final: 0.7065 (mp) REVERT: C 69 ARG cc_start: 0.8965 (tpt170) cc_final: 0.8615 (ttm-80) REVERT: C 238 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8192 (mtmm) REVERT: C 275 LEU cc_start: 0.7270 (mp) cc_final: 0.6962 (mp) REVERT: D 22 ILE cc_start: 0.6068 (OUTLIER) cc_final: 0.5851 (mp) REVERT: D 238 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8328 (mtmt) REVERT: E 69 ARG cc_start: 0.8990 (tpt170) cc_final: 0.8633 (ttm-80) REVERT: E 275 LEU cc_start: 0.7484 (mp) cc_final: 0.7207 (mp) REVERT: F 275 LEU cc_start: 0.7240 (mp) cc_final: 0.6947 (mp) outliers start: 67 outliers final: 31 residues processed: 386 average time/residue: 0.3467 time to fit residues: 202.2402 Evaluate side-chains 361 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 325 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain J residue 253 PHE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 170 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN A 82 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.142453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.110406 restraints weight = 20087.347| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.31 r_work: 0.2695 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18678 Z= 0.273 Angle : 0.524 5.561 24780 Z= 0.277 Chirality : 0.044 0.144 2730 Planarity : 0.004 0.030 2904 Dihedral : 12.662 59.932 3494 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.29 % Allowed : 1.37 % Favored : 98.33 % Rotamer: Outliers : 2.65 % Allowed : 13.85 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.18), residues: 2040 helix: 2.25 (0.13), residues: 1404 sheet: -0.12 (0.37), residues: 204 loop : -0.90 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 277 HIS 0.004 0.001 HIS L 75 PHE 0.012 0.001 PHE A 81 TYR 0.009 0.002 TYR F 67 ARG 0.003 0.001 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 335 time to evaluate : 1.897 Fit side-chains REVERT: G 52 MET cc_start: 0.9208 (mmt) cc_final: 0.8927 (mmt) REVERT: I 69 ARG cc_start: 0.8896 (tpt170) cc_final: 0.8622 (tpt90) REVERT: I 204 VAL cc_start: 0.9053 (t) cc_final: 0.8744 (m) REVERT: I 230 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8108 (tp30) REVERT: J 52 MET cc_start: 0.9215 (mmt) cc_final: 0.8950 (mmt) REVERT: L 204 VAL cc_start: 0.9067 (t) cc_final: 0.8766 (m) REVERT: L 230 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7923 (mm-30) REVERT: L 237 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8652 (mm) REVERT: A 69 ARG cc_start: 0.8972 (tpt170) cc_final: 0.8549 (ttm-80) REVERT: A 238 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8412 (mtmt) REVERT: B 69 ARG cc_start: 0.8915 (tpt170) cc_final: 0.8488 (ttm-80) REVERT: B 275 LEU cc_start: 0.7353 (mp) cc_final: 0.7090 (mp) REVERT: C 69 ARG cc_start: 0.8840 (tpt170) cc_final: 0.8443 (ttm-80) REVERT: C 275 LEU cc_start: 0.7232 (mp) cc_final: 0.6977 (mp) REVERT: D 238 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8513 (mtmt) REVERT: E 69 ARG cc_start: 0.8926 (tpt170) cc_final: 0.8490 (ttm-80) REVERT: E 275 LEU cc_start: 0.7401 (mp) cc_final: 0.7158 (mp) REVERT: F 275 LEU cc_start: 0.7188 (mp) cc_final: 0.6962 (mp) outliers start: 50 outliers final: 35 residues processed: 354 average time/residue: 0.3189 time to fit residues: 171.8790 Evaluate side-chains 358 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 320 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 54.0418 > 50: distance: 64 - 82: 7.194 distance: 68 - 86: 24.687 distance: 71 - 76: 3.370 distance: 72 - 94: 34.266 distance: 76 - 77: 3.457 distance: 78 - 79: 3.491 distance: 79 - 100: 21.546 distance: 80 - 81: 4.972 distance: 82 - 83: 3.615 distance: 83 - 84: 4.356 distance: 84 - 85: 13.395 distance: 84 - 86: 11.869 distance: 85 - 107: 13.742 distance: 86 - 87: 11.184 distance: 87 - 88: 13.997 distance: 87 - 90: 4.360 distance: 88 - 89: 20.532 distance: 88 - 94: 21.306 distance: 89 - 114: 10.285 distance: 90 - 91: 4.220 distance: 90 - 92: 5.589 distance: 91 - 93: 9.410 distance: 94 - 95: 34.668 distance: 95 - 96: 6.631 distance: 95 - 98: 27.803 distance: 96 - 97: 4.824 distance: 96 - 100: 9.057 distance: 97 - 122: 13.226 distance: 98 - 99: 31.974 distance: 100 - 101: 5.127 distance: 101 - 102: 8.655 distance: 101 - 104: 3.492 distance: 102 - 103: 4.835 distance: 102 - 107: 5.815 distance: 104 - 105: 4.575 distance: 104 - 106: 4.102 distance: 107 - 108: 5.320 distance: 108 - 109: 5.125 distance: 108 - 111: 4.741 distance: 109 - 110: 5.367 distance: 109 - 114: 3.001 distance: 110 - 138: 9.487 distance: 111 - 112: 3.516 distance: 111 - 113: 8.711 distance: 115 - 116: 3.526 distance: 115 - 118: 3.481 distance: 116 - 117: 4.190 distance: 117 - 143: 8.680 distance: 118 - 119: 3.763 distance: 119 - 120: 5.394 distance: 119 - 121: 6.195 distance: 124 - 125: 4.941 distance: 125 - 151: 4.020 distance: 126 - 127: 3.168 distance: 127 - 128: 4.055 distance: 127 - 129: 4.453 distance: 131 - 134: 3.346 distance: 133 - 158: 4.953 distance: 134 - 135: 6.657 distance: 135 - 136: 8.842 distance: 139 - 142: 4.275 distance: 141 - 164: 5.304