Starting phenix.real_space_refine on Sat Jul 4 22:47:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pil_13441/07_2026/7pil_13441.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pil_13441/07_2026/7pil_13441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pil_13441/07_2026/7pil_13441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pil_13441/07_2026/7pil_13441.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7pil_13441/07_2026/7pil_13441.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pil_13441/07_2026/7pil_13441.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pil_13441/07_2026/7pil_13441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pil_13441/07_2026/7pil_13441.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 6 5.49 5 Mg 32 5.21 5 S 90 5.16 5 C 15852 2.51 5 N 3119 2.21 5 O 3380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22480 Number of models: 1 Model: "" Number of chains: 66 Chain: "AA" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 392 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "AB" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AC" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AD" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AE" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AF" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AG" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AH" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AI" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AJ" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AK" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AL" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AM" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AN" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 432 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "BA" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BB" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BC" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "BD" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BE" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BF" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BG" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BH" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BI" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BJ" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BK" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BL" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BM" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BN" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 317 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "H" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1867 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} Chain: "L" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2445 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "UU" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 363 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "X" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 422 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "AA" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 143 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AB" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'3PE': 1, 'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AC" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 201 Unusual residues: {'3PE': 1, 'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AD" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AE" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AF" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AG" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AH" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AI" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AJ" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AK" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 216 Unusual residues: {'BCL': 2, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AL" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AM" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 216 Unusual residues: {'BCL': 2, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AN" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BB" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BC" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BD" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BE" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "BF" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BG" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BH" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BI" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BJ" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BL" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BN" 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: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 278 Unusual residues: {'BCL': 2, 'BPH': 1, 'U10': 1, 'UQ1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 422 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CD4': 1, 'LMT': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.36, per 1000 atoms: 0.19 Number of scatterers: 22480 At special positions: 0 Unit cell: (138.45, 129.35, 96.2, 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 1 26.01 S 90 16.00 P 6 15.00 Mg 32 11.99 O 3380 8.00 N 3119 7.00 C 15852 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.3 seconds 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4258 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 7 sheets defined 73.5% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'AA' and resid 3 through 10 Processing helix chain 'AA' and resid 12 through 37 Processing helix chain 'AB' and resid 3 through 10 Processing helix chain 'AB' and resid 12 through 37 Processing helix chain 'AB' and resid 42 through 51 Processing helix chain 'AC' and resid 3 through 10 Processing helix chain 'AC' and resid 12 through 37 removed outlier: 3.508A pdb=" N VALAC 18 " --> pdb=" O ARGAC 14 " (cutoff:3.500A) Processing helix chain 'AC' and resid 42 through 51 Processing helix chain 'AD' and resid 3 through 5 No H-bonds generated for 'chain 'AD' and resid 3 through 5' Processing helix chain 'AD' and resid 6 through 11 Processing helix chain 'AD' and resid 12 through 37 Processing helix chain 'AD' and resid 42 through 51 Processing helix chain 'AE' and resid 1 through 5 removed outlier: 4.183A pdb=" N TYRAE 5 " --> pdb=" O SERAE 2 " (cutoff:3.500A) Processing helix chain 'AE' and resid 6 through 11 removed outlier: 3.507A pdb=" N ILEAE 10 " --> pdb=" O LYSAE 6 " (cutoff:3.500A) Processing helix chain 'AE' and resid 12 through 37 Processing helix chain 'AE' and resid 42 through 51 Processing helix chain 'AF' and resid 3 through 5 No H-bonds generated for 'chain 'AF' and resid 3 through 5' Processing helix chain 'AF' and resid 6 through 11 removed outlier: 3.648A pdb=" N ILEAF 10 " --> pdb=" O LYSAF 6 " (cutoff:3.500A) Processing helix chain 'AF' and resid 12 through 38 Processing helix chain 'AF' and resid 42 through 51 Processing helix chain 'AG' and resid 3 through 5 No H-bonds generated for 'chain 'AG' and resid 3 through 5' Processing helix chain 'AG' and resid 6 through 11 removed outlier: 3.565A pdb=" N ILEAG 10 " --> pdb=" O LYSAG 6 " (cutoff:3.500A) Processing helix chain 'AG' and resid 12 through 38 Processing helix chain 'AG' and resid 42 through 51 Processing helix chain 'AH' and resid 3 through 5 No H-bonds generated for 'chain 'AH' and resid 3 through 5' Processing helix chain 'AH' and resid 6 through 11 removed outlier: 3.527A pdb=" N ILEAH 10 " --> pdb=" O LYSAH 6 " (cutoff:3.500A) Processing helix chain 'AH' and resid 12 through 38 Processing helix chain 'AH' and resid 42 through 51 Processing helix chain 'AI' and resid 3 through 10 Processing helix chain 'AI' and resid 12 through 38 Processing helix chain 'AI' and resid 42 through 51 Processing helix chain 'AJ' and resid 1 through 5 removed outlier: 4.286A pdb=" N TYRAJ 5 " --> pdb=" O SERAJ 2 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 6 through 11 removed outlier: 3.501A pdb=" N ILEAJ 10 " --> pdb=" O LYSAJ 6 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 12 through 37 Processing helix chain 'AJ' and resid 42 through 51 Processing helix chain 'AK' and resid 3 through 10 Processing helix chain 'AK' and resid 12 through 37 Processing helix chain 'AK' and resid 42 through 51 Processing helix chain 'AL' and resid 1 through 5 removed outlier: 4.159A pdb=" N TYRAL 5 " --> pdb=" O SERAL 2 " (cutoff:3.500A) Processing helix chain 'AL' and resid 6 through 11 removed outlier: 3.561A pdb=" N ILEAL 10 " --> pdb=" O LYSAL 6 " (cutoff:3.500A) Processing helix chain 'AL' and resid 12 through 37 Processing helix chain 'AL' and resid 42 through 51 Processing helix chain 'AM' and resid 1 through 10 removed outlier: 4.310A pdb=" N TYRAM 5 " --> pdb=" O SERAM 2 " (cutoff:3.500A) Processing helix chain 'AM' and resid 12 through 37 Processing helix chain 'AM' and resid 42 through 51 Processing helix chain 'AN' and resid 6 through 11 Processing helix chain 'AN' and resid 12 through 37 Processing helix chain 'AN' and resid 42 through 51 Processing helix chain 'BA' and resid 12 through 45 Processing helix chain 'BB' and resid 12 through 45 Processing helix chain 'BC' and resid 12 through 45 Processing helix chain 'BD' and resid 12 through 45 Processing helix chain 'BE' and resid 12 through 45 Processing helix chain 'BF' and resid 12 through 45 Processing helix chain 'BG' and resid 12 through 45 Processing helix chain 'BH' and resid 12 through 45 Processing helix chain 'BI' and resid 12 through 45 Processing helix chain 'BJ' and resid 12 through 45 removed outlier: 3.511A pdb=" N VALBJ 22 " --> pdb=" O GLUBJ 18 " (cutoff:3.500A) Processing helix chain 'BK' and resid 12 through 45 Processing helix chain 'BL' and resid 12 through 45 removed outlier: 3.517A pdb=" N SERBL 25 " --> pdb=" O SERBL 21 " (cutoff:3.500A) Processing helix chain 'BM' and resid 12 through 45 Processing helix chain 'BN' and resid 12 through 45 removed outlier: 3.581A pdb=" N SERBN 25 " --> pdb=" O SERBN 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 35 Processing helix chain 'H' and resid 67 through 70 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 209 through 216 removed outlier: 3.548A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 244 removed outlier: 4.176A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 10 Processing helix chain 'L' and resid 31 through 57 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 79 through 82 Processing helix chain 'L' and resid 83 through 112 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.718A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 Processing helix chain 'L' and resid 151 through 163 Processing helix chain 'L' and resid 164 through 165 No H-bonds generated for 'chain 'L' and resid 164 through 165' Processing helix chain 'L' and resid 166 through 169 Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 221 Processing helix chain 'L' and resid 225 through 250 removed outlier: 3.874A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 262 Processing helix chain 'L' and resid 263 through 268 removed outlier: 3.670A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 29 Processing helix chain 'M' and resid 38 through 42 Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 89 through 92 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 112 through 140 Processing helix chain 'M' and resid 144 through 162 removed outlier: 3.585A pdb=" N SER M 152 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.565A pdb=" N GLU M 173 " --> pdb=" O SER M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 193 removed outlier: 3.610A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 Processing helix chain 'M' and resid 263 through 287 removed outlier: 3.605A pdb=" N ARG M 267 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'UU' and resid 5 through 30 Processing helix chain 'UU' and resid 31 through 48 removed outlier: 3.642A pdb=" N GLYUU 35 " --> pdb=" O HISUU 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 55 Processing helix chain 'X' and resid 56 through 59 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7 removed outlier: 4.218A pdb=" N PHE H 7 " --> pdb=" O PHE H 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 62 through 65 Processing sheet with id=AA3, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.431A pdb=" N GLY H 162 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU H 183 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL H 164 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL H 181 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP H 166 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU H 179 " --> pdb=" O ASP H 166 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP H 168 " --> pdb=" O ARG H 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.733A pdb=" N VAL H 153 " --> pdb=" O ALA H 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 141 through 144 removed outlier: 6.602A pdb=" N GLN M 11 " --> pdb=" O SER H 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 25 through 26 1286 hydrogen bonds defined for protein. 3654 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 6439 1.37 - 1.57: 16588 1.57 - 1.78: 15 1.78 - 1.99: 174 1.99 - 2.19: 128 Bond restraints: 23344 Sorted by residual: bond pdb=" O6 CD4 M 405 " pdb=" P1 CD4 M 405 " ideal model delta sigma weight residual 1.492 1.606 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" O11 CD4 M 405 " pdb=" P2 CD4 M 405 " ideal model delta sigma weight residual 1.505 1.606 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C4A BPH M 402 " pdb=" NA BPH M 402 " ideal model delta sigma weight residual 1.312 1.384 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C4A BPH L 301 " pdb=" NA BPH L 301 " ideal model delta sigma weight residual 1.312 1.383 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C2 UQ1 L 303 " pdb=" O2 UQ1 L 303 " ideal model delta sigma weight residual 1.341 1.399 -0.058 2.00e-02 2.50e+03 8.27e+00 ... (remaining 23339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 31294 2.89 - 5.79: 662 5.79 - 8.68: 82 8.68 - 11.58: 13 11.58 - 14.47: 1 Bond angle restraints: 32052 Sorted by residual: angle pdb=" C3 UQ1 L 303 " pdb=" O3 UQ1 L 303 " pdb=" CM3 UQ1 L 303 " ideal model delta sigma weight residual 115.37 129.84 -14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" C6 UQ1 L 303 " pdb=" C7 UQ1 L 303 " pdb=" C8 UQ1 L 303 " ideal model delta sigma weight residual 110.15 121.69 -11.54 3.00e+00 1.11e-01 1.48e+01 angle pdb=" O11 CD4 M 405 " pdb=" P2 CD4 M 405 " pdb=" O12 CD4 M 405 " ideal model delta sigma weight residual 119.01 108.58 10.43 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C4 U10 M 404 " pdb=" O4 U10 M 404 " pdb=" C4M U10 M 404 " ideal model delta sigma weight residual 120.00 130.35 -10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C18 CD4 M 405 " pdb=" C17 CD4 M 405 " pdb=" O3 CD4 M 405 " ideal model delta sigma weight residual 110.43 120.76 -10.33 3.00e+00 1.11e-01 1.18e+01 ... (remaining 32047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 12066 35.95 - 71.91: 235 71.91 - 107.86: 37 107.86 - 143.81: 11 143.81 - 179.77: 9 Dihedral angle restraints: 12358 sinusoidal: 5733 harmonic: 6625 Sorted by residual: dihedral pdb=" C1 BCLAI 101 " pdb=" C2 BCLAI 101 " pdb=" C3 BCLAI 101 " pdb=" C5 BCLAI 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.23 -179.77 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCLAC 102 " pdb=" C2 BCLAC 102 " pdb=" C3 BCLAC 102 " pdb=" C5 BCLAC 102 " ideal model delta sinusoidal sigma weight residual 180.00 1.82 178.18 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCLAB 101 " pdb=" C2 BCLAB 101 " pdb=" C3 BCLAB 101 " pdb=" C5 BCLAB 101 " ideal model delta sinusoidal sigma weight residual 180.00 1.87 178.13 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 12355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2110 0.044 - 0.087: 772 0.087 - 0.131: 203 0.131 - 0.174: 60 0.174 - 0.218: 11 Chirality restraints: 3156 Sorted by residual: chirality pdb=" C2C BPH M 402 " pdb=" C1C BPH M 402 " pdb=" C3C BPH M 402 " pdb=" CMC BPH M 402 " both_signs ideal model delta sigma weight residual False -2.81 -2.59 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C3B LMTAA1003 " pdb=" C2B LMTAA1003 " pdb=" C4B LMTAA1003 " pdb=" O3B LMTAA1003 " both_signs ideal model delta sigma weight residual False 2.50 2.29 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C3B LMT X 101 " pdb=" C2B LMT X 101 " pdb=" C4B LMT X 101 " pdb=" O3B LMT X 101 " both_signs ideal model delta sigma weight residual False 2.50 2.30 0.20 2.00e-01 2.50e+01 9.60e-01 ... (remaining 3153 not shown) Planarity restraints: 3928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCLAL1001 " 0.075 1.50e-02 4.44e+03 6.30e-02 8.81e+01 pdb=" C2 BCLAL1001 " -0.094 1.50e-02 4.44e+03 pdb=" C3 BCLAL1001 " -0.040 1.50e-02 4.44e+03 pdb=" C4 BCLAL1001 " -0.002 1.50e-02 4.44e+03 pdb=" C5 BCLAL1001 " 0.062 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCLAD 102 " -0.070 1.50e-02 4.44e+03 5.86e-02 7.63e+01 pdb=" C2 BCLAD 102 " 0.091 1.50e-02 4.44e+03 pdb=" C3 BCLAD 102 " 0.032 1.50e-02 4.44e+03 pdb=" C4 BCLAD 102 " 0.002 1.50e-02 4.44e+03 pdb=" C5 BCLAD 102 " -0.055 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCLAM1001 " 0.068 1.50e-02 4.44e+03 5.76e-02 7.37e+01 pdb=" C2 BCLAM1001 " -0.080 1.50e-02 4.44e+03 pdb=" C3 BCLAM1001 " -0.045 1.50e-02 4.44e+03 pdb=" C4 BCLAM1001 " -0.001 1.50e-02 4.44e+03 pdb=" C5 BCLAM1001 " 0.059 1.50e-02 4.44e+03 ... (remaining 3925 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 91 2.63 - 3.19: 18454 3.19 - 3.76: 36847 3.76 - 4.33: 53079 4.33 - 4.90: 84521 Nonbonded interactions: 192992 Sorted by model distance: nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 408 " model vdw 2.058 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 408 " model vdw 2.107 2.260 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 408 " model vdw 2.237 2.340 nonbonded pdb=" NE2 HIS M 219 " pdb="FE FE M 408 " model vdw 2.269 2.340 nonbonded pdb=" NE2 HIS L 230 " pdb="FE FE M 408 " model vdw 2.339 2.340 ... (remaining 192987 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 'AA' and resid 4 through 46) selection = (chain 'AL' and resid 4 through 46) selection = (chain 'AN' and resid 4 through 46) } ncs_group { reference = (chain 'AB' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AC' and resid 1 through 55) selection = (chain 'AD' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AE' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AF' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AG' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AH' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AI' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AJ' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AK' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AM' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) } ncs_group { reference = (chain 'BA' and resid 11 through 48) selection = (chain 'BB' and resid 11 through 48) selection = (chain 'BC' and resid 11 through 48) selection = (chain 'BD' and resid 11 through 48) selection = (chain 'BE' and resid 11 through 48) selection = (chain 'BF' and resid 11 through 48) selection = (chain 'BG' and resid 11 through 48) selection = (chain 'BH' and resid 11 through 48) selection = (chain 'BI' and resid 11 through 48) selection = (chain 'BJ' and resid 11 through 48) selection = (chain 'BK' and resid 11 through 48) selection = (chain 'BL' and resid 11 through 48) selection = (chain 'BM' and resid 11 through 48) selection = (chain 'BN' and resid 11 through 48) } 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: 12.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.500 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.050 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:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.402 23376 Z= 1.494 Angle : 0.997 14.469 32052 Z= 0.474 Chirality : 0.050 0.218 3156 Planarity : 0.009 0.138 3928 Dihedral : 16.306 179.766 8100 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.21 % Allowed : 0.95 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.15), residues: 2225 helix: 1.03 (0.11), residues: 1420 sheet: 0.96 (0.96), residues: 22 loop : 0.39 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.004 ARGAD 15 TYR 0.040 0.005 TYRBL 8 PHE 0.029 0.003 PHEAJ 11 TRP 0.039 0.003 TRPBK 47 HIS 0.013 0.002 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.24 (23344) covalent geometry : angle 0.99744 / 0.47 (32052) hydrogen bonds : bond 0.15210 / 9.67 ( 1284) hydrogen bonds : angle 5.40553 / 3.90 ( 3654) Misc. bond : bond 0.39830 / 23.29 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 470 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: AE 15 ARG cc_start: 0.7176 (ttm-80) cc_final: 0.6254 (ttt-90) REVERT: AE 52 ASN cc_start: 0.7978 (m-40) cc_final: 0.7707 (m110) REVERT: AI 9 MET cc_start: 0.7656 (mtp) cc_final: 0.7445 (mtp) REVERT: AJ 54 VAL cc_start: 0.6622 (t) cc_final: 0.6396 (m) REVERT: BG 42 TYR cc_start: 0.8539 (t80) cc_final: 0.8326 (t80) REVERT: H 60 LYS cc_start: 0.7995 (mtpt) cc_final: 0.7699 (mtmm) REVERT: M 292 ASP cc_start: 0.7867 (p0) cc_final: 0.7547 (p0) REVERT: X 29 LYS cc_start: 0.7482 (mtpp) cc_final: 0.7174 (tttp) outliers start: 4 outliers final: 3 residues processed: 473 average time/residue: 0.5813 time to fit residues: 314.8971 Evaluate side-chains 353 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 350 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 216 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AA 20 GLN AI 20 GLN AL 20 GLN BA 15 GLN BC 17 GLN BE 15 GLN L 62 GLN X 61 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116025 restraints weight = 23159.754| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 0.95 r_work: 0.3059 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 23376 Z= 0.340 Angle : 1.006 18.333 32052 Z= 0.418 Chirality : 0.053 0.264 3156 Planarity : 0.006 0.094 3928 Dihedral : 18.316 179.760 4108 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.74 % Allowed : 8.33 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.17), residues: 2225 helix: 1.57 (0.12), residues: 1529 sheet: 0.31 (1.11), residues: 19 loop : 0.57 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAN 15 TYR 0.032 0.003 TYRAG 41 PHE 0.039 0.003 PHE H 20 TRP 0.030 0.003 TRPBK 47 HIS 0.013 0.003 HIS M 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00840 / 0.34 (23344) covalent geometry : angle 1.00594 / 0.42 (32052) hydrogen bonds : bond 0.07297 / 4.71 ( 1284) hydrogen bonds : angle 4.03281 / 2.88 ( 3654) Misc. bond : bond 0.00499 / 0.31 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 347 time to evaluate : 0.818 Fit side-chains REVERT: AE 15 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.6584 (tmt-80) REVERT: AE 45 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: AF 30 MET cc_start: 0.8004 (mmm) cc_final: 0.7739 (mmp) REVERT: AG 3 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7965 (mtpt) REVERT: AG 5 TYR cc_start: 0.8500 (p90) cc_final: 0.8271 (p90) REVERT: AJ 54 VAL cc_start: 0.6851 (t) cc_final: 0.6601 (m) REVERT: AL 9 MET cc_start: 0.7288 (mmm) cc_final: 0.6802 (mtp) REVERT: AL 10 ILE cc_start: 0.7538 (mm) cc_final: 0.6853 (tt) REVERT: AM 50 LYS cc_start: 0.7721 (tttm) cc_final: 0.7490 (tttm) REVERT: BE 17 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7787 (mt0) REVERT: BM 28 TRP cc_start: 0.6790 (m100) cc_final: 0.5532 (m-90) REVERT: M 292 ASP cc_start: 0.8315 (p0) cc_final: 0.8005 (p0) REVERT: X 21 LEU cc_start: 0.8294 (mt) cc_final: 0.7968 (mm) REVERT: X 29 LYS cc_start: 0.7756 (mtpp) cc_final: 0.6930 (tttp) outliers start: 52 outliers final: 23 residues processed: 366 average time/residue: 0.6216 time to fit residues: 261.9372 Evaluate side-chains 350 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 324 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 38 THR Chi-restraints excluded: chain AB residue 30 MET Chi-restraints excluded: chain AE residue 45 GLU Chi-restraints excluded: chain AG residue 3 LYS Chi-restraints excluded: chain AG residue 40 SER Chi-restraints excluded: chain AH residue 9 MET Chi-restraints excluded: chain AJ residue 10 ILE Chi-restraints excluded: chain AJ residue 40 SER Chi-restraints excluded: chain BE residue 17 GLN Chi-restraints excluded: chain BE residue 31 SER Chi-restraints excluded: chain BG residue 31 SER Chi-restraints excluded: chain BH residue 11 LEU Chi-restraints excluded: chain BI residue 19 LEU Chi-restraints excluded: chain BJ residue 17 GLN Chi-restraints excluded: chain BK residue 12 THR Chi-restraints excluded: chain BK residue 25 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain UU residue 42 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 chunk 105 optimal weight: 0.0010 chunk 11 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AF 20 GLN AL 20 GLN ** AM 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121821 restraints weight = 22948.716| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 0.81 r_work: 0.3142 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23376 Z= 0.129 Angle : 0.656 13.715 32052 Z= 0.270 Chirality : 0.038 0.148 3156 Planarity : 0.004 0.042 3928 Dihedral : 16.544 179.942 4108 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.90 % Allowed : 9.07 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.17), residues: 2225 helix: 2.56 (0.12), residues: 1509 sheet: 1.97 (1.45), residues: 12 loop : 0.94 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAF 14 TYR 0.012 0.001 TYR M 198 PHE 0.021 0.002 PHE H 20 TRP 0.019 0.002 TRPBK 47 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (23344) covalent geometry : angle 0.65643 / 0.27 (32052) hydrogen bonds : bond 0.05258 / 3.40 ( 1284) hydrogen bonds : angle 3.49941 / 2.47 ( 3654) Misc. bond : bond 0.00161 / 0.10 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 361 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: AE 6 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8160 (mptt) REVERT: AE 15 ARG cc_start: 0.7556 (ttm-80) cc_final: 0.6545 (tmt-80) REVERT: AF 30 MET cc_start: 0.7913 (mmm) cc_final: 0.7661 (mmp) REVERT: AG 3 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7767 (mtpt) REVERT: AG 5 TYR cc_start: 0.8477 (p90) cc_final: 0.8190 (p90) REVERT: AH 1 MET cc_start: 0.5359 (mpm) cc_final: 0.4965 (tmm) REVERT: AK 9 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7630 (mpp) REVERT: AL 10 ILE cc_start: 0.7453 (mm) cc_final: 0.6799 (tt) REVERT: AM 50 LYS cc_start: 0.7699 (tttm) cc_final: 0.7482 (tttm) REVERT: BE 17 GLN cc_start: 0.7995 (mt0) cc_final: 0.7656 (mt0) REVERT: BF 8 TYR cc_start: 0.6647 (m-10) cc_final: 0.6318 (m-10) REVERT: BG 18 GLU cc_start: 0.7534 (tp30) cc_final: 0.7269 (tp30) REVERT: BI 17 GLN cc_start: 0.8016 (tp40) cc_final: 0.7650 (tt0) REVERT: BI 29 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8102 (tt) REVERT: M 292 ASP cc_start: 0.8235 (p0) cc_final: 0.7967 (p0) REVERT: X 21 LEU cc_start: 0.8233 (mt) cc_final: 0.7915 (mm) REVERT: X 29 LYS cc_start: 0.7708 (mtpp) cc_final: 0.7002 (tttp) outliers start: 36 outliers final: 12 residues processed: 376 average time/residue: 0.5811 time to fit residues: 252.5971 Evaluate side-chains 343 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 327 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 6 LYS Chi-restraints excluded: chain AG residue 3 LYS Chi-restraints excluded: chain AG residue 40 SER Chi-restraints excluded: chain AJ residue 10 ILE Chi-restraints excluded: chain AK residue 9 MET Chi-restraints excluded: chain BF residue 21 SER Chi-restraints excluded: chain BI residue 19 LEU Chi-restraints excluded: chain BI residue 29 LEU Chi-restraints excluded: chain BK residue 25 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain M residue 303 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 160 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AL 20 GLN ** AM 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.146197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117835 restraints weight = 22849.004| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.01 r_work: 0.3110 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23376 Z= 0.174 Angle : 0.731 15.081 32052 Z= 0.298 Chirality : 0.041 0.152 3156 Planarity : 0.004 0.043 3928 Dihedral : 16.655 179.864 4105 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.80 % Allowed : 9.23 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.17), residues: 2225 helix: 2.47 (0.12), residues: 1515 sheet: -0.61 (0.98), residues: 24 loop : 0.77 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 103 TYR 0.017 0.002 TYRAG 41 PHE 0.027 0.002 PHE H 20 TRP 0.019 0.002 TRPBK 47 HIS 0.008 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (23344) covalent geometry : angle 0.73061 / 0.30 (32052) hydrogen bonds : bond 0.05818 / 3.76 ( 1284) hydrogen bonds : angle 3.59032 / 2.54 ( 3654) Misc. bond : bond 0.00283 / 0.17 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 0.807 Fit side-chains REVERT: AE 6 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8187 (mptt) REVERT: AE 15 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.6551 (tmt-80) REVERT: AE 45 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: AF 30 MET cc_start: 0.7951 (mmm) cc_final: 0.7639 (mmp) REVERT: AG 3 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7845 (mtpt) REVERT: AG 5 TYR cc_start: 0.8503 (p90) cc_final: 0.8155 (p90) REVERT: AH 1 MET cc_start: 0.5263 (mpm) cc_final: 0.4788 (tmm) REVERT: AK 9 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7511 (mpp) REVERT: AL 10 ILE cc_start: 0.7419 (mm) cc_final: 0.6810 (tt) REVERT: AM 1 MET cc_start: 0.5460 (OUTLIER) cc_final: 0.4989 (tmt) REVERT: AM 20 GLN cc_start: 0.7070 (tp40) cc_final: 0.6864 (tp-100) REVERT: AM 50 LYS cc_start: 0.7678 (tttm) cc_final: 0.7414 (tttm) REVERT: BE 17 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7632 (mt0) REVERT: BF 8 TYR cc_start: 0.6491 (m-10) cc_final: 0.6190 (m-10) REVERT: BG 18 GLU cc_start: 0.7541 (tp30) cc_final: 0.7206 (tp30) REVERT: BI 17 GLN cc_start: 0.7974 (tp40) cc_final: 0.7609 (tt0) REVERT: BI 29 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8061 (tt) REVERT: BN 24 MET cc_start: 0.5435 (OUTLIER) cc_final: 0.4963 (mmt) REVERT: M 52 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8246 (mp) REVERT: M 292 ASP cc_start: 0.8230 (p0) cc_final: 0.7938 (p0) REVERT: X 16 LYS cc_start: 0.4988 (OUTLIER) cc_final: 0.4752 (ttpp) REVERT: X 21 LEU cc_start: 0.8228 (mt) cc_final: 0.7930 (mm) REVERT: X 29 LYS cc_start: 0.7838 (mtpp) cc_final: 0.7071 (tttp) outliers start: 53 outliers final: 22 residues processed: 353 average time/residue: 0.5832 time to fit residues: 236.6405 Evaluate side-chains 354 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 322 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 30 MET Chi-restraints excluded: chain AE residue 6 LYS Chi-restraints excluded: chain AE residue 45 GLU Chi-restraints excluded: chain AG residue 3 LYS Chi-restraints excluded: chain AG residue 40 SER Chi-restraints excluded: chain AH residue 3 LYS Chi-restraints excluded: chain AJ residue 10 ILE Chi-restraints excluded: chain AJ residue 40 SER Chi-restraints excluded: chain AK residue 9 MET Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain BE residue 17 GLN Chi-restraints excluded: chain BF residue 21 SER Chi-restraints excluded: chain BG residue 31 SER Chi-restraints excluded: chain BI residue 14 GLU Chi-restraints excluded: chain BI residue 19 LEU Chi-restraints excluded: chain BI residue 29 LEU Chi-restraints excluded: chain BJ residue 17 GLN Chi-restraints excluded: chain BK residue 12 THR Chi-restraints excluded: chain BK residue 25 SER Chi-restraints excluded: chain BN residue 24 MET Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain X residue 16 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 82 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 193 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AJ 20 GLN AL 20 GLN ** AM 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117904 restraints weight = 22737.962| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.03 r_work: 0.3077 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 23376 Z= 0.214 Angle : 0.792 16.209 32052 Z= 0.321 Chirality : 0.043 0.169 3156 Planarity : 0.005 0.056 3928 Dihedral : 16.902 179.828 4105 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.80 % Allowed : 10.07 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.17), residues: 2225 helix: 2.25 (0.12), residues: 1520 sheet: -0.61 (0.98), residues: 24 loop : 0.64 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGAN 15 TYR 0.020 0.002 TYRAG 41 PHE 0.029 0.002 PHE H 20 TRP 0.021 0.002 TRPBK 47 HIS 0.009 0.002 HIS M 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.21 (23344) covalent geometry : angle 0.79157 / 0.32 (32052) hydrogen bonds : bond 0.06165 / 3.99 ( 1284) hydrogen bonds : angle 3.68670 / 2.61 ( 3654) Misc. bond : bond 0.00330 / 0.20 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 334 time to evaluate : 0.844 Fit side-chains REVERT: AE 15 ARG cc_start: 0.7672 (ttm-80) cc_final: 0.6566 (tmt-80) REVERT: AE 45 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: AF 30 MET cc_start: 0.8014 (mmm) cc_final: 0.7730 (mmp) REVERT: AG 3 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7884 (mtpt) REVERT: AG 5 TYR cc_start: 0.8514 (p90) cc_final: 0.8180 (p90) REVERT: AH 1 MET cc_start: 0.5376 (mpm) cc_final: 0.4839 (tmm) REVERT: AH 45 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: AK 9 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7558 (mpp) REVERT: AL 9 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6817 (mmm) REVERT: AL 10 ILE cc_start: 0.7392 (mm) cc_final: 0.6824 (tt) REVERT: AM 1 MET cc_start: 0.5473 (OUTLIER) cc_final: 0.4790 (tmt) REVERT: AM 20 GLN cc_start: 0.7097 (tp40) cc_final: 0.6871 (tp-100) REVERT: AM 50 LYS cc_start: 0.7656 (tttm) cc_final: 0.7409 (tttm) REVERT: BE 17 GLN cc_start: 0.8077 (mt0) cc_final: 0.7733 (mt0) REVERT: BF 8 TYR cc_start: 0.6589 (m-10) cc_final: 0.6269 (m-10) REVERT: BG 18 GLU cc_start: 0.7648 (tp30) cc_final: 0.7282 (tp30) REVERT: BI 17 GLN cc_start: 0.8042 (tt0) cc_final: 0.7626 (tt0) REVERT: BI 29 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8077 (tt) REVERT: BN 24 MET cc_start: 0.5396 (OUTLIER) cc_final: 0.4940 (mmt) REVERT: H 206 ASN cc_start: 0.7853 (m-40) cc_final: 0.7636 (t0) REVERT: M 52 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8304 (mp) REVERT: M 292 ASP cc_start: 0.8240 (p0) cc_final: 0.7986 (p0) REVERT: X 16 LYS cc_start: 0.5121 (OUTLIER) cc_final: 0.4773 (ttpp) REVERT: X 21 LEU cc_start: 0.8286 (mt) cc_final: 0.7980 (mm) REVERT: X 29 LYS cc_start: 0.7879 (mtpp) cc_final: 0.7039 (tttp) outliers start: 53 outliers final: 27 residues processed: 353 average time/residue: 0.6213 time to fit residues: 251.9190 Evaluate side-chains 357 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 320 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 30 MET Chi-restraints excluded: chain AE residue 45 GLU Chi-restraints excluded: chain AG residue 3 LYS Chi-restraints excluded: chain AG residue 40 SER Chi-restraints excluded: chain AH residue 3 LYS Chi-restraints excluded: chain AH residue 45 GLU Chi-restraints excluded: chain AJ residue 10 ILE Chi-restraints excluded: chain AK residue 9 MET Chi-restraints excluded: chain AL residue 9 MET Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain BA residue 11 LEU Chi-restraints excluded: chain BB residue 12 THR Chi-restraints excluded: chain BF residue 21 SER Chi-restraints excluded: chain BF residue 25 SER Chi-restraints excluded: chain BH residue 11 LEU Chi-restraints excluded: chain BI residue 6 LEU Chi-restraints excluded: chain BI residue 14 GLU Chi-restraints excluded: chain BI residue 19 LEU Chi-restraints excluded: chain BI residue 29 LEU Chi-restraints excluded: chain BJ residue 17 GLN Chi-restraints excluded: chain BK residue 12 THR Chi-restraints excluded: chain BK residue 25 SER Chi-restraints excluded: chain BN residue 24 MET Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain X residue 16 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 122 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AL 20 GLN ** AM 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120995 restraints weight = 22839.674| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 0.99 r_work: 0.3144 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23376 Z= 0.131 Angle : 0.648 14.158 32052 Z= 0.263 Chirality : 0.038 0.147 3156 Planarity : 0.004 0.037 3928 Dihedral : 15.985 179.929 4105 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.69 % Allowed : 10.50 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.17), residues: 2225 helix: 2.60 (0.12), residues: 1521 sheet: -0.45 (1.00), residues: 24 loop : 0.77 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAF 14 TYR 0.017 0.001 TYRAF 5 PHE 0.021 0.001 PHE H 20 TRP 0.018 0.002 TRPAN 43 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (23344) covalent geometry : angle 0.64800 / 0.26 (32052) hydrogen bonds : bond 0.05185 / 3.35 ( 1284) hydrogen bonds : angle 3.47592 / 2.45 ( 3654) Misc. bond : bond 0.00203 / 0.11 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 334 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: AE 15 ARG cc_start: 0.7538 (ttm-80) cc_final: 0.6531 (tmt-80) REVERT: AE 45 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: AF 14 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.6796 (ttp-110) REVERT: AF 30 MET cc_start: 0.7922 (mmm) cc_final: 0.7649 (mmp) REVERT: AG 3 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7804 (mtpt) REVERT: AG 5 TYR cc_start: 0.8490 (p90) cc_final: 0.8196 (p90) REVERT: AH 1 MET cc_start: 0.5324 (mpm) cc_final: 0.4792 (tmm) REVERT: AK 9 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7552 (mpp) REVERT: AL 9 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6808 (mmm) REVERT: AL 10 ILE cc_start: 0.7325 (mm) cc_final: 0.6740 (tt) REVERT: AM 1 MET cc_start: 0.5593 (tmt) cc_final: 0.5342 (tpt) REVERT: AM 20 GLN cc_start: 0.7112 (tp40) cc_final: 0.6881 (tp-100) REVERT: BA 13 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8021 (t70) REVERT: BB 11 LEU cc_start: 0.8188 (mt) cc_final: 0.7988 (mp) REVERT: BF 8 TYR cc_start: 0.6585 (m-10) cc_final: 0.6194 (m-10) REVERT: BI 17 GLN cc_start: 0.7940 (tt0) cc_final: 0.7539 (tt0) REVERT: BI 29 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8045 (tt) REVERT: BN 24 MET cc_start: 0.5400 (OUTLIER) cc_final: 0.4959 (mmt) REVERT: M 263 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: M 292 ASP cc_start: 0.8173 (p0) cc_final: 0.7905 (p0) REVERT: X 16 LYS cc_start: 0.5128 (OUTLIER) cc_final: 0.4890 (ttpp) REVERT: X 21 LEU cc_start: 0.8235 (mt) cc_final: 0.7941 (mm) REVERT: X 29 LYS cc_start: 0.7806 (mtpp) cc_final: 0.6988 (tttp) outliers start: 51 outliers final: 20 residues processed: 352 average time/residue: 0.6296 time to fit residues: 254.7320 Evaluate side-chains 351 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 322 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 45 GLU Chi-restraints excluded: chain AG residue 3 LYS Chi-restraints excluded: chain AG residue 40 SER Chi-restraints excluded: chain AH residue 3 LYS Chi-restraints excluded: chain AJ residue 10 ILE Chi-restraints excluded: chain AJ residue 40 SER Chi-restraints excluded: chain AK residue 9 MET Chi-restraints excluded: chain AL residue 9 MET Chi-restraints excluded: chain BA residue 13 ASP Chi-restraints excluded: chain BB residue 18 GLU Chi-restraints excluded: chain BF residue 21 SER Chi-restraints excluded: chain BH residue 11 LEU Chi-restraints excluded: chain BI residue 6 LEU Chi-restraints excluded: chain BI residue 14 GLU Chi-restraints excluded: chain BI residue 19 LEU Chi-restraints excluded: chain BI residue 29 LEU Chi-restraints excluded: chain BK residue 12 THR Chi-restraints excluded: chain BK residue 25 SER Chi-restraints excluded: chain BN residue 24 MET Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 42 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 147 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AJ 20 GLN AL 20 GLN ** AM 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117145 restraints weight = 22789.096| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.00 r_work: 0.3101 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 23376 Z= 0.245 Angle : 0.834 17.015 32052 Z= 0.337 Chirality : 0.045 0.192 3156 Planarity : 0.005 0.064 3928 Dihedral : 16.816 179.759 4105 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.11 % Allowed : 10.28 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.17), residues: 2225 helix: 2.17 (0.12), residues: 1520 sheet: -0.60 (0.97), residues: 24 loop : 0.55 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAN 15 TYR 0.022 0.003 TYR M 101 PHE 0.031 0.002 PHE H 20 TRP 0.021 0.002 TRPAN 43 HIS 0.010 0.002 HIS M 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.25 (23344) covalent geometry : angle 0.83426 / 0.34 (32052) hydrogen bonds : bond 0.06332 / 4.09 ( 1284) hydrogen bonds : angle 3.73349 / 2.65 ( 3654) Misc. bond : bond 0.00368 / 0.22 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 329 time to evaluate : 0.838 Fit side-chains REVERT: AE 6 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8280 (mptt) REVERT: AE 15 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.6600 (tmt-80) REVERT: AE 45 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: AF 9 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8014 (mtt) REVERT: AF 30 MET cc_start: 0.7934 (mmm) cc_final: 0.7661 (mmp) REVERT: AG 3 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7880 (mtpt) REVERT: AG 5 TYR cc_start: 0.8524 (p90) cc_final: 0.8197 (p90) REVERT: AH 1 MET cc_start: 0.5362 (mpm) cc_final: 0.4756 (tmm) REVERT: AK 9 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7507 (mpp) REVERT: AL 9 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6835 (mmm) REVERT: AL 10 ILE cc_start: 0.7416 (mm) cc_final: 0.6859 (tt) REVERT: AM 20 GLN cc_start: 0.7102 (tp40) cc_final: 0.6840 (tp-100) REVERT: BF 8 TYR cc_start: 0.6555 (m-10) cc_final: 0.6185 (m-10) REVERT: BI 17 GLN cc_start: 0.7990 (tt0) cc_final: 0.7569 (tt0) REVERT: BI 29 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8076 (tt) REVERT: BM 31 SER cc_start: 0.7919 (p) cc_final: 0.7710 (m) REVERT: BN 24 MET cc_start: 0.5455 (OUTLIER) cc_final: 0.5020 (mmt) REVERT: M 263 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: M 292 ASP cc_start: 0.8186 (p0) cc_final: 0.7930 (p0) REVERT: X 16 LYS cc_start: 0.5169 (OUTLIER) cc_final: 0.4401 (tttt) REVERT: X 21 LEU cc_start: 0.8288 (mt) cc_final: 0.7987 (mm) REVERT: X 29 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7050 (tttp) outliers start: 59 outliers final: 29 residues processed: 355 average time/residue: 0.6100 time to fit residues: 248.6502 Evaluate side-chains 355 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 316 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 6 LYS Chi-restraints excluded: chain AE residue 45 GLU Chi-restraints excluded: chain AF residue 9 MET Chi-restraints excluded: chain AG residue 3 LYS Chi-restraints excluded: chain AG residue 40 SER Chi-restraints excluded: chain AH residue 3 LYS Chi-restraints excluded: chain AJ residue 10 ILE Chi-restraints excluded: chain AK residue 9 MET Chi-restraints excluded: chain AL residue 9 MET Chi-restraints excluded: chain AN residue 45 GLU Chi-restraints excluded: chain BA residue 11 LEU Chi-restraints excluded: chain BB residue 12 THR Chi-restraints excluded: chain BB residue 18 GLU Chi-restraints excluded: chain BF residue 21 SER Chi-restraints excluded: chain BG residue 31 SER Chi-restraints excluded: chain BH residue 11 LEU Chi-restraints excluded: chain BI residue 6 LEU Chi-restraints excluded: chain BI residue 14 GLU Chi-restraints excluded: chain BI residue 19 LEU Chi-restraints excluded: chain BI residue 29 LEU Chi-restraints excluded: chain BJ residue 17 GLN Chi-restraints excluded: chain BJ residue 29 LEU Chi-restraints excluded: chain BK residue 12 THR Chi-restraints excluded: chain BK residue 25 SER Chi-restraints excluded: chain BN residue 24 MET Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 42 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 103 optimal weight: 7.9990 chunk 154 optimal weight: 0.0470 chunk 49 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 214 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AL 20 GLN ** AM 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.117394 restraints weight = 22504.319| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.01 r_work: 0.3109 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23376 Z= 0.171 Angle : 0.728 15.292 32052 Z= 0.295 Chirality : 0.040 0.166 3156 Planarity : 0.004 0.043 3928 Dihedral : 16.337 179.895 4105 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.64 % Allowed : 10.81 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.17), residues: 2225 helix: 2.33 (0.12), residues: 1520 sheet: -0.53 (0.99), residues: 24 loop : 0.60 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAF 14 TYR 0.017 0.002 TYR M 101 PHE 0.026 0.002 PHE H 20 TRP 0.023 0.002 TRPAN 43 HIS 0.008 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (23344) covalent geometry : angle 0.72793 / 0.30 (32052) hydrogen bonds : bond 0.05726 / 3.71 ( 1284) hydrogen bonds : angle 3.60834 / 2.55 ( 3654) Misc. bond : bond 0.00266 / 0.16 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 330 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: AE 15 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.6520 (tmt-80) REVERT: AE 45 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: AF 9 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7950 (mtt) REVERT: AF 14 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.6791 (ttp-110) REVERT: AF 30 MET cc_start: 0.7928 (mmm) cc_final: 0.7646 (mmp) REVERT: AG 3 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7913 (mtpt) REVERT: AG 5 TYR cc_start: 0.8496 (p90) cc_final: 0.8177 (p90) REVERT: AH 1 MET cc_start: 0.5304 (mpm) cc_final: 0.4717 (tmm) REVERT: AI 3 LYS cc_start: 0.7659 (tppp) cc_final: 0.7420 (tppp) REVERT: AK 9 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7515 (mpp) REVERT: AL 10 ILE cc_start: 0.7343 (mm) cc_final: 0.6768 (tt) REVERT: AM 20 GLN cc_start: 0.7024 (tp40) cc_final: 0.6750 (tp-100) REVERT: BF 8 TYR cc_start: 0.6477 (m-10) cc_final: 0.6139 (m-10) REVERT: BI 17 GLN cc_start: 0.7913 (tt0) cc_final: 0.7490 (tt0) REVERT: BI 29 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8047 (tt) REVERT: BN 24 MET cc_start: 0.5364 (OUTLIER) cc_final: 0.4938 (mmt) REVERT: M 52 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8302 (mp) REVERT: M 263 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: M 292 ASP cc_start: 0.8200 (p0) cc_final: 0.7943 (p0) REVERT: X 16 LYS cc_start: 0.5080 (OUTLIER) cc_final: 0.4345 (tttt) REVERT: X 21 LEU cc_start: 0.8265 (mt) cc_final: 0.7965 (mm) REVERT: X 29 LYS cc_start: 0.7868 (mtpp) cc_final: 0.7052 (tttp) outliers start: 50 outliers final: 29 residues processed: 350 average time/residue: 0.6264 time to fit residues: 251.5417 Evaluate side-chains 361 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 323 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 45 GLU Chi-restraints excluded: chain AF residue 9 MET Chi-restraints excluded: chain AG residue 3 LYS Chi-restraints excluded: chain AG residue 40 SER Chi-restraints excluded: chain AH residue 3 LYS Chi-restraints excluded: chain AJ residue 10 ILE Chi-restraints excluded: chain AK residue 9 MET Chi-restraints excluded: chain AL residue 9 MET Chi-restraints excluded: chain BA residue 11 LEU Chi-restraints excluded: chain BB residue 18 GLU Chi-restraints excluded: chain BE residue 25 SER Chi-restraints excluded: chain BF residue 21 SER Chi-restraints excluded: chain BH residue 11 LEU Chi-restraints excluded: chain BI residue 6 LEU Chi-restraints excluded: chain BI residue 14 GLU Chi-restraints excluded: chain BI residue 19 LEU Chi-restraints excluded: chain BI residue 29 LEU Chi-restraints excluded: chain BJ residue 17 GLN Chi-restraints excluded: chain BJ residue 29 LEU Chi-restraints excluded: chain BK residue 12 THR Chi-restraints excluded: chain BK residue 25 SER Chi-restraints excluded: chain BN residue 24 MET Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 42 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 81 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 213 optimal weight: 0.5980 chunk 69 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AB 20 GLN AJ 20 GLN AL 20 GLN ** AM 20 GLN ** 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 = 0.3702 r_free = 0.3702 target = 0.146461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117581 restraints weight = 22561.786| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.01 r_work: 0.3114 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23376 Z= 0.167 Angle : 0.723 15.074 32052 Z= 0.293 Chirality : 0.040 0.162 3156 Planarity : 0.004 0.043 3928 Dihedral : 16.179 179.908 4105 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.43 % Allowed : 11.39 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.17), residues: 2225 helix: 2.36 (0.12), residues: 1520 sheet: -0.52 (1.00), residues: 24 loop : 0.63 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAF 14 TYR 0.017 0.002 TYR M 101 PHE 0.025 0.002 PHE H 20 TRP 0.022 0.002 TRPAN 43 HIS 0.008 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (23344) covalent geometry : angle 0.72301 / 0.29 (32052) hydrogen bonds : bond 0.05675 / 3.67 ( 1284) hydrogen bonds : angle 3.59732 / 2.55 ( 3654) Misc. bond : bond 0.00264 / 0.16 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 332 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: AE 15 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.6505 (tmt-80) REVERT: AE 45 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: AF 9 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7905 (mtt) REVERT: AF 14 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.6753 (ttp-110) REVERT: AF 30 MET cc_start: 0.7924 (mmm) cc_final: 0.7646 (mmp) REVERT: AG 3 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7902 (mtpt) REVERT: AG 5 TYR cc_start: 0.8503 (p90) cc_final: 0.8189 (p90) REVERT: AH 1 MET cc_start: 0.5341 (mpm) cc_final: 0.4715 (tmm) REVERT: AH 45 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: AI 3 LYS cc_start: 0.7595 (tppp) cc_final: 0.7333 (tppp) REVERT: AI 6 LYS cc_start: 0.7789 (mttt) cc_final: 0.7581 (mttt) REVERT: AK 9 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7539 (mpp) REVERT: AL 10 ILE cc_start: 0.7373 (mm) cc_final: 0.6776 (tt) REVERT: AM 20 GLN cc_start: 0.7079 (tp40) cc_final: 0.6804 (tp-100) REVERT: BF 8 TYR cc_start: 0.6488 (m-10) cc_final: 0.6120 (m-10) REVERT: BI 17 GLN cc_start: 0.7872 (tt0) cc_final: 0.7453 (tt0) REVERT: BI 29 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8053 (tt) REVERT: BN 24 MET cc_start: 0.5428 (OUTLIER) cc_final: 0.4989 (mmt) REVERT: M 52 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8293 (mp) REVERT: M 263 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: M 292 ASP cc_start: 0.8198 (p0) cc_final: 0.7939 (p0) REVERT: X 16 LYS cc_start: 0.5103 (OUTLIER) cc_final: 0.4348 (tttt) REVERT: X 21 LEU cc_start: 0.8253 (mt) cc_final: 0.7961 (mm) REVERT: X 29 LYS cc_start: 0.7858 (mtpp) cc_final: 0.7042 (tttp) outliers start: 46 outliers final: 31 residues processed: 348 average time/residue: 0.6408 time to fit residues: 256.3878 Evaluate side-chains 362 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 321 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 45 GLU Chi-restraints excluded: chain AF residue 9 MET Chi-restraints excluded: chain AG residue 3 LYS Chi-restraints excluded: chain AG residue 40 SER Chi-restraints excluded: chain AH residue 3 LYS Chi-restraints excluded: chain AH residue 45 GLU Chi-restraints excluded: chain AJ residue 10 ILE Chi-restraints excluded: chain AJ residue 40 SER Chi-restraints excluded: chain AK residue 9 MET Chi-restraints excluded: chain AL residue 9 MET Chi-restraints excluded: chain AN residue 31 ILE Chi-restraints excluded: chain AN residue 45 GLU Chi-restraints excluded: chain BB residue 18 GLU Chi-restraints excluded: chain BE residue 25 SER Chi-restraints excluded: chain BF residue 21 SER Chi-restraints excluded: chain BH residue 11 LEU Chi-restraints excluded: chain BI residue 6 LEU Chi-restraints excluded: chain BI residue 14 GLU Chi-restraints excluded: chain BI residue 19 LEU Chi-restraints excluded: chain BI residue 29 LEU Chi-restraints excluded: chain BJ residue 17 GLN Chi-restraints excluded: chain BJ residue 29 LEU Chi-restraints excluded: chain BK residue 12 THR Chi-restraints excluded: chain BK residue 25 SER Chi-restraints excluded: chain BN residue 24 MET Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 109 optimal weight: 8.9990 chunk 192 optimal weight: 0.0970 chunk 101 optimal weight: 0.0060 chunk 49 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AL 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120905 restraints weight = 22591.860| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.00 r_work: 0.3153 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23376 Z= 0.119 Angle : 0.629 13.441 32052 Z= 0.257 Chirality : 0.037 0.144 3156 Planarity : 0.003 0.037 3928 Dihedral : 15.566 179.973 4105 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.00 % Allowed : 12.03 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.17), residues: 2225 helix: 2.66 (0.12), residues: 1517 sheet: -0.38 (1.01), residues: 24 loop : 0.76 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAF 14 TYR 0.009 0.001 TYR M 198 PHE 0.020 0.001 PHE X 47 TRP 0.019 0.002 TRP M 252 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (23344) covalent geometry : angle 0.62939 / 0.26 (32052) hydrogen bonds : bond 0.04936 / 3.20 ( 1284) hydrogen bonds : angle 3.44978 / 2.43 ( 3654) Misc. bond : bond 0.00156 / 0.09 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 329 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AE 15 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.6494 (tmt-80) REVERT: AE 45 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: AF 14 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.6686 (ttp-110) REVERT: AF 30 MET cc_start: 0.7922 (mmm) cc_final: 0.7638 (mmp) REVERT: AG 3 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7817 (mtpt) REVERT: AH 1 MET cc_start: 0.5336 (mpm) cc_final: 0.4697 (tmm) REVERT: AI 3 LYS cc_start: 0.7444 (tppp) cc_final: 0.7219 (tppp) REVERT: AK 9 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7498 (mpp) REVERT: AL 6 LYS cc_start: 0.7738 (mttt) cc_final: 0.7497 (mtmm) REVERT: AL 10 ILE cc_start: 0.7303 (mm) cc_final: 0.6690 (tt) REVERT: AM 20 GLN cc_start: 0.7047 (tp40) cc_final: 0.6800 (tp-100) REVERT: BF 8 TYR cc_start: 0.6452 (m-10) cc_final: 0.6063 (m-10) REVERT: BI 17 GLN cc_start: 0.7847 (tt0) cc_final: 0.7417 (tt0) REVERT: BI 28 TRP cc_start: 0.7717 (m100) cc_final: 0.7309 (m100) REVERT: BI 29 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8054 (tt) REVERT: BJ 17 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.6917 (tm-30) REVERT: M 263 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: M 292 ASP cc_start: 0.8186 (p0) cc_final: 0.7924 (p0) REVERT: X 21 LEU cc_start: 0.8217 (mt) cc_final: 0.7928 (mm) REVERT: X 29 LYS cc_start: 0.7789 (mtpp) cc_final: 0.6956 (tttp) outliers start: 38 outliers final: 20 residues processed: 339 average time/residue: 0.6390 time to fit residues: 248.5409 Evaluate side-chains 343 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 317 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 45 GLU Chi-restraints excluded: chain AG residue 3 LYS Chi-restraints excluded: chain AG residue 40 SER Chi-restraints excluded: chain AJ residue 10 ILE Chi-restraints excluded: chain AJ residue 40 SER Chi-restraints excluded: chain AK residue 9 MET Chi-restraints excluded: chain AL residue 9 MET Chi-restraints excluded: chain BE residue 25 SER Chi-restraints excluded: chain BF residue 21 SER Chi-restraints excluded: chain BG residue 31 SER Chi-restraints excluded: chain BI residue 14 GLU Chi-restraints excluded: chain BI residue 19 LEU Chi-restraints excluded: chain BI residue 29 LEU Chi-restraints excluded: chain BJ residue 17 GLN Chi-restraints excluded: chain BK residue 12 THR Chi-restraints excluded: chain BK residue 25 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain X residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 129 optimal weight: 0.3980 chunk 213 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AH 20 GLN AJ 20 GLN AL 20 GLN ** AM 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.145167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116244 restraints weight = 22514.496| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.01 r_work: 0.3095 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 23376 Z= 0.223 Angle : 0.809 16.139 32052 Z= 0.328 Chirality : 0.044 0.187 3156 Planarity : 0.005 0.057 3928 Dihedral : 16.578 179.815 4105 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.11 % Allowed : 12.61 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.17), residues: 2225 helix: 2.23 (0.12), residues: 1520 sheet: 2.10 (1.43), residues: 12 loop : 0.53 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGAN 15 TYR 0.026 0.002 TYRAG 5 PHE 0.029 0.002 PHE H 20 TRP 0.020 0.002 TRPAN 43 HIS 0.010 0.002 HIS M 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.22 (23344) covalent geometry : angle 0.80927 / 0.33 (32052) hydrogen bonds : bond 0.06178 / 4.00 ( 1284) hydrogen bonds : angle 3.70637 / 2.63 ( 3654) Misc. bond : bond 0.00347 / 0.21 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9082.09 seconds wall clock time: 155 minutes 16.15 seconds (9316.15 seconds total)