Starting phenix.real_space_refine on Sat Jul 4 20:10:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hjv_34839/07_2026/8hjv_34839.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hjv_34839/07_2026/8hjv_34839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8hjv_34839/07_2026/8hjv_34839.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hjv_34839/07_2026/8hjv_34839.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hjv_34839/07_2026/8hjv_34839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hjv_34839/07_2026/8hjv_34839.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hjv_34839/07_2026/8hjv_34839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hjv_34839/07_2026/8hjv_34839.map" } resolution = 3.1 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= 0.005 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 5 7.16 5 P 3 5.49 5 Mg 48 5.21 5 S 71 5.16 5 C 15527 2.51 5 N 3231 2.21 5 O 3308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 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: 22193 Number of models: 1 Model: "" Number of chains: 68 Chain: "0" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "1" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 271 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "2" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "3" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "5" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "7" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "8" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "9" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "D" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "E" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "F" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "H" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "I" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "J" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "K" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "L" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2337 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 16, 'TRANS': 277} Chain breaks: 1 Chain: "M" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2488 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 16, 'TRANS': 289} Chain: "N" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "O" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "P" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "Q" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "R" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "S" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "T" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "U" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "V" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 232 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "W" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "Y" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 259 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "C" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2216 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 23, 'TRANS': 267} Chain: "Z" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 362 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "0" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 329 Unusual residues: {'BCL': 1, 'BPH': 3, 'MQE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 347 Unusual residues: {' FE': 1, 'BCL': 2, 'MQE': 2, 'PGV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'MQE:plan-2': 1, 'MQE:plan-3': 1, 'MQE:plan-4': 1, 'MQE:plan-5': 1, 'MQE:plan-6': 1, 'MQE:plan-9': 1, 'MQE:plan-10': 1, 'MQE:plan-11': 1, 'MQE:plan-12': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 47 Chain: "N" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'HEM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.55, per 1000 atoms: 0.21 Number of scatterers: 22193 At special positions: 0 Unit cell: (131.271, 138.415, 132.164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 71 16.00 P 3 15.00 Mg 48 11.99 O 3308 8.00 N 3231 7.00 C 15527 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=65, symmetry=0 Number of additional bonds: simple=65, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 677.8 milliseconds 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4246 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 2 sheets defined 67.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain '0' and resid 20 through 51 removed outlier: 4.038A pdb=" N LEU 0 24 " --> pdb=" O ASN 0 20 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL 0 25 " --> pdb=" O ALA 0 21 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 34 removed outlier: 4.006A pdb=" N GLY 1 34 " --> pdb=" O VAL 1 30 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 51 removed outlier: 3.751A pdb=" N TRP 2 23 " --> pdb=" O ASN 2 19 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU 2 24 " --> pdb=" O ASN 2 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL 2 25 " --> pdb=" O ALA 2 21 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 34 removed outlier: 3.606A pdb=" N SER 3 11 " --> pdb=" O GLU 3 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) Processing helix chain '4' and resid 11 through 15 Processing helix chain '4' and resid 20 through 51 removed outlier: 4.037A pdb=" N LEU 4 24 " --> pdb=" O ASN 4 20 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL 4 25 " --> pdb=" O ALA 4 21 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 34 removed outlier: 3.605A pdb=" N SER 5 11 " --> pdb=" O GLU 5 7 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) Processing helix chain '6' and resid 20 through 51 removed outlier: 4.051A pdb=" N LEU 6 24 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL 6 25 " --> pdb=" O ALA 6 21 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 34 removed outlier: 3.605A pdb=" N SER 7 11 " --> pdb=" O GLU 7 7 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '8' and resid 11 through 15 Processing helix chain '8' and resid 20 through 51 removed outlier: 4.281A pdb=" N LEU 8 24 " --> pdb=" O ASN 8 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL 8 25 " --> pdb=" O ALA 8 21 " (cutoff:3.500A) Processing helix chain '9' and resid 7 through 34 removed outlier: 3.605A pdb=" N SER 9 11 " --> pdb=" O GLU 9 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY 9 34 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 34 removed outlier: 3.606A pdb=" N SER A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 51 removed outlier: 4.038A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR B 51 " --> pdb=" O CYS B 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 34 removed outlier: 3.606A pdb=" N SER D 11 " --> pdb=" O GLU D 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY D 34 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 51 removed outlier: 4.035A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP E 48 " --> pdb=" O HIS E 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 34 removed outlier: 3.606A pdb=" N SER F 11 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY F 34 " --> pdb=" O VAL F 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 51 removed outlier: 4.122A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 34 removed outlier: 3.606A pdb=" N SER H 11 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY H 34 " --> pdb=" O VAL H 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 15 Processing helix chain 'I' and resid 20 through 51 removed outlier: 4.054A pdb=" N LEU I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 34 removed outlier: 3.607A pdb=" N SER J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 51 removed outlier: 4.242A pdb=" N LEU K 24 " --> pdb=" O ASN K 20 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 43 removed outlier: 4.313A pdb=" N ILE L 39 " --> pdb=" O PRO L 35 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU L 40 " --> pdb=" O PHE L 36 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR L 43 " --> pdb=" O ILE L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 56 removed outlier: 3.772A pdb=" N PHE L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 93 removed outlier: 3.510A pdb=" N ILE L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLY L 91 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL L 92 " --> pdb=" O LEU L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 113 Processing helix chain 'L' and resid 122 through 151 Processing helix chain 'L' and resid 154 through 172 removed outlier: 3.565A pdb=" N ILE L 158 " --> pdb=" O MET L 154 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL L 163 " --> pdb=" O ALA L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 179 Processing helix chain 'L' and resid 191 through 203 removed outlier: 3.685A pdb=" N TYR L 203 " --> pdb=" O ILE L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 208 Processing helix chain 'L' and resid 209 through 236 removed outlier: 3.647A pdb=" N GLU L 236 " --> pdb=" O ALA L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 253 Processing helix chain 'L' and resid 259 through 288 removed outlier: 3.704A pdb=" N ILE L 263 " --> pdb=" O GLY L 259 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N HIS L 264 " --> pdb=" O GLU L 260 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG L 265 " --> pdb=" O ILE L 261 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU L 276 " --> pdb=" O ALA L 272 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR L 287 " --> pdb=" O PHE L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 306 removed outlier: 3.943A pdb=" N PHE L 298 " --> pdb=" O PHE L 295 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP L 300 " --> pdb=" O GLY L 297 " (cutoff:3.500A) Proline residue: L 303 - end of helix Processing helix chain 'M' and resid 338 through 342 Processing helix chain 'M' and resid 359 through 366 removed outlier: 3.698A pdb=" N GLY M 366 " --> pdb=" O GLN M 362 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 402 removed outlier: 3.646A pdb=" N ILE M 381 " --> pdb=" O LEU M 377 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER M 382 " --> pdb=" O TRP M 378 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY M 398 " --> pdb=" O LEU M 394 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN M 400 " --> pdb=" O ASP M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 404 through 411 Processing helix chain 'M' and resid 412 through 415 removed outlier: 3.599A pdb=" N LEU M 415 " --> pdb=" O PHE M 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 412 through 415' Processing helix chain 'M' and resid 435 through 464 removed outlier: 4.067A pdb=" N LEU M 439 " --> pdb=" O GLY M 435 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA M 440 " --> pdb=" O GLY M 436 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY M 464 " --> pdb=" O ALA M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 467 through 485 removed outlier: 3.740A pdb=" N TRP M 471 " --> pdb=" O THR M 467 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU M 479 " --> pdb=" O SER M 475 " (cutoff:3.500A) Processing helix chain 'M' and resid 493 through 497 removed outlier: 3.740A pdb=" N ALA M 496 " --> pdb=" O ASN M 493 " (cutoff:3.500A) Processing helix chain 'M' and resid 501 through 517 removed outlier: 3.544A pdb=" N ILE M 505 " --> pdb=" O GLY M 501 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU M 506 " --> pdb=" O PHE M 502 " (cutoff:3.500A) Processing helix chain 'M' and resid 518 through 521 Processing helix chain 'M' and resid 522 through 549 Processing helix chain 'M' and resid 550 through 553 Processing helix chain 'M' and resid 556 through 563 removed outlier: 3.951A pdb=" N MET M 562 " --> pdb=" O PHE M 558 " (cutoff:3.500A) Processing helix chain 'M' and resid 565 through 580 removed outlier: 3.661A pdb=" N TRP M 575 " --> pdb=" O ALA M 571 " (cutoff:3.500A) Processing helix chain 'M' and resid 586 through 609 removed outlier: 3.850A pdb=" N ILE M 590 " --> pdb=" O TYR M 586 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA M 600 " --> pdb=" O ALA M 596 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU M 609 " --> pdb=" O ILE M 605 " (cutoff:3.500A) Processing helix chain 'M' and resid 616 through 624 removed outlier: 3.721A pdb=" N THR M 623 " --> pdb=" O ALA M 619 " (cutoff:3.500A) Processing helix chain 'M' and resid 634 through 638 removed outlier: 4.117A pdb=" N GLN M 637 " --> pdb=" O ASP M 634 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 34 removed outlier: 3.606A pdb=" N SER N 11 " --> pdb=" O GLU N 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY N 34 " --> pdb=" O VAL N 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 51 removed outlier: 4.104A pdb=" N LEU O 24 " --> pdb=" O ASN O 20 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR O 51 " --> pdb=" O CYS O 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 34 removed outlier: 3.606A pdb=" N SER P 11 " --> pdb=" O GLU P 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY P 34 " --> pdb=" O VAL P 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 50 removed outlier: 4.050A pdb=" N LEU Q 24 " --> pdb=" O ASN Q 20 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL Q 25 " --> pdb=" O ALA Q 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 34 removed outlier: 3.607A pdb=" N SER R 11 " --> pdb=" O GLU R 7 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 50 removed outlier: 4.075A pdb=" N LEU S 24 " --> pdb=" O ASN S 20 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 34 removed outlier: 3.792A pdb=" N SER T 11 " --> pdb=" O GLU T 7 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY T 34 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 51 removed outlier: 3.752A pdb=" N TRP U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU U 24 " --> pdb=" O ASN U 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 32 removed outlier: 3.660A pdb=" N VAL V 12 " --> pdb=" O PHE V 8 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 51 removed outlier: 3.752A pdb=" N TRP W 23 " --> pdb=" O ASN W 19 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU W 24 " --> pdb=" O ASN W 20 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL W 25 " --> pdb=" O ALA W 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 30 Proline residue: Y 19 - end of helix Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 71 through 85 removed outlier: 3.697A pdb=" N ALA C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 85 " --> pdb=" O TYR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 138 through 156 Processing helix chain 'C' and resid 218 through 236 Processing helix chain 'C' and resid 239 through 243 removed outlier: 4.030A pdb=" N CYS C 243 " --> pdb=" O CYS C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 274 removed outlier: 4.413A pdb=" N HIS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 298 removed outlier: 4.208A pdb=" N HIS C 297 " --> pdb=" O CYS C 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 47 removed outlier: 3.840A pdb=" N VAL Z 25 " --> pdb=" O ALA Z 21 " (cutoff:3.500A) Proline residue: Z 26 - end of helix removed outlier: 4.093A pdb=" N ILE Z 31 " --> pdb=" O LEU Z 27 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG Z 39 " --> pdb=" O ILE Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 58 removed outlier: 3.735A pdb=" N ASN Z 58 " --> pdb=" O PRO Z 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 7 through 9 Processing sheet with id=AA2, first strand: chain 'L' and resid 32 through 34 removed outlier: 4.073A pdb=" N TYR Z 49 " --> pdb=" O ILE L 34 " (cutoff:3.500A) 1114 hydrogen bonds defined for protein. 3276 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: 3.45 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.30: 2963 1.30 - 1.49: 10509 1.49 - 1.69: 9434 1.69 - 1.88: 119 1.88 - 2.08: 208 Bond restraints: 23233 Sorted by residual: bond pdb=" C HIS W 26 " pdb=" N ASP W 27 " ideal model delta sigma weight residual 1.334 1.221 0.113 1.27e-02 6.20e+03 7.91e+01 bond pdb=" C HIS U 44 " pdb=" N VAL U 45 " ideal model delta sigma weight residual 1.334 1.441 -0.107 1.26e-02 6.30e+03 7.20e+01 bond pdb=" C VAL 0 25 " pdb=" N HIS 0 26 " ideal model delta sigma weight residual 1.335 1.449 -0.115 1.36e-02 5.41e+03 7.10e+01 bond pdb=" C ILE 3 26 " pdb=" N HIS 3 27 " ideal model delta sigma weight residual 1.334 1.228 0.106 1.27e-02 6.20e+03 7.01e+01 bond pdb=" C HIS 1 27 " pdb=" N PHE 1 28 " ideal model delta sigma weight residual 1.334 1.442 -0.107 1.33e-02 5.65e+03 6.50e+01 ... (remaining 23228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 29974 3.78 - 7.57: 2117 7.57 - 11.35: 344 11.35 - 15.14: 74 15.14 - 18.92: 3 Bond angle restraints: 32512 Sorted by residual: angle pdb=" N TRP Q 48 " pdb=" CA TRP Q 48 " pdb=" C TRP Q 48 " ideal model delta sigma weight residual 112.12 100.96 11.16 1.34e+00 5.57e-01 6.94e+01 angle pdb=" N ALA C 51 " pdb=" CA ALA C 51 " pdb=" C ALA C 51 " ideal model delta sigma weight residual 109.72 119.92 -10.20 1.25e+00 6.40e-01 6.66e+01 angle pdb=" N TRP S 48 " pdb=" CA TRP S 48 " pdb=" C TRP S 48 " ideal model delta sigma weight residual 112.93 103.45 9.48 1.33e+00 5.65e-01 5.08e+01 angle pdb=" N TRP B 48 " pdb=" CA TRP B 48 " pdb=" C TRP B 48 " ideal model delta sigma weight residual 113.12 104.50 8.62 1.25e+00 6.40e-01 4.76e+01 angle pdb=" N ASP W 8 " pdb=" CA ASP W 8 " pdb=" C ASP W 8 " ideal model delta sigma weight residual 110.68 120.17 -9.49 1.39e+00 5.18e-01 4.66e+01 ... (remaining 32507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.16: 10883 29.16 - 58.33: 908 58.33 - 87.49: 115 87.49 - 116.66: 22 116.66 - 145.82: 7 Dihedral angle restraints: 11935 sinusoidal: 5402 harmonic: 6533 Sorted by residual: dihedral pdb=" C1 BCL V 101 " pdb=" CGA BCL V 101 " pdb=" O2A BCL V 101 " pdb=" CBA BCL V 101 " ideal model delta sinusoidal sigma weight residual 180.00 51.14 128.86 1 6.00e+00 2.78e-02 4.34e+02 dihedral pdb=" C1 BCL L 401 " pdb=" CGA BCL L 401 " pdb=" O2A BCL L 401 " pdb=" CBA BCL L 401 " ideal model delta sinusoidal sigma weight residual -180.00 -65.07 -114.93 1 6.00e+00 2.78e-02 3.79e+02 dihedral pdb=" CBD BCL W 101 " pdb=" CGD BCL W 101 " pdb=" O2D BCL W 101 " pdb=" CED BCL W 101 " ideal model delta sinusoidal sigma weight residual -180.00 -94.58 -85.42 1 5.00e+00 4.00e-02 3.53e+02 ... (remaining 11932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.125: 3301 1.125 - 2.250: 0 2.250 - 3.374: 0 3.374 - 4.499: 0 4.499 - 5.624: 27 Chirality restraints: 3328 Sorted by residual: chirality pdb=" C18 BCL Q 101 " pdb=" C17 BCL Q 101 " pdb=" C19 BCL Q 101 " pdb=" C20 BCL Q 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.91 5.62 2.00e-01 2.50e+01 7.91e+02 chirality pdb=" C18 BCL E 101 " pdb=" C17 BCL E 101 " pdb=" C19 BCL E 101 " pdb=" C20 BCL E 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.91 5.62 2.00e-01 2.50e+01 7.90e+02 chirality pdb=" C18 BCL I 101 " pdb=" C17 BCL I 101 " pdb=" C19 BCL I 101 " pdb=" C20 BCL I 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.91 5.62 2.00e-01 2.50e+01 7.89e+02 ... (remaining 3325 not shown) Planarity restraints: 3826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL 2 101 " -0.355 1.50e-02 4.44e+03 3.03e-01 2.04e+03 pdb=" C2 BCL 2 101 " 0.475 1.50e-02 4.44e+03 pdb=" C3 BCL 2 101 " 0.193 1.50e-02 4.44e+03 pdb=" C4 BCL 2 101 " -0.258 1.50e-02 4.44e+03 pdb=" C5 BCL 2 101 " -0.055 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL L 401 " 0.353 1.50e-02 4.44e+03 2.99e-01 1.98e+03 pdb=" C2 BCL L 401 " -0.446 1.50e-02 4.44e+03 pdb=" C3 BCL L 401 " -0.220 1.50e-02 4.44e+03 pdb=" C4 BCL L 401 " 0.043 1.50e-02 4.44e+03 pdb=" C5 BCL L 401 " 0.270 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C3D BCL V 101 " -0.051 5.00e-03 4.00e+04 9.42e-02 1.42e+03 pdb=" CAD BCL V 101 " 0.162 5.00e-03 4.00e+04 pdb=" CBD BCL V 101 " -0.044 5.00e-03 4.00e+04 pdb=" OBD BCL V 101 " -0.067 5.00e-03 4.00e+04 ... (remaining 3823 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 119 2.50 - 3.10: 15855 3.10 - 3.70: 32319 3.70 - 4.30: 47300 4.30 - 4.90: 77676 Nonbonded interactions: 173269 Sorted by model distance: nonbonded pdb=" NH1 ARG Z 39 " pdb=" CG LYS Z 43 " model vdw 1.901 3.520 nonbonded pdb=" OE2 GLU M 557 " pdb="FE FE M1004 " model vdw 1.961 2.260 nonbonded pdb=" OE1 GLU M 557 " pdb="FE FE M1004 " model vdw 2.016 2.260 nonbonded pdb=" ND2 ASN M 518 " pdb=" CE2 TYR M 521 " model vdw 2.053 3.420 nonbonded pdb=" NH2 ARG M 570 " pdb=" ND2 ASN Z 58 " model vdw 2.072 3.200 ... (remaining 173264 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 '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'B' selection = chain 'E' selection = chain 'G' selection = (chain 'I' and resid 7 through 102) selection = chain 'K' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = (chain '1' and resid 7 through 41) selection = (chain '3' and resid 7 through 41) selection = (chain '5' and resid 7 through 41) selection = (chain '7' and resid 7 through 41) selection = (chain '9' and resid 7 through 41) selection = (chain 'A' and resid 7 through 41) selection = (chain 'D' and resid 7 through 41) selection = (chain 'F' and resid 7 through 41) selection = (chain 'H' and resid 7 through 41) selection = (chain 'J' and resid 7 through 41) selection = (chain 'N' and resid 7 through 41) selection = (chain 'P' and resid 7 through 41) selection = (chain 'R' and resid 7 through 41) selection = (chain 'T' and resid 7 through 41) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.390 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.023 0.711 23298 Z= 1.470 Angle : 2.022 18.919 32512 Z= 0.872 Chirality : 0.517 5.624 3328 Planarity : 0.039 0.303 3826 Dihedral : 20.482 145.824 7689 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.99 % Allowed : 13.11 % Favored : 85.90 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.16), residues: 2193 helix: 0.51 (0.13), residues: 1327 sheet: None (None), residues: 0 loop : -2.33 (0.18), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 4 TYR 0.014 0.002 TYR M 408 PHE 0.022 0.002 PHE H 6 TRP 0.018 0.002 TRP 2 53 HIS 0.008 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.01926 / 0.86 (23233) covalent geometry : angle 2.02177 / 0.87 (32512) hydrogen bonds : bond 0.15682 / 10.37 ( 1114) hydrogen bonds : angle 5.49188 / 4.14 ( 3276) Misc. bond : bond 0.22750 / 16.09 ( 65) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 575 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: 0 15 LYS cc_start: 0.7862 (tppt) cc_final: 0.7295 (tptp) REVERT: 1 24 LEU cc_start: 0.8218 (mt) cc_final: 0.8000 (mp) REVERT: 2 52 PRO cc_start: 0.6655 (Cg_endo) cc_final: 0.6433 (Cg_exo) REVERT: 4 9 LEU cc_start: 0.7346 (mt) cc_final: 0.6973 (tp) REVERT: 5 27 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7946 (m90) REVERT: 6 28 ILE cc_start: 0.8113 (mt) cc_final: 0.7881 (mm) REVERT: A 27 HIS cc_start: 0.8413 (OUTLIER) cc_final: 0.7977 (m90) REVERT: A 40 ARG cc_start: 0.5896 (ttm-80) cc_final: 0.5676 (ttt90) REVERT: B 34 TYR cc_start: 0.7889 (m-10) cc_final: 0.7613 (m-10) REVERT: E 31 LYS cc_start: 0.7821 (mttt) cc_final: 0.7451 (mmmt) REVERT: E 46 LEU cc_start: 0.8081 (mt) cc_final: 0.7825 (mt) REVERT: H 7 GLU cc_start: 0.6269 (mt-10) cc_final: 0.5319 (mp0) REVERT: I 31 LYS cc_start: 0.7125 (mttt) cc_final: 0.6775 (mtpt) REVERT: J 6 PHE cc_start: 0.6033 (m-80) cc_final: 0.5729 (m-80) REVERT: K 8 ASP cc_start: 0.7899 (p0) cc_final: 0.7524 (p0) REVERT: K 13 GLN cc_start: 0.6634 (tt0) cc_final: 0.6399 (mp10) REVERT: K 24 LEU cc_start: 0.7343 (mt) cc_final: 0.6939 (mt) REVERT: K 51 THR cc_start: 0.7993 (p) cc_final: 0.7784 (m) REVERT: L 16 LEU cc_start: 0.5427 (tp) cc_final: 0.5224 (tp) REVERT: L 58 ASP cc_start: 0.6848 (t70) cc_final: 0.6049 (t70) REVERT: L 302 MET cc_start: 0.7224 (mmm) cc_final: 0.6992 (mmm) REVERT: M 503 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7384 (ttp-170) REVERT: M 632 ASN cc_start: 0.7674 (p0) cc_final: 0.7458 (p0) REVERT: P 27 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.7886 (m90) REVERT: R 27 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7656 (m90) REVERT: S 15 LYS cc_start: 0.7134 (ttmm) cc_final: 0.6803 (tptt) REVERT: W 31 LYS cc_start: 0.6744 (mttt) cc_final: 0.6317 (mmmt) REVERT: W 41 VAL cc_start: 0.7041 (t) cc_final: 0.6828 (m) REVERT: C 148 MET cc_start: 0.8797 (ttp) cc_final: 0.8553 (ttp) outliers start: 19 outliers final: 6 residues processed: 591 average time/residue: 0.1380 time to fit residues: 127.8951 Evaluate side-chains 340 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 329 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 27 HIS Chi-restraints excluded: chain 5 residue 27 HIS Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain M residue 503 ARG Chi-restraints excluded: chain P residue 27 HIS Chi-restraints excluded: chain R residue 27 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 22 GLN B 13 GLN E 7 ASN G 7 ASN H 37 ASN K 19 ASN L 306 ASN T 37 ASN U 19 ASN W 20 ASN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 155 ASN C 233 ASN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.124180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.104701 restraints weight = 41020.386| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.36 r_work: 0.3211 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.418 23298 Z= 0.185 Angle : 0.987 16.524 32512 Z= 0.361 Chirality : 0.043 0.199 3328 Planarity : 0.005 0.046 3826 Dihedral : 21.030 179.313 3819 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.66 % Allowed : 15.67 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.41 (0.18), residues: 2193 helix: 2.49 (0.13), residues: 1349 sheet: None (None), residues: 0 loop : -1.83 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 1 40 TYR 0.017 0.001 TYR M 521 PHE 0.016 0.001 PHE L 62 TRP 0.016 0.001 TRP D 38 HIS 0.006 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 (23233) covalent geometry : angle 0.98719 / 0.36 (32512) hydrogen bonds : bond 0.06445 / 4.25 ( 1114) hydrogen bonds : angle 3.69165 / 2.76 ( 3276) Misc. bond : bond 0.07539 / 4.23 ( 65) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 354 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: 0 15 LYS cc_start: 0.8101 (tppt) cc_final: 0.7324 (tptp) REVERT: 2 52 PRO cc_start: 0.6324 (Cg_endo) cc_final: 0.5915 (Cg_exo) REVERT: 4 9 LEU cc_start: 0.7619 (mt) cc_final: 0.7193 (tp) REVERT: 6 28 ILE cc_start: 0.8166 (mt) cc_final: 0.7936 (mm) REVERT: B 34 TYR cc_start: 0.8042 (m-10) cc_final: 0.7783 (m-10) REVERT: E 31 LYS cc_start: 0.7879 (mttt) cc_final: 0.7548 (mmmt) REVERT: G 8 ASP cc_start: 0.6280 (p0) cc_final: 0.6043 (p0) REVERT: H 7 GLU cc_start: 0.6472 (mt-10) cc_final: 0.5390 (mp0) REVERT: I 22 GLN cc_start: 0.8225 (mt0) cc_final: 0.7844 (mt0) REVERT: K 13 GLN cc_start: 0.6966 (tt0) cc_final: 0.6395 (mp10) REVERT: K 24 LEU cc_start: 0.7415 (mt) cc_final: 0.6872 (mt) REVERT: L 16 LEU cc_start: 0.5445 (tp) cc_final: 0.5185 (tp) REVERT: L 39 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7686 (pt) REVERT: M 357 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.6719 (t70) REVERT: M 387 PHE cc_start: 0.7616 (t80) cc_final: 0.7189 (t80) REVERT: M 396 ASP cc_start: 0.8494 (t0) cc_final: 0.8236 (t0) REVERT: M 632 ASN cc_start: 0.7722 (p0) cc_final: 0.7515 (p0) REVERT: O 55 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6679 (ptp-110) REVERT: P 24 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7895 (mp) REVERT: P 27 HIS cc_start: 0.9092 (OUTLIER) cc_final: 0.8755 (m90) REVERT: Q 34 TYR cc_start: 0.7112 (m-10) cc_final: 0.6739 (m-10) REVERT: R 27 HIS cc_start: 0.9089 (OUTLIER) cc_final: 0.8296 (m90) REVERT: S 15 LYS cc_start: 0.7481 (ttmm) cc_final: 0.6942 (tptt) REVERT: U 41 VAL cc_start: 0.8483 (t) cc_final: 0.8213 (p) REVERT: V 22 MET cc_start: 0.6528 (mmp) cc_final: 0.6139 (mmp) REVERT: W 31 LYS cc_start: 0.6596 (mttt) cc_final: 0.6144 (mmmt) REVERT: W 55 ARG cc_start: 0.6323 (ttp-170) cc_final: 0.6090 (ttm170) REVERT: Y 17 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7782 (t80) REVERT: C 31 MET cc_start: 0.5526 (mtp) cc_final: 0.5202 (mtt) REVERT: C 54 LEU cc_start: 0.7209 (tp) cc_final: 0.6770 (tp) REVERT: C 63 THR cc_start: 0.8640 (t) cc_final: 0.8384 (m) REVERT: C 122 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.7092 (m-70) REVERT: C 145 MET cc_start: 0.8293 (mmt) cc_final: 0.7854 (mmt) REVERT: C 148 MET cc_start: 0.8928 (ttp) cc_final: 0.8653 (ttp) REVERT: C 229 MET cc_start: 0.8676 (mmt) cc_final: 0.8339 (mmt) REVERT: C 244 HIS cc_start: 0.8711 (OUTLIER) cc_final: 0.8086 (t-90) outliers start: 70 outliers final: 39 residues processed: 399 average time/residue: 0.1325 time to fit residues: 85.8784 Evaluate side-chains 353 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 305 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 27 HIS Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 7 residue 14 VAL Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 9 residue 15 SER Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain M residue 357 HIS Chi-restraints excluded: chain M residue 367 GLU Chi-restraints excluded: chain M residue 429 ASN Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 27 HIS Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 27 HIS Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 27 HIS Chi-restraints excluded: chain T residue 11 SER Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 10 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.0470 chunk 103 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 186 optimal weight: 9.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 22 GLN B 13 GLN S 22 GLN C 87 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.124662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.104893 restraints weight = 41016.586| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.34 r_work: 0.3218 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.351 23298 Z= 0.138 Angle : 0.892 16.536 32512 Z= 0.320 Chirality : 0.041 0.180 3328 Planarity : 0.004 0.036 3826 Dihedral : 19.471 179.962 3809 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.13 % Allowed : 16.19 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.20 (0.18), residues: 2193 helix: 3.25 (0.13), residues: 1350 sheet: None (None), residues: 0 loop : -1.77 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 363 TYR 0.019 0.001 TYR O 34 PHE 0.015 0.001 PHE L 62 TRP 0.015 0.001 TRP D 38 HIS 0.004 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (23233) covalent geometry : angle 0.89194 / 0.32 (32512) hydrogen bonds : bond 0.04957 / 3.28 ( 1114) hydrogen bonds : angle 3.31248 / 2.47 ( 3276) Misc. bond : bond 0.05041 / 2.35 ( 65) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 343 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: 0 15 LYS cc_start: 0.8072 (tppt) cc_final: 0.7144 (tptp) REVERT: 4 9 LEU cc_start: 0.7574 (mt) cc_final: 0.7171 (tp) REVERT: 6 28 ILE cc_start: 0.8032 (mt) cc_final: 0.7790 (mm) REVERT: 8 34 TYR cc_start: 0.8007 (m-10) cc_final: 0.7757 (m-10) REVERT: B 34 TYR cc_start: 0.8112 (m-10) cc_final: 0.7876 (m-10) REVERT: E 31 LYS cc_start: 0.7843 (mttt) cc_final: 0.7532 (mmmt) REVERT: G 8 ASP cc_start: 0.6133 (p0) cc_final: 0.5888 (p0) REVERT: H 7 GLU cc_start: 0.6411 (mt-10) cc_final: 0.5447 (mp0) REVERT: I 22 GLN cc_start: 0.8130 (mt0) cc_final: 0.7895 (mt0) REVERT: K 13 GLN cc_start: 0.6981 (tt0) cc_final: 0.6395 (mp10) REVERT: K 24 LEU cc_start: 0.7365 (mt) cc_final: 0.7050 (mt) REVERT: L 16 LEU cc_start: 0.5519 (tp) cc_final: 0.5224 (tp) REVERT: L 39 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7600 (pt) REVERT: L 58 ASP cc_start: 0.6423 (t70) cc_final: 0.6220 (t70) REVERT: L 82 LEU cc_start: 0.8665 (mt) cc_final: 0.8462 (mt) REVERT: L 219 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8307 (mt) REVERT: M 357 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6673 (t70) REVERT: M 387 PHE cc_start: 0.7628 (t80) cc_final: 0.7191 (t80) REVERT: M 630 TRP cc_start: 0.8488 (OUTLIER) cc_final: 0.8061 (t60) REVERT: M 632 ASN cc_start: 0.7733 (p0) cc_final: 0.7503 (p0) REVERT: P 24 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8046 (mp) REVERT: R 27 HIS cc_start: 0.9113 (OUTLIER) cc_final: 0.8268 (m90) REVERT: S 15 LYS cc_start: 0.7380 (ttmm) cc_final: 0.6939 (tptt) REVERT: V 22 MET cc_start: 0.6942 (mmp) cc_final: 0.6683 (mmp) REVERT: W 30 VAL cc_start: 0.6580 (t) cc_final: 0.6159 (m) REVERT: W 31 LYS cc_start: 0.6614 (mttt) cc_final: 0.6077 (mmmt) REVERT: W 55 ARG cc_start: 0.6327 (ttp-170) cc_final: 0.6054 (ttm170) REVERT: Y 17 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7864 (t80) REVERT: C 54 LEU cc_start: 0.7218 (tp) cc_final: 0.6887 (tp) REVERT: C 69 TYR cc_start: 0.7054 (p90) cc_final: 0.6636 (p90) REVERT: C 122 HIS cc_start: 0.7486 (OUTLIER) cc_final: 0.6894 (m-70) REVERT: C 145 MET cc_start: 0.8467 (mmt) cc_final: 0.8036 (mmt) REVERT: C 148 MET cc_start: 0.8958 (ttp) cc_final: 0.8672 (ttp) REVERT: C 229 MET cc_start: 0.8701 (mmt) cc_final: 0.8484 (mmt) REVERT: C 244 HIS cc_start: 0.8727 (OUTLIER) cc_final: 0.7755 (t-90) outliers start: 60 outliers final: 28 residues processed: 383 average time/residue: 0.1201 time to fit residues: 75.2880 Evaluate side-chains 339 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 302 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 3 residue 27 HIS Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 357 HIS Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 553 LYS Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain N residue 27 HIS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 27 HIS Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 58 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 80 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 7 ASN B 13 GLN L 183 HIS L 205 ASN R 37 ASN W 19 ASN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN C 168 GLN Z 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.100321 restraints weight = 40642.576| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.29 r_work: 0.3137 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.349 23298 Z= 0.155 Angle : 0.935 17.225 32512 Z= 0.336 Chirality : 0.041 0.211 3328 Planarity : 0.004 0.039 3826 Dihedral : 18.998 179.786 3807 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.71 % Allowed : 16.29 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.18 (0.18), residues: 2193 helix: 3.25 (0.13), residues: 1349 sheet: None (None), residues: 0 loop : -1.80 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 570 TYR 0.016 0.002 TYR C 120 PHE 0.017 0.001 PHE M 519 TRP 0.017 0.001 TRP D 38 HIS 0.006 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.15 (23233) covalent geometry : angle 0.93545 / 0.34 (32512) hydrogen bonds : bond 0.05429 / 3.59 ( 1114) hydrogen bonds : angle 3.33563 / 2.48 ( 3276) Misc. bond : bond 0.06399 / 3.48 ( 65) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 306 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 15 LYS cc_start: 0.8071 (tppt) cc_final: 0.7174 (tptp) REVERT: 4 9 LEU cc_start: 0.7644 (mt) cc_final: 0.7175 (tp) REVERT: 6 15 LYS cc_start: 0.7952 (mttt) cc_final: 0.7699 (mmtt) REVERT: 6 28 ILE cc_start: 0.8117 (mt) cc_final: 0.7877 (mm) REVERT: 8 15 LYS cc_start: 0.7331 (tppt) cc_final: 0.6918 (tppp) REVERT: 8 41 VAL cc_start: 0.8447 (t) cc_final: 0.8028 (p) REVERT: E 31 LYS cc_start: 0.7929 (mttt) cc_final: 0.7609 (mmmt) REVERT: G 8 ASP cc_start: 0.6225 (p0) cc_final: 0.6019 (p0) REVERT: H 7 GLU cc_start: 0.6458 (mt-10) cc_final: 0.5543 (mp0) REVERT: H 31 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7336 (mt) REVERT: I 22 GLN cc_start: 0.8104 (mt0) cc_final: 0.7785 (mt0) REVERT: K 13 GLN cc_start: 0.6959 (tt0) cc_final: 0.6453 (mp10) REVERT: K 20 ASN cc_start: 0.7103 (t0) cc_final: 0.6849 (m-40) REVERT: L 16 LEU cc_start: 0.5713 (tp) cc_final: 0.5382 (tp) REVERT: L 39 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7758 (pt) REVERT: L 64 ILE cc_start: 0.8203 (tt) cc_final: 0.7765 (tp) REVERT: L 82 LEU cc_start: 0.8637 (mt) cc_final: 0.8385 (mt) REVERT: L 88 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7828 (mt) REVERT: M 387 PHE cc_start: 0.7635 (t80) cc_final: 0.7212 (t80) REVERT: M 630 TRP cc_start: 0.8475 (OUTLIER) cc_final: 0.7970 (t60) REVERT: M 632 ASN cc_start: 0.7849 (p0) cc_final: 0.7630 (p0) REVERT: O 42 ILE cc_start: 0.9122 (mt) cc_final: 0.8896 (mm) REVERT: P 24 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8233 (mp) REVERT: S 15 LYS cc_start: 0.7308 (ttmm) cc_final: 0.7029 (tptt) REVERT: S 37 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7759 (mm) REVERT: V 22 MET cc_start: 0.7091 (mmp) cc_final: 0.6696 (mmp) REVERT: W 15 LYS cc_start: 0.6785 (ttmm) cc_final: 0.6503 (tttt) REVERT: W 30 VAL cc_start: 0.6700 (t) cc_final: 0.6291 (m) REVERT: W 31 LYS cc_start: 0.6562 (mttt) cc_final: 0.6123 (mmmt) REVERT: W 55 ARG cc_start: 0.6434 (ttp-170) cc_final: 0.6134 (ttm170) REVERT: Y 17 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7875 (t80) REVERT: C 122 HIS cc_start: 0.7311 (OUTLIER) cc_final: 0.6711 (m-70) REVERT: C 145 MET cc_start: 0.8432 (mmt) cc_final: 0.7948 (mmt) REVERT: C 229 MET cc_start: 0.8824 (mmt) cc_final: 0.8594 (mmt) REVERT: C 244 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.7930 (t-90) outliers start: 71 outliers final: 43 residues processed: 355 average time/residue: 0.1346 time to fit residues: 77.2526 Evaluate side-chains 337 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 285 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 6 residue 7 ASN Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 9 residue 15 SER Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 553 LYS Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 53 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 196 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 4 22 GLN 4 26 HIS 6 7 ASN B 13 GLN K 7 ASN K 19 ASN M 525 HIS P 37 ASN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN C 269 HIS Z 58 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.092830 restraints weight = 41046.094| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.33 r_work: 0.3011 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.298 23298 Z= 0.315 Angle : 1.091 20.983 32512 Z= 0.407 Chirality : 0.049 0.288 3328 Planarity : 0.005 0.054 3826 Dihedral : 19.152 179.571 3803 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.54 % Allowed : 15.46 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.44 (0.18), residues: 2193 helix: 2.59 (0.13), residues: 1353 sheet: None (None), residues: 0 loop : -1.98 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 4 TYR 0.031 0.003 TYR M 424 PHE 0.032 0.002 PHE M 519 TRP 0.021 0.002 TRP M 552 HIS 0.008 0.002 HIS E 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.26 (23233) covalent geometry : angle 1.09089 / 0.41 (32512) hydrogen bonds : bond 0.07577 / 5.02 ( 1114) hydrogen bonds : angle 3.73149 / 2.77 ( 3276) Misc. bond : bond 0.06788 / 4.61 ( 65) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 302 time to evaluate : 0.744 Fit side-chains REVERT: 0 15 LYS cc_start: 0.8113 (tppt) cc_final: 0.7399 (tptp) REVERT: 2 37 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7185 (tt) REVERT: 6 7 ASN cc_start: 0.5928 (OUTLIER) cc_final: 0.5639 (m-40) REVERT: 6 15 LYS cc_start: 0.8038 (mttt) cc_final: 0.7692 (mmtt) REVERT: 6 28 ILE cc_start: 0.8392 (mt) cc_final: 0.8143 (mm) REVERT: 8 15 LYS cc_start: 0.7671 (tppt) cc_final: 0.7243 (tppp) REVERT: B 9 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7550 (tt) REVERT: D 4 ARG cc_start: 0.4461 (ttm170) cc_final: 0.4234 (ttm-80) REVERT: E 31 LYS cc_start: 0.8063 (mttt) cc_final: 0.7713 (mmmt) REVERT: H 7 GLU cc_start: 0.6406 (mt-10) cc_final: 0.5684 (mp0) REVERT: I 13 GLN cc_start: 0.6673 (tt0) cc_final: 0.6300 (mt0) REVERT: I 18 PHE cc_start: 0.8177 (m-80) cc_final: 0.7949 (m-80) REVERT: K 20 ASN cc_start: 0.7097 (t0) cc_final: 0.6855 (m-40) REVERT: L 16 LEU cc_start: 0.5714 (tp) cc_final: 0.5412 (tp) REVERT: L 64 ILE cc_start: 0.8728 (tt) cc_final: 0.8315 (tp) REVERT: L 302 MET cc_start: 0.8109 (mmm) cc_final: 0.7617 (mtp) REVERT: M 387 PHE cc_start: 0.7655 (t80) cc_final: 0.7298 (t80) REVERT: Q 55 ARG cc_start: 0.7056 (ttm110) cc_final: 0.6433 (ttp-170) REVERT: S 15 LYS cc_start: 0.7286 (ttmm) cc_final: 0.6972 (tptt) REVERT: S 37 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7854 (mm) REVERT: U 38 ILE cc_start: 0.7735 (mt) cc_final: 0.7432 (mm) REVERT: U 41 VAL cc_start: 0.8585 (t) cc_final: 0.8284 (p) REVERT: V 25 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5829 (mm) REVERT: W 30 VAL cc_start: 0.6970 (t) cc_final: 0.6582 (m) REVERT: W 38 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.7079 (mp) REVERT: W 55 ARG cc_start: 0.6679 (ttp-170) cc_final: 0.6250 (ttm170) REVERT: Y 17 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7600 (t80) REVERT: C 63 THR cc_start: 0.8774 (t) cc_final: 0.8490 (m) REVERT: C 122 HIS cc_start: 0.7719 (OUTLIER) cc_final: 0.6960 (m-70) REVERT: C 229 MET cc_start: 0.8916 (mmt) cc_final: 0.8624 (mmt) outliers start: 87 outliers final: 51 residues processed: 367 average time/residue: 0.1349 time to fit residues: 79.2334 Evaluate side-chains 336 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 277 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 7 ASN Chi-restraints excluded: chain 6 residue 10 VAL Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 58 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 180 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 7 ASN 8 22 GLN M 446 HIS C 130 GLN Z 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.098044 restraints weight = 40617.110| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.28 r_work: 0.3095 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.269 23298 Z= 0.132 Angle : 0.865 16.835 32512 Z= 0.320 Chirality : 0.039 0.205 3328 Planarity : 0.004 0.101 3826 Dihedral : 18.159 179.700 3801 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.35 % Allowed : 18.43 % Favored : 79.22 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 2.12 (0.18), residues: 2193 helix: 3.20 (0.13), residues: 1357 sheet: None (None), residues: 0 loop : -1.87 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 40 TYR 0.014 0.001 TYR C 120 PHE 0.016 0.001 PHE L 249 TRP 0.022 0.001 TRP M 552 HIS 0.005 0.001 HIS M 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (23233) covalent geometry : angle 0.86502 / 0.32 (32512) hydrogen bonds : bond 0.05249 / 3.47 ( 1114) hydrogen bonds : angle 3.33155 / 2.48 ( 3276) Misc. bond : bond 0.04687 / 2.36 ( 65) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 295 time to evaluate : 0.837 Fit side-chains REVERT: 0 15 LYS cc_start: 0.8062 (tppt) cc_final: 0.7307 (tptp) REVERT: 4 9 LEU cc_start: 0.7766 (mt) cc_final: 0.7258 (tp) REVERT: 6 15 LYS cc_start: 0.7994 (mttt) cc_final: 0.7703 (mmtt) REVERT: 6 28 ILE cc_start: 0.8258 (mt) cc_final: 0.8015 (mm) REVERT: 8 15 LYS cc_start: 0.7470 (tppt) cc_final: 0.7086 (tppp) REVERT: D 4 ARG cc_start: 0.4589 (ttm170) cc_final: 0.3981 (ttm170) REVERT: E 31 LYS cc_start: 0.7954 (mttt) cc_final: 0.7624 (mmmt) REVERT: H 7 GLU cc_start: 0.6414 (mt-10) cc_final: 0.5760 (mp0) REVERT: L 16 LEU cc_start: 0.5698 (tp) cc_final: 0.5440 (tp) REVERT: L 39 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7868 (pt) REVERT: L 64 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8142 (tp) REVERT: L 302 MET cc_start: 0.7893 (mmm) cc_final: 0.7687 (mtm) REVERT: M 387 PHE cc_start: 0.7593 (t80) cc_final: 0.7227 (t80) REVERT: M 630 TRP cc_start: 0.8474 (OUTLIER) cc_final: 0.8026 (t60) REVERT: O 22 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: Q 55 ARG cc_start: 0.7006 (ttm110) cc_final: 0.6543 (mtp180) REVERT: S 15 LYS cc_start: 0.7269 (ttmm) cc_final: 0.6901 (tptt) REVERT: U 13 GLN cc_start: 0.6842 (tt0) cc_final: 0.6638 (tt0) REVERT: U 46 LEU cc_start: 0.8163 (tt) cc_final: 0.7116 (mt) REVERT: W 55 ARG cc_start: 0.6584 (ttp-170) cc_final: 0.6098 (ttm170) REVERT: Y 17 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7856 (t80) REVERT: C 63 THR cc_start: 0.8639 (t) cc_final: 0.8303 (m) REVERT: C 122 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.6974 (m-70) REVERT: C 145 MET cc_start: 0.8382 (mmt) cc_final: 0.8037 (mmt) REVERT: C 229 MET cc_start: 0.8863 (mmt) cc_final: 0.8475 (mmt) outliers start: 45 outliers final: 27 residues processed: 328 average time/residue: 0.1469 time to fit residues: 76.7814 Evaluate side-chains 301 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 268 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain Q residue 31 LYS Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 50 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 167 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 7 ASN 8 22 GLN B 13 GLN K 19 ASN Z 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092678 restraints weight = 40861.381| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.42 r_work: 0.3047 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.304 23298 Z= 0.225 Angle : 0.994 19.827 32512 Z= 0.374 Chirality : 0.046 0.234 3328 Planarity : 0.005 0.098 3826 Dihedral : 18.140 179.618 3801 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.81 % Allowed : 16.81 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.68 (0.18), residues: 2193 helix: 2.79 (0.13), residues: 1353 sheet: None (None), residues: 0 loop : -1.91 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 4 TYR 0.024 0.002 TYR M 424 PHE 0.028 0.002 PHE M 519 TRP 0.019 0.002 TRP D 38 HIS 0.009 0.002 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.22 (23233) covalent geometry : angle 0.99354 / 0.37 (32512) hydrogen bonds : bond 0.06937 / 4.60 ( 1114) hydrogen bonds : angle 3.61540 / 2.69 ( 3276) Misc. bond : bond 0.06714 / 3.79 ( 65) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 276 time to evaluate : 0.815 Fit side-chains REVERT: 0 15 LYS cc_start: 0.8057 (tppt) cc_final: 0.7308 (tptp) REVERT: 0 22 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7313 (mp10) REVERT: 6 15 LYS cc_start: 0.8070 (mttt) cc_final: 0.7734 (mmtt) REVERT: 6 28 ILE cc_start: 0.8406 (mt) cc_final: 0.8153 (mm) REVERT: D 4 ARG cc_start: 0.4590 (ttm170) cc_final: 0.4332 (ttm-80) REVERT: E 31 LYS cc_start: 0.7976 (mttt) cc_final: 0.7647 (mmmt) REVERT: G 8 ASP cc_start: 0.6596 (p0) cc_final: 0.6388 (p0) REVERT: H 7 GLU cc_start: 0.6295 (mt-10) cc_final: 0.5808 (mp0) REVERT: L 16 LEU cc_start: 0.5476 (tp) cc_final: 0.5259 (tp) REVERT: L 64 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8358 (tp) REVERT: M 387 PHE cc_start: 0.7584 (t80) cc_final: 0.7259 (t80) REVERT: O 22 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7094 (mp10) REVERT: Q 55 ARG cc_start: 0.7117 (ttm110) cc_final: 0.6591 (mtp180) REVERT: U 38 ILE cc_start: 0.7756 (mt) cc_final: 0.7426 (mm) REVERT: U 41 VAL cc_start: 0.8456 (t) cc_final: 0.8170 (p) REVERT: V 17 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7223 (tp) REVERT: Y 17 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7570 (t80) REVERT: C 63 THR cc_start: 0.8743 (t) cc_final: 0.8427 (m) REVERT: C 122 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6530 (m-70) REVERT: C 229 MET cc_start: 0.8927 (mmt) cc_final: 0.8618 (mmt) outliers start: 73 outliers final: 53 residues processed: 329 average time/residue: 0.1473 time to fit residues: 77.5017 Evaluate side-chains 333 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 274 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 6 residue 7 ASN Chi-restraints excluded: chain 6 residue 10 VAL Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 7 residue 14 VAL Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 8 residue 41 VAL Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 350 THR Chi-restraints excluded: chain M residue 409 LEU Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 31 LYS Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 44 HIS Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain Z residue 12 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 181 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 199 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 7 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095327 restraints weight = 40641.389| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.43 r_work: 0.3078 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.287 23298 Z= 0.144 Angle : 0.850 16.348 32512 Z= 0.318 Chirality : 0.041 0.213 3328 Planarity : 0.004 0.099 3826 Dihedral : 17.553 179.673 3801 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.19 % Allowed : 17.18 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 2.04 (0.18), residues: 2193 helix: 3.10 (0.13), residues: 1352 sheet: None (None), residues: 0 loop : -1.80 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 40 TYR 0.013 0.001 TYR M 424 PHE 0.014 0.001 PHE L 185 TRP 0.014 0.001 TRP D 38 HIS 0.007 0.001 HIS M 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (23233) covalent geometry : angle 0.84953 / 0.32 (32512) hydrogen bonds : bond 0.05689 / 3.76 ( 1114) hydrogen bonds : angle 3.40216 / 2.53 ( 3276) Misc. bond : bond 0.06042 / 3.19 ( 65) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 286 time to evaluate : 0.792 Fit side-chains REVERT: 0 22 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: 4 9 LEU cc_start: 0.7802 (mt) cc_final: 0.7272 (tp) REVERT: 6 15 LYS cc_start: 0.7960 (mttt) cc_final: 0.7671 (mmtt) REVERT: 6 28 ILE cc_start: 0.8352 (mt) cc_final: 0.8095 (mm) REVERT: D 4 ARG cc_start: 0.4652 (ttm170) cc_final: 0.4073 (ttm170) REVERT: E 31 LYS cc_start: 0.7968 (mttt) cc_final: 0.7593 (mmmt) REVERT: H 7 GLU cc_start: 0.6315 (mt-10) cc_final: 0.5649 (mp0) REVERT: L 16 LEU cc_start: 0.5389 (tp) cc_final: 0.5172 (tp) REVERT: L 64 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8336 (tp) REVERT: L 254 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7321 (mt) REVERT: M 387 PHE cc_start: 0.7607 (t80) cc_final: 0.7224 (t80) REVERT: M 630 TRP cc_start: 0.8483 (OUTLIER) cc_final: 0.7995 (t60) REVERT: O 22 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7034 (mp10) REVERT: Q 55 ARG cc_start: 0.7140 (ttm110) cc_final: 0.6618 (mtp180) REVERT: U 13 GLN cc_start: 0.7011 (tt0) cc_final: 0.6782 (tt0) REVERT: V 17 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7270 (tp) REVERT: Y 17 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7682 (t80) REVERT: C 63 THR cc_start: 0.8691 (t) cc_final: 0.8359 (m) REVERT: C 87 GLN cc_start: 0.7478 (mp10) cc_final: 0.7159 (mp10) REVERT: C 122 HIS cc_start: 0.7353 (OUTLIER) cc_final: 0.6662 (m-70) REVERT: C 229 MET cc_start: 0.8898 (mmt) cc_final: 0.8511 (mmt) outliers start: 61 outliers final: 41 residues processed: 328 average time/residue: 0.1480 time to fit residues: 77.4897 Evaluate side-chains 325 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 276 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 6 residue 10 VAL Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 350 THR Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 31 LYS Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 139 optimal weight: 0.0770 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 171 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 188 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.098799 restraints weight = 40069.213| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.42 r_work: 0.3142 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.287 23298 Z= 0.119 Angle : 0.784 16.061 32512 Z= 0.295 Chirality : 0.039 0.201 3328 Planarity : 0.004 0.100 3826 Dihedral : 16.832 179.725 3801 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.45 % Allowed : 17.91 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 2.38 (0.19), residues: 2193 helix: 3.37 (0.13), residues: 1353 sheet: None (None), residues: 0 loop : -1.65 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 40 TYR 0.012 0.001 TYR C 120 PHE 0.013 0.001 PHE L 62 TRP 0.014 0.001 TRP D 38 HIS 0.006 0.001 HIS M 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (23233) covalent geometry : angle 0.78442 / 0.30 (32512) hydrogen bonds : bond 0.04618 / 3.04 ( 1114) hydrogen bonds : angle 3.22810 / 2.40 ( 3276) Misc. bond : bond 0.05226 / 2.25 ( 65) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 284 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: 4 9 LEU cc_start: 0.7801 (mt) cc_final: 0.7293 (tp) REVERT: 6 15 LYS cc_start: 0.7955 (mttt) cc_final: 0.7679 (mmtt) REVERT: 6 28 ILE cc_start: 0.8234 (mt) cc_final: 0.7992 (mm) REVERT: D 4 ARG cc_start: 0.4753 (ttm170) cc_final: 0.4189 (ttm170) REVERT: E 31 LYS cc_start: 0.7965 (mttt) cc_final: 0.7672 (mmmt) REVERT: H 7 GLU cc_start: 0.6324 (mt-10) cc_final: 0.5669 (mp0) REVERT: L 39 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7981 (pt) REVERT: L 58 ASP cc_start: 0.6671 (t70) cc_final: 0.6468 (t70) REVERT: L 64 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8330 (tp) REVERT: M 357 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.6625 (t70) REVERT: M 387 PHE cc_start: 0.7640 (t80) cc_final: 0.7296 (t80) REVERT: M 630 TRP cc_start: 0.8462 (OUTLIER) cc_final: 0.8017 (t60) REVERT: O 22 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7078 (mp10) REVERT: Q 55 ARG cc_start: 0.7216 (ttm110) cc_final: 0.6682 (mtp180) REVERT: U 46 LEU cc_start: 0.8091 (tt) cc_final: 0.7154 (mt) REVERT: Y 17 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7864 (t80) REVERT: C 101 GLN cc_start: 0.7219 (mt0) cc_final: 0.6970 (pt0) REVERT: C 122 HIS cc_start: 0.7180 (OUTLIER) cc_final: 0.6563 (m-70) REVERT: C 145 MET cc_start: 0.8137 (mmt) cc_final: 0.7675 (mmt) REVERT: C 229 MET cc_start: 0.8860 (mmt) cc_final: 0.8519 (mmt) outliers start: 47 outliers final: 32 residues processed: 319 average time/residue: 0.1489 time to fit residues: 76.2160 Evaluate side-chains 306 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 357 HIS Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 68 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 195 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097048 restraints weight = 40189.642| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.29 r_work: 0.3081 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.268 23298 Z= 0.161 Angle : 0.845 17.385 32512 Z= 0.319 Chirality : 0.041 0.214 3328 Planarity : 0.004 0.093 3826 Dihedral : 16.878 179.707 3801 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.19 % Allowed : 18.33 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 2.20 (0.18), residues: 2193 helix: 3.19 (0.13), residues: 1353 sheet: None (None), residues: 0 loop : -1.67 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 40 TYR 0.016 0.002 TYR M 424 PHE 0.018 0.001 PHE M 519 TRP 0.015 0.001 TRP D 38 HIS 0.007 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (23233) covalent geometry : angle 0.84541 / 0.32 (32512) hydrogen bonds : bond 0.05588 / 3.70 ( 1114) hydrogen bonds : angle 3.36087 / 2.50 ( 3276) Misc. bond : bond 0.05645 / 2.62 ( 65) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: 0 22 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7366 (mp10) REVERT: 4 9 LEU cc_start: 0.7786 (mt) cc_final: 0.7294 (tp) REVERT: 6 15 LYS cc_start: 0.7982 (mttt) cc_final: 0.7644 (mmtt) REVERT: 6 28 ILE cc_start: 0.8336 (mt) cc_final: 0.8080 (mm) REVERT: D 4 ARG cc_start: 0.4737 (ttm170) cc_final: 0.4164 (ttm170) REVERT: E 31 LYS cc_start: 0.7987 (mttt) cc_final: 0.7673 (mmmt) REVERT: H 7 GLU cc_start: 0.6345 (mt-10) cc_final: 0.5734 (mp0) REVERT: L 64 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8349 (tp) REVERT: M 387 PHE cc_start: 0.7628 (t80) cc_final: 0.7266 (t80) REVERT: M 630 TRP cc_start: 0.8492 (OUTLIER) cc_final: 0.7968 (t60) REVERT: O 22 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: Q 55 ARG cc_start: 0.7256 (ttm110) cc_final: 0.6718 (mtp180) REVERT: Y 17 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7750 (t80) REVERT: C 122 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.6549 (m-70) REVERT: C 145 MET cc_start: 0.8222 (mmt) cc_final: 0.7706 (mmt) REVERT: C 229 MET cc_start: 0.8876 (mmt) cc_final: 0.8532 (mmt) outliers start: 42 outliers final: 33 residues processed: 302 average time/residue: 0.1518 time to fit residues: 73.0189 Evaluate side-chains 305 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 266 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 116 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 7 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 19 ASN A 37 ASN ** C 130 GLN ** 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 = 0.3512 r_free = 0.3512 target = 0.114637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.095119 restraints weight = 40309.517| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.21 r_work: 0.3057 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.291 23298 Z= 0.188 Angle : 0.902 18.272 32512 Z= 0.346 Chirality : 0.043 0.227 3328 Planarity : 0.005 0.099 3826 Dihedral : 17.078 179.690 3801 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.40 % Allowed : 18.22 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.90 (0.18), residues: 2193 helix: 2.95 (0.13), residues: 1352 sheet: None (None), residues: 0 loop : -1.77 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 1 40 TYR 0.021 0.002 TYR M 424 PHE 0.020 0.002 PHE M 519 TRP 0.017 0.002 TRP D 38 HIS 0.008 0.001 HIS M 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 (23233) covalent geometry : angle 0.90231 / 0.35 (32512) hydrogen bonds : bond 0.06467 / 4.29 ( 1114) hydrogen bonds : angle 3.51352 / 2.61 ( 3276) Misc. bond : bond 0.05941 / 2.74 ( 65) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5831.09 seconds wall clock time: 100 minutes 12.92 seconds (6012.92 seconds total)