Starting phenix.real_space_refine on Sun Aug 24 21:57:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hjv_34839/08_2025/8hjv_34839.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hjv_34839/08_2025/8hjv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hjv_34839/08_2025/8hjv_34839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hjv_34839/08_2025/8hjv_34839.map" model { file = "/net/cci-nas-00/data/ceres_data/8hjv_34839/08_2025/8hjv_34839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hjv_34839/08_2025/8hjv_34839.cif" } 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-2.0-5787/lib/python3.9/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: 69 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: 4.51, per 1000 atoms: 0.20 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: 1.91 Conformation dependent library (CDL) restraints added in 682.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.52 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: 2.90 Time building geometry restraints manager: 2.39 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 - 35.05: 11353 35.05 - 70.10: 724 70.10 - 105.15: 54 105.15 - 140.19: 7 140.19 - 175.24: 3 Dihedral angle restraints: 12141 sinusoidal: 5608 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 12138 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: 1.130 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: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.470 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 : 20.900 175.242 7895 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 aren 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 covalent geometry : bond 0.01926 (23233) covalent geometry : angle 2.02177 (32512) hydrogen bonds : bond 0.15682 ( 1114) hydrogen bonds : angle 5.49188 ( 3276) Misc. bond : bond 0.22750 ( 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 : 0.717 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: 0.1324 time to fit residues: 122.3336 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 : 0.483 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN B 13 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.124246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.104767 restraints weight = 41031.636| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.34 r_work: 0.3208 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.431 23298 Z= 0.174 Angle : 1.014 16.808 32512 Z= 0.368 Chirality : 0.043 0.196 3328 Planarity : 0.005 0.045 3826 Dihedral : 21.539 179.973 4025 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.60 % Allowed : 15.77 % Favored : 80.63 % 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 aren not related in a simple way. whole: 1.40 (0.18), residues: 2193 helix: 2.48 (0.13), residues: 1349 sheet: None (None), residues: 0 loop : -1.84 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 1 40 TYR 0.019 0.001 TYR M 521 PHE 0.015 0.001 PHE L 62 TRP 0.018 0.001 TRP D 38 HIS 0.006 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00471 (23233) covalent geometry : angle 1.01397 (32512) hydrogen bonds : bond 0.06455 ( 1114) hydrogen bonds : angle 3.69608 ( 3276) Misc. bond : bond 0.07624 ( 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: 69 poor density : 355 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: 0 15 LYS cc_start: 0.8098 (tppt) cc_final: 0.7325 (tptp) REVERT: 2 52 PRO cc_start: 0.6328 (Cg_endo) cc_final: 0.5917 (Cg_exo) REVERT: 4 9 LEU cc_start: 0.7598 (mt) cc_final: 0.7179 (tp) REVERT: 6 28 ILE cc_start: 0.8125 (mt) cc_final: 0.7900 (mm) REVERT: B 34 TYR cc_start: 0.8049 (m-10) cc_final: 0.7796 (m-10) REVERT: E 31 LYS cc_start: 0.7897 (mttt) cc_final: 0.7562 (mmmt) REVERT: G 8 ASP cc_start: 0.6266 (p0) cc_final: 0.6014 (p0) REVERT: H 7 GLU cc_start: 0.6463 (mt-10) cc_final: 0.5399 (mp0) REVERT: I 22 GLN cc_start: 0.8263 (mt0) cc_final: 0.7908 (mt0) REVERT: K 13 GLN cc_start: 0.6934 (tt0) cc_final: 0.6377 (mp10) REVERT: K 24 LEU cc_start: 0.7425 (mt) cc_final: 0.6881 (mt) REVERT: L 16 LEU cc_start: 0.5458 (tp) cc_final: 0.5204 (tp) REVERT: L 39 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7695 (pt) REVERT: M 357 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6728 (t70) REVERT: M 387 PHE cc_start: 0.7634 (t80) cc_final: 0.7206 (t80) REVERT: M 396 ASP cc_start: 0.8499 (t0) cc_final: 0.8240 (t0) REVERT: M 632 ASN cc_start: 0.7714 (p0) cc_final: 0.7504 (p0) REVERT: O 55 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6667 (ptp-110) REVERT: P 24 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7907 (mp) REVERT: P 27 HIS cc_start: 0.9084 (OUTLIER) cc_final: 0.8771 (m90) REVERT: Q 34 TYR cc_start: 0.7129 (m-10) cc_final: 0.6761 (m-10) REVERT: R 27 HIS cc_start: 0.9093 (OUTLIER) cc_final: 0.8225 (m90) REVERT: S 15 LYS cc_start: 0.7474 (ttmm) cc_final: 0.6938 (tptt) REVERT: V 22 MET cc_start: 0.6533 (mmp) cc_final: 0.6148 (mmp) REVERT: W 31 LYS cc_start: 0.6613 (mttt) cc_final: 0.6161 (mmmt) REVERT: W 55 ARG cc_start: 0.6324 (ttp-170) cc_final: 0.6078 (ttm170) REVERT: Y 17 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7798 (t80) REVERT: C 31 MET cc_start: 0.5556 (mtp) cc_final: 0.5208 (mtt) REVERT: C 122 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.7104 (m-70) REVERT: C 145 MET cc_start: 0.8295 (mmt) cc_final: 0.7853 (mmt) REVERT: C 229 MET cc_start: 0.8683 (mmt) cc_final: 0.8353 (mmt) REVERT: C 244 HIS cc_start: 0.8715 (OUTLIER) cc_final: 0.8173 (t-90) outliers start: 69 outliers final: 41 residues processed: 399 average time/residue: 0.1236 time to fit residues: 80.0077 Evaluate side-chains 355 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 305 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 42 ILE 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 9 residue 17 LEU 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 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 M residue 553 LYS 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: 7.9990 chunk 104 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 106 optimal weight: 0.2980 chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 0.0370 chunk 103 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 186 optimal weight: 8.9990 overall best weight: 2.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN B 13 GLN L 205 ASN S 22 GLN W 19 ASN C 87 GLN ** 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 = 0.3604 r_free = 0.3604 target = 0.121095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101047 restraints weight = 41034.869| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.59 r_work: 0.3141 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.388 23298 Z= 0.157 Angle : 0.933 17.125 32512 Z= 0.336 Chirality : 0.042 0.207 3328 Planarity : 0.004 0.038 3826 Dihedral : 20.040 179.907 4015 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.34 % Allowed : 15.77 % Favored : 80.89 % 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 aren not related in a simple way. whole: 2.07 (0.18), residues: 2193 helix: 3.14 (0.13), residues: 1351 sheet: None (None), residues: 0 loop : -1.81 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 40 TYR 0.020 0.002 TYR C 120 PHE 0.015 0.001 PHE L 62 TRP 0.019 0.001 TRP M 552 HIS 0.006 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00389 (23233) covalent geometry : angle 0.93259 (32512) hydrogen bonds : bond 0.05467 ( 1114) hydrogen bonds : angle 3.37621 ( 3276) Misc. bond : bond 0.06000 ( 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 396 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 332 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 15 LYS cc_start: 0.8145 (tppt) cc_final: 0.7248 (tptp) REVERT: 4 9 LEU cc_start: 0.7603 (mt) cc_final: 0.7172 (tp) REVERT: 6 15 LYS cc_start: 0.7925 (mttt) cc_final: 0.7699 (mmtt) REVERT: 6 28 ILE cc_start: 0.8137 (mt) cc_final: 0.7879 (mm) REVERT: B 34 TYR cc_start: 0.8177 (m-10) cc_final: 0.7939 (m-10) REVERT: E 31 LYS cc_start: 0.7926 (mttt) cc_final: 0.7593 (mmmt) REVERT: G 8 ASP cc_start: 0.6264 (p0) cc_final: 0.6034 (p0) REVERT: H 7 GLU cc_start: 0.6521 (mt-10) cc_final: 0.5545 (mp0) REVERT: I 22 GLN cc_start: 0.8129 (mt0) cc_final: 0.7891 (mt0) REVERT: K 13 GLN cc_start: 0.6955 (tt0) cc_final: 0.6430 (mp10) REVERT: K 19 ASN cc_start: 0.6295 (m-40) cc_final: 0.5960 (m-40) REVERT: L 16 LEU cc_start: 0.5575 (tp) cc_final: 0.5268 (tp) REVERT: L 39 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7768 (pt) REVERT: L 58 ASP cc_start: 0.6615 (t70) cc_final: 0.6346 (t70) REVERT: L 64 ILE cc_start: 0.8212 (tt) cc_final: 0.7832 (tp) REVERT: L 82 LEU cc_start: 0.8683 (mt) cc_final: 0.8461 (mt) REVERT: M 357 HIS cc_start: 0.7441 (OUTLIER) cc_final: 0.6690 (t70) REVERT: M 387 PHE cc_start: 0.7666 (t80) cc_final: 0.7228 (t80) REVERT: M 630 TRP cc_start: 0.8488 (OUTLIER) cc_final: 0.7986 (t60) REVERT: O 42 ILE cc_start: 0.9099 (mt) cc_final: 0.8888 (mm) REVERT: P 24 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8218 (mp) REVERT: R 27 HIS cc_start: 0.9208 (OUTLIER) cc_final: 0.8320 (m90) REVERT: S 15 LYS cc_start: 0.7458 (ttmm) cc_final: 0.7047 (tptt) REVERT: V 22 MET cc_start: 0.7018 (mmp) cc_final: 0.6715 (mmp) REVERT: W 30 VAL cc_start: 0.6625 (t) cc_final: 0.6202 (m) REVERT: W 31 LYS cc_start: 0.6633 (mttt) cc_final: 0.6136 (mmmt) REVERT: W 41 VAL cc_start: 0.6791 (t) cc_final: 0.6530 (m) REVERT: W 55 ARG cc_start: 0.6430 (ttp-170) cc_final: 0.6137 (ttm170) REVERT: Y 17 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7809 (t80) REVERT: C 54 LEU cc_start: 0.7232 (tp) cc_final: 0.6907 (tp) REVERT: C 69 TYR cc_start: 0.7102 (p90) cc_final: 0.6693 (p90) REVERT: C 82 ILE cc_start: 0.7949 (mt) cc_final: 0.7735 (mt) REVERT: C 122 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.6919 (m-70) REVERT: C 145 MET cc_start: 0.8404 (mmt) cc_final: 0.7986 (mmt) REVERT: C 229 MET cc_start: 0.8845 (mmt) cc_final: 0.8563 (mmt) REVERT: C 244 HIS cc_start: 0.8771 (OUTLIER) cc_final: 0.7726 (t-90) outliers start: 64 outliers final: 36 residues processed: 378 average time/residue: 0.1253 time to fit residues: 76.9745 Evaluate side-chains 334 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 2 residue 30 VAL 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 D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain L residue 30 SER 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 613 LEU Chi-restraints excluded: chain M residue 630 TRP 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 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 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 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 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 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: 0.9990 chunk 41 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN L 183 HIS ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.119905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.100257 restraints weight = 40754.229| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.31 r_work: 0.3137 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.322 23298 Z= 0.137 Angle : 0.888 17.133 32512 Z= 0.316 Chirality : 0.040 0.209 3328 Planarity : 0.004 0.041 3826 Dihedral : 19.263 179.769 4013 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.50 % Allowed : 16.40 % Favored : 80.10 % 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 aren not related in a simple way. whole: 2.22 (0.18), residues: 2193 helix: 3.30 (0.13), residues: 1348 sheet: None (None), residues: 0 loop : -1.81 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 4 TYR 0.015 0.001 TYR C 120 PHE 0.014 0.001 PHE L 185 TRP 0.018 0.001 TRP D 38 HIS 0.005 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00331 (23233) covalent geometry : angle 0.88800 (32512) hydrogen bonds : bond 0.05135 ( 1114) hydrogen bonds : angle 3.26804 ( 3276) Misc. bond : bond 0.06027 ( 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 371 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 304 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 15 LYS cc_start: 0.8046 (tppt) cc_final: 0.7187 (tptp) REVERT: 2 7 ASN cc_start: 0.4235 (p0) cc_final: 0.4027 (p0) REVERT: 4 9 LEU cc_start: 0.7755 (mt) cc_final: 0.7237 (tp) REVERT: 6 15 LYS cc_start: 0.7979 (mttt) cc_final: 0.7719 (mmtt) REVERT: 6 28 ILE cc_start: 0.8129 (mt) cc_final: 0.7888 (mm) REVERT: 8 15 LYS cc_start: 0.7296 (tppt) cc_final: 0.6892 (tppp) REVERT: 8 41 VAL cc_start: 0.8400 (t) cc_final: 0.8018 (p) REVERT: E 31 LYS cc_start: 0.7932 (mttt) cc_final: 0.7613 (mmmt) REVERT: G 8 ASP cc_start: 0.6309 (p0) cc_final: 0.6084 (p0) REVERT: H 7 GLU cc_start: 0.6446 (mt-10) cc_final: 0.5550 (mp0) REVERT: H 18 LEU cc_start: 0.8358 (tp) cc_final: 0.8156 (tt) REVERT: I 22 GLN cc_start: 0.8106 (mt0) cc_final: 0.7796 (mt0) REVERT: K 13 GLN cc_start: 0.6906 (tt0) cc_final: 0.6455 (mp10) REVERT: L 16 LEU cc_start: 0.5699 (tp) cc_final: 0.5376 (tp) REVERT: L 39 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7735 (pt) REVERT: L 64 ILE cc_start: 0.8252 (tt) cc_final: 0.7846 (tp) REVERT: L 82 LEU cc_start: 0.8628 (mt) cc_final: 0.8372 (mt) REVERT: M 387 PHE cc_start: 0.7575 (t80) cc_final: 0.7162 (t80) REVERT: M 630 TRP cc_start: 0.8494 (OUTLIER) cc_final: 0.8073 (t60) REVERT: P 24 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8261 (mp) REVERT: S 15 LYS cc_start: 0.7314 (ttmm) cc_final: 0.7016 (tptt) REVERT: S 37 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7935 (mm) REVERT: V 22 MET cc_start: 0.6987 (mmp) cc_final: 0.6581 (mmp) REVERT: W 30 VAL cc_start: 0.6749 (t) cc_final: 0.6331 (m) REVERT: W 31 LYS cc_start: 0.6496 (mttt) cc_final: 0.6041 (mmmt) REVERT: W 38 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6670 (mp) REVERT: W 41 VAL cc_start: 0.6834 (t) cc_final: 0.6568 (m) REVERT: W 55 ARG cc_start: 0.6468 (ttp-170) cc_final: 0.6132 (ttm170) REVERT: Y 17 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7873 (t80) REVERT: C 87 GLN cc_start: 0.7624 (mp10) cc_final: 0.7379 (mp10) REVERT: C 145 MET cc_start: 0.8425 (mmt) cc_final: 0.8045 (mmt) REVERT: C 229 MET cc_start: 0.8835 (mmt) cc_final: 0.8558 (mmt) REVERT: C 244 HIS cc_start: 0.8837 (OUTLIER) cc_final: 0.7920 (t-90) REVERT: C 266 MET cc_start: 0.8923 (ttm) cc_final: 0.8692 (ttp) outliers start: 67 outliers final: 45 residues processed: 353 average time/residue: 0.1291 time to fit residues: 74.3905 Evaluate side-chains 336 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 284 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 30 VAL 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 54 ILE 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 10 VAL 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 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 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 630 TRP 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 24 LEU 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 W residue 10 VAL 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 188 GLU Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 196 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 145 optimal weight: 0.0770 chunk 182 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 180 optimal weight: 0.0570 chunk 137 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN P 37 ASN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.119264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099777 restraints weight = 40969.776| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.28 r_work: 0.3125 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.281 23298 Z= 0.139 Angle : 0.875 16.567 32512 Z= 0.316 Chirality : 0.040 0.205 3328 Planarity : 0.004 0.038 3826 Dihedral : 18.928 179.745 4009 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.50 % Allowed : 16.40 % Favored : 80.10 % 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 aren not related in a simple way. whole: 2.30 (0.18), residues: 2193 helix: 3.35 (0.13), residues: 1349 sheet: None (None), residues: 0 loop : -1.76 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 570 TYR 0.013 0.001 TYR C 120 PHE 0.013 0.001 PHE L 185 TRP 0.016 0.001 TRP D 38 HIS 0.005 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00335 (23233) covalent geometry : angle 0.87488 (32512) hydrogen bonds : bond 0.05020 ( 1114) hydrogen bonds : angle 3.23349 ( 3276) Misc. bond : bond 0.05151 ( 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 363 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 296 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: 0 15 LYS cc_start: 0.7996 (tppt) cc_final: 0.7200 (tptp) REVERT: 2 7 ASN cc_start: 0.4083 (p0) cc_final: 0.3847 (p0) REVERT: 4 9 LEU cc_start: 0.7702 (mt) cc_final: 0.7330 (tp) REVERT: 6 15 LYS cc_start: 0.7980 (mttt) cc_final: 0.7667 (mmmt) REVERT: 6 28 ILE cc_start: 0.8189 (mt) cc_final: 0.7942 (mm) REVERT: 8 15 LYS cc_start: 0.7366 (tppt) cc_final: 0.6992 (tppp) REVERT: 8 41 VAL cc_start: 0.8406 (t) cc_final: 0.7996 (p) REVERT: E 31 LYS cc_start: 0.7973 (mttt) cc_final: 0.7673 (mmmt) REVERT: G 8 ASP cc_start: 0.6306 (p0) cc_final: 0.6069 (p0) REVERT: H 7 GLU cc_start: 0.6269 (mt-10) cc_final: 0.5492 (mp0) REVERT: L 16 LEU cc_start: 0.5864 (tp) cc_final: 0.5560 (tp) REVERT: L 39 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7734 (pt) REVERT: L 64 ILE cc_start: 0.8269 (tt) cc_final: 0.7871 (tp) REVERT: L 82 LEU cc_start: 0.8608 (mt) cc_final: 0.8330 (mt) REVERT: L 254 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6915 (mt) REVERT: L 302 MET cc_start: 0.7741 (mmm) cc_final: 0.6946 (mtp) REVERT: M 387 PHE cc_start: 0.7575 (t80) cc_final: 0.7175 (t80) REVERT: M 630 TRP cc_start: 0.8494 (OUTLIER) cc_final: 0.8038 (t60) REVERT: S 15 LYS cc_start: 0.7263 (ttmm) cc_final: 0.6993 (tptt) REVERT: S 37 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7840 (mm) REVERT: V 22 MET cc_start: 0.7177 (mmp) cc_final: 0.6828 (mmp) REVERT: W 30 VAL cc_start: 0.6663 (t) cc_final: 0.6290 (m) REVERT: W 55 ARG cc_start: 0.6527 (ttp-170) cc_final: 0.6138 (ttm170) REVERT: Y 17 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7889 (t80) REVERT: C 122 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.6975 (m-70) REVERT: C 145 MET cc_start: 0.8431 (mmt) cc_final: 0.7975 (mmt) REVERT: C 229 MET cc_start: 0.8857 (mmt) cc_final: 0.8599 (mmt) outliers start: 67 outliers final: 47 residues processed: 344 average time/residue: 0.1253 time to fit residues: 69.9472 Evaluate side-chains 330 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 277 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 30 VAL 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 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL 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 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 76 SER 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 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 409 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 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG 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 V residue 18 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 161 optimal weight: 0.0270 chunk 127 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 180 optimal weight: 0.4980 overall best weight: 3.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 26 HIS B 13 GLN K 7 ASN M 525 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094883 restraints weight = 40995.263| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.35 r_work: 0.3043 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.300 23298 Z= 0.273 Angle : 0.955 19.561 32512 Z= 0.351 Chirality : 0.043 0.234 3328 Planarity : 0.005 0.045 3826 Dihedral : 18.648 179.662 4009 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.07 % Allowed : 15.98 % Favored : 79.95 % 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 aren not related in a simple way. whole: 1.95 (0.18), residues: 2193 helix: 3.02 (0.13), residues: 1354 sheet: None (None), residues: 0 loop : -1.83 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 40 TYR 0.022 0.002 TYR M 424 PHE 0.023 0.002 PHE M 519 TRP 0.017 0.001 TRP D 38 HIS 0.007 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00472 (23233) covalent geometry : angle 0.95530 (32512) hydrogen bonds : bond 0.06360 ( 1114) hydrogen bonds : angle 3.47327 ( 3276) Misc. bond : bond 0.07099 ( 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 359 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 281 time to evaluate : 0.661 Fit side-chains REVERT: 0 15 LYS cc_start: 0.8109 (tppt) cc_final: 0.7348 (tptp) REVERT: 2 7 ASN cc_start: 0.4150 (p0) cc_final: 0.3889 (p0) REVERT: 4 9 LEU cc_start: 0.7758 (mt) cc_final: 0.7354 (tp) REVERT: 6 15 LYS cc_start: 0.8024 (mttt) cc_final: 0.7649 (mmtt) REVERT: 6 28 ILE cc_start: 0.8299 (mt) cc_final: 0.8059 (mm) REVERT: 8 15 LYS cc_start: 0.7536 (tppt) cc_final: 0.7138 (tppp) REVERT: 8 41 VAL cc_start: 0.8581 (t) cc_final: 0.8159 (p) REVERT: B 9 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7564 (tt) REVERT: D 4 ARG cc_start: 0.4444 (ttm170) cc_final: 0.4214 (ttm-80) REVERT: E 31 LYS cc_start: 0.8015 (mttt) cc_final: 0.7616 (mmmt) REVERT: G 8 ASP cc_start: 0.6506 (p0) cc_final: 0.6302 (p0) REVERT: H 7 GLU cc_start: 0.6299 (mt-10) cc_final: 0.5619 (mp0) REVERT: L 16 LEU cc_start: 0.5706 (tp) cc_final: 0.5466 (tp) REVERT: L 39 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7857 (pt) REVERT: L 64 ILE cc_start: 0.8600 (tt) cc_final: 0.8195 (tp) REVERT: L 253 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7470 (mm) REVERT: L 254 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7214 (mt) REVERT: L 302 MET cc_start: 0.7911 (mmm) cc_final: 0.7675 (mtm) REVERT: M 387 PHE cc_start: 0.7547 (t80) cc_final: 0.7143 (t80) REVERT: M 630 TRP cc_start: 0.8519 (OUTLIER) cc_final: 0.7964 (t60) REVERT: Q 55 ARG cc_start: 0.6999 (ttm110) cc_final: 0.6514 (mtp180) REVERT: S 15 LYS cc_start: 0.7309 (ttmm) cc_final: 0.6912 (tptt) REVERT: S 37 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7802 (mm) REVERT: U 13 GLN cc_start: 0.6766 (tt0) cc_final: 0.6556 (tt0) REVERT: U 41 VAL cc_start: 0.8548 (t) cc_final: 0.8265 (p) REVERT: V 25 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5728 (mm) REVERT: W 30 VAL cc_start: 0.6757 (t) cc_final: 0.6400 (m) REVERT: W 38 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6921 (mp) REVERT: W 55 ARG cc_start: 0.6592 (ttp-170) cc_final: 0.6212 (ttm170) REVERT: Y 17 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7676 (t80) REVERT: C 63 THR cc_start: 0.8748 (t) cc_final: 0.8404 (m) REVERT: C 122 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6751 (m-70) REVERT: C 145 MET cc_start: 0.8378 (mmt) cc_final: 0.8012 (mmt) REVERT: C 229 MET cc_start: 0.8962 (mmt) cc_final: 0.8602 (mmt) outliers start: 78 outliers final: 46 residues processed: 339 average time/residue: 0.1225 time to fit residues: 67.2282 Evaluate side-chains 323 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 267 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE 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 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 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 254 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 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 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 244 HIS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain Z residue 58 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 50 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 167 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 22 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.095132 restraints weight = 40409.155| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.27 r_work: 0.3055 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.315 23298 Z= 0.177 Angle : 0.900 17.065 32512 Z= 0.335 Chirality : 0.042 0.226 3328 Planarity : 0.004 0.047 3826 Dihedral : 18.203 179.674 4007 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.45 % Allowed : 17.08 % 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 aren not related in a simple way. whole: 1.98 (0.18), residues: 2193 helix: 3.04 (0.13), residues: 1353 sheet: None (None), residues: 0 loop : -1.81 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 570 TYR 0.018 0.002 TYR M 424 PHE 0.020 0.001 PHE M 519 TRP 0.016 0.001 TRP D 38 HIS 0.006 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00443 (23233) covalent geometry : angle 0.89975 (32512) hydrogen bonds : bond 0.06101 ( 1114) hydrogen bonds : angle 3.44692 ( 3276) Misc. bond : bond 0.06728 ( 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 348 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 282 time to evaluate : 0.715 Fit side-chains REVERT: 0 15 LYS cc_start: 0.8078 (tppt) cc_final: 0.7321 (tptp) REVERT: 2 37 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7074 (tt) REVERT: 4 9 LEU cc_start: 0.7751 (mt) cc_final: 0.7359 (tp) REVERT: 6 15 LYS cc_start: 0.8061 (mttt) cc_final: 0.7733 (mmtt) REVERT: 6 28 ILE cc_start: 0.8353 (mt) cc_final: 0.8102 (mm) REVERT: 8 15 LYS cc_start: 0.7581 (tppt) cc_final: 0.7167 (tppp) REVERT: 8 41 VAL cc_start: 0.8536 (t) cc_final: 0.8143 (p) REVERT: D 4 ARG cc_start: 0.4548 (ttm170) cc_final: 0.4347 (ttm-80) REVERT: E 31 LYS cc_start: 0.8011 (mttt) cc_final: 0.7645 (mmmt) REVERT: G 8 ASP cc_start: 0.6429 (p0) cc_final: 0.6215 (p0) REVERT: H 7 GLU cc_start: 0.6355 (mt-10) cc_final: 0.5726 (mp0) REVERT: L 64 ILE cc_start: 0.8665 (tt) cc_final: 0.8293 (tp) REVERT: L 254 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7081 (mt) REVERT: L 302 MET cc_start: 0.7949 (mmm) cc_final: 0.7701 (mtm) REVERT: M 387 PHE cc_start: 0.7541 (t80) cc_final: 0.7216 (t80) REVERT: M 551 LYS cc_start: 0.6372 (mmtt) cc_final: 0.6140 (tptp) REVERT: Q 55 ARG cc_start: 0.7138 (ttm110) cc_final: 0.6643 (mtp180) REVERT: S 15 LYS cc_start: 0.7146 (ttmm) cc_final: 0.6946 (tptp) REVERT: U 22 GLN cc_start: 0.6542 (mp10) cc_final: 0.6240 (pm20) REVERT: W 30 VAL cc_start: 0.6863 (t) cc_final: 0.6530 (m) REVERT: W 38 ILE cc_start: 0.7245 (OUTLIER) cc_final: 0.7030 (mp) REVERT: Y 17 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7725 (t80) REVERT: C 63 THR cc_start: 0.8738 (t) cc_final: 0.8404 (m) REVERT: C 122 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.6727 (m-70) REVERT: C 145 MET cc_start: 0.8375 (mmt) cc_final: 0.8062 (mmt) REVERT: C 229 MET cc_start: 0.8893 (mmt) cc_final: 0.8518 (mmt) outliers start: 66 outliers final: 51 residues processed: 333 average time/residue: 0.1309 time to fit residues: 69.9915 Evaluate side-chains 328 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 272 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 5 residue 24 LEU 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 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 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 K residue 7 ASN 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 76 SER 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 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 613 LEU 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 Q residue 28 ILE 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 10 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 41 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 70 ILE 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 244 HIS Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 181 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 7 ASN K 19 ASN C 130 GLN Z 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.096257 restraints weight = 40198.664| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.45 r_work: 0.3102 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.276 23298 Z= 0.144 Angle : 0.830 16.019 32512 Z= 0.311 Chirality : 0.040 0.217 3328 Planarity : 0.004 0.042 3826 Dihedral : 17.564 179.693 4007 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.39 % Allowed : 17.02 % Favored : 79.58 % 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 aren not related in a simple way. whole: 2.19 (0.18), residues: 2193 helix: 3.24 (0.13), residues: 1350 sheet: None (None), residues: 0 loop : -1.78 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 40 TYR 0.012 0.001 TYR C 120 PHE 0.014 0.001 PHE L 185 TRP 0.015 0.001 TRP D 38 HIS 0.005 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00357 (23233) covalent geometry : angle 0.82992 (32512) hydrogen bonds : bond 0.05393 ( 1114) hydrogen bonds : angle 3.32961 ( 3276) Misc. bond : bond 0.05867 ( 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 350 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 285 time to evaluate : 0.731 Fit side-chains REVERT: 0 15 LYS cc_start: 0.8028 (tppt) cc_final: 0.7281 (tptp) REVERT: 4 9 LEU cc_start: 0.7854 (mt) cc_final: 0.7438 (tp) REVERT: 6 15 LYS cc_start: 0.7969 (mttt) cc_final: 0.7649 (mmtt) REVERT: 6 28 ILE cc_start: 0.8298 (mt) cc_final: 0.8035 (mm) REVERT: 8 41 VAL cc_start: 0.8501 (t) cc_final: 0.8125 (p) REVERT: D 4 ARG cc_start: 0.4548 (ttm170) cc_final: 0.4049 (ttm170) REVERT: E 31 LYS cc_start: 0.7952 (mttt) cc_final: 0.7611 (mmmt) REVERT: H 7 GLU cc_start: 0.6244 (mt-10) cc_final: 0.5625 (mp0) REVERT: L 64 ILE cc_start: 0.8687 (tt) cc_final: 0.8314 (tp) REVERT: L 253 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7472 (mm) REVERT: L 254 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7091 (mt) REVERT: L 302 MET cc_start: 0.7893 (mmm) cc_final: 0.7611 (mtm) REVERT: M 387 PHE cc_start: 0.7600 (t80) cc_final: 0.7239 (t80) REVERT: M 630 TRP cc_start: 0.8496 (OUTLIER) cc_final: 0.8075 (t60) REVERT: Q 55 ARG cc_start: 0.7163 (ttm110) cc_final: 0.6645 (mtp180) REVERT: S 15 LYS cc_start: 0.7242 (ttmm) cc_final: 0.6918 (tptp) REVERT: U 13 GLN cc_start: 0.6963 (tt0) cc_final: 0.6747 (tt0) REVERT: V 17 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7238 (tp) REVERT: W 30 VAL cc_start: 0.6867 (t) cc_final: 0.6538 (m) REVERT: W 38 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6855 (mp) REVERT: Y 17 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7755 (t80) REVERT: C 63 THR cc_start: 0.8672 (t) cc_final: 0.8323 (m) REVERT: C 122 HIS cc_start: 0.7288 (OUTLIER) cc_final: 0.6668 (m-70) REVERT: C 229 MET cc_start: 0.8900 (mmt) cc_final: 0.8488 (mmt) outliers start: 65 outliers final: 50 residues processed: 333 average time/residue: 0.1314 time to fit residues: 69.8793 Evaluate side-chains 331 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 274 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 5 residue 24 LEU 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 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 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 20 LEU Chi-restraints excluded: chain H residue 39 LEU 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 76 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 253 ILE 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 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 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 Q residue 28 ILE 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 25 VAL Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 44 HIS 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 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 58 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 139 optimal weight: 0.6980 chunk 28 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 19 ASN Z 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.117696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097785 restraints weight = 40283.785| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.33 r_work: 0.3099 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.273 23298 Z= 0.142 Angle : 0.847 21.165 32512 Z= 0.323 Chirality : 0.040 0.211 3328 Planarity : 0.004 0.043 3826 Dihedral : 17.569 179.710 4007 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.29 % Allowed : 17.08 % Favored : 79.63 % 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 aren not related in a simple way. whole: 2.23 (0.18), residues: 2193 helix: 3.25 (0.13), residues: 1352 sheet: None (None), residues: 0 loop : -1.73 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 40 TYR 0.016 0.001 TYR G 34 PHE 0.014 0.001 PHE L 185 TRP 0.016 0.001 TRP M 552 HIS 0.005 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00345 (23233) covalent geometry : angle 0.84672 (32512) hydrogen bonds : bond 0.05324 ( 1114) hydrogen bonds : angle 3.33496 ( 3276) Misc. bond : bond 0.05410 ( 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 349 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 286 time to evaluate : 0.464 Fit side-chains REVERT: 0 22 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7344 (mp10) REVERT: 2 37 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7108 (tt) REVERT: 4 9 LEU cc_start: 0.7858 (mt) cc_final: 0.7423 (tp) REVERT: 6 8 ASP cc_start: 0.6894 (p0) cc_final: 0.6643 (p0) REVERT: 6 15 LYS cc_start: 0.8008 (mttt) cc_final: 0.7688 (mmtt) REVERT: 6 28 ILE cc_start: 0.8300 (mt) cc_final: 0.8041 (mm) REVERT: 8 41 VAL cc_start: 0.8496 (t) cc_final: 0.8109 (p) REVERT: D 4 ARG cc_start: 0.4586 (ttm170) cc_final: 0.4084 (ttm170) REVERT: D 18 LEU cc_start: 0.8882 (tp) cc_final: 0.8655 (tt) REVERT: E 31 LYS cc_start: 0.7983 (mttt) cc_final: 0.7683 (mmmt) REVERT: H 7 GLU cc_start: 0.6302 (mt-10) cc_final: 0.5675 (mp0) REVERT: L 58 ASP cc_start: 0.6803 (t70) cc_final: 0.6523 (t70) REVERT: L 64 ILE cc_start: 0.8661 (tt) cc_final: 0.8301 (tp) REVERT: L 253 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7466 (mm) REVERT: L 254 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7036 (mt) REVERT: L 302 MET cc_start: 0.7896 (mmm) cc_final: 0.7605 (mtm) REVERT: M 387 PHE cc_start: 0.7621 (t80) cc_final: 0.7268 (t80) REVERT: M 630 TRP cc_start: 0.8488 (OUTLIER) cc_final: 0.8043 (t60) REVERT: Q 55 ARG cc_start: 0.7165 (ttm110) cc_final: 0.6647 (mtp180) REVERT: S 15 LYS cc_start: 0.7233 (ttmm) cc_final: 0.6916 (tptp) REVERT: U 46 LEU cc_start: 0.8113 (tt) cc_final: 0.7122 (mt) REVERT: V 17 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7266 (tp) REVERT: V 25 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5939 (mm) REVERT: W 30 VAL cc_start: 0.6917 (t) cc_final: 0.6599 (m) REVERT: W 38 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6893 (mp) REVERT: Y 17 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7779 (t80) REVERT: C 63 THR cc_start: 0.8676 (t) cc_final: 0.8326 (m) REVERT: C 122 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.6735 (m-70) REVERT: C 145 MET cc_start: 0.8222 (mmt) cc_final: 0.7829 (mmt) REVERT: C 229 MET cc_start: 0.8872 (mmt) cc_final: 0.8533 (mmt) outliers start: 63 outliers final: 50 residues processed: 330 average time/residue: 0.1204 time to fit residues: 63.7512 Evaluate side-chains 338 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 278 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 2 residue 30 VAL 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 5 residue 24 LEU 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 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 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 20 LEU Chi-restraints excluded: chain H residue 39 LEU 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 76 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 253 ILE 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 409 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 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 Q residue 28 ILE 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 V residue 25 LEU Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 44 HIS 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 106 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 68 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095942 restraints weight = 40244.665| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.29 r_work: 0.3072 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.275 23298 Z= 0.174 Angle : 0.890 18.153 32512 Z= 0.340 Chirality : 0.042 0.226 3328 Planarity : 0.004 0.047 3826 Dihedral : 17.489 179.700 4007 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.60 % Allowed : 16.87 % Favored : 79.53 % 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 aren not related in a simple way. whole: 1.90 (0.18), residues: 2193 helix: 2.97 (0.13), residues: 1368 sheet: None (None), residues: 0 loop : -1.91 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 40 TYR 0.019 0.002 TYR M 424 PHE 0.019 0.002 PHE M 519 TRP 0.016 0.001 TRP D 38 HIS 0.007 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00433 (23233) covalent geometry : angle 0.88990 (32512) hydrogen bonds : bond 0.06064 ( 1114) hydrogen bonds : angle 3.45454 ( 3276) Misc. bond : bond 0.05529 ( 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 350 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 281 time to evaluate : 0.572 Fit side-chains REVERT: 0 22 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7283 (mp10) REVERT: 2 37 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7019 (tt) REVERT: 4 9 LEU cc_start: 0.7841 (mt) cc_final: 0.7407 (tp) REVERT: 6 15 LYS cc_start: 0.8000 (mttt) cc_final: 0.7718 (mmtt) REVERT: 6 28 ILE cc_start: 0.8357 (mt) cc_final: 0.8104 (mm) REVERT: 8 41 VAL cc_start: 0.8553 (t) cc_final: 0.8164 (p) REVERT: 9 16 THR cc_start: 0.8379 (m) cc_final: 0.8152 (m) REVERT: D 4 ARG cc_start: 0.4716 (ttm170) cc_final: 0.4217 (ttm170) REVERT: D 18 LEU cc_start: 0.8936 (tp) cc_final: 0.8705 (tt) REVERT: E 31 LYS cc_start: 0.8000 (mttt) cc_final: 0.7673 (mmmt) REVERT: H 7 GLU cc_start: 0.6237 (mt-10) cc_final: 0.5816 (mp0) REVERT: L 64 ILE cc_start: 0.8712 (tt) cc_final: 0.8377 (tp) REVERT: L 253 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7482 (mm) REVERT: L 254 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7169 (mt) REVERT: L 302 MET cc_start: 0.7971 (mmm) cc_final: 0.7692 (mtm) REVERT: M 357 HIS cc_start: 0.7589 (OUTLIER) cc_final: 0.6680 (t70) REVERT: M 387 PHE cc_start: 0.7658 (t80) cc_final: 0.7327 (t80) REVERT: M 630 TRP cc_start: 0.8489 (OUTLIER) cc_final: 0.8059 (t60) REVERT: Q 55 ARG cc_start: 0.7116 (ttm110) cc_final: 0.6640 (mtp180) REVERT: S 15 LYS cc_start: 0.7209 (ttmm) cc_final: 0.6897 (tptp) REVERT: V 17 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7276 (tp) REVERT: V 25 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5867 (mm) REVERT: W 30 VAL cc_start: 0.6957 (t) cc_final: 0.6629 (m) REVERT: W 38 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6990 (mp) REVERT: Y 17 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7724 (t80) REVERT: C 63 THR cc_start: 0.8705 (t) cc_final: 0.8373 (m) REVERT: C 122 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.6756 (m-70) REVERT: C 145 MET cc_start: 0.8268 (mmt) cc_final: 0.7878 (mmt) REVERT: C 229 MET cc_start: 0.8889 (mmt) cc_final: 0.8584 (mmt) outliers start: 69 outliers final: 52 residues processed: 330 average time/residue: 0.1293 time to fit residues: 68.6416 Evaluate side-chains 336 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 273 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 2 residue 30 VAL 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 5 residue 24 LEU 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 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 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 30 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 253 ILE 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 357 HIS Chi-restraints excluded: chain M residue 409 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 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 Q residue 28 ILE 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 V residue 25 LEU Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 44 HIS 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 99 THR Chi-restraints excluded: chain C residue 106 MET 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 266 MET 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: 4.9990 chunk 15 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 45 optimal weight: 0.0870 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097112 restraints weight = 40337.723| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.29 r_work: 0.3083 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.285 23298 Z= 0.149 Angle : 0.835 16.846 32512 Z= 0.319 Chirality : 0.041 0.211 3328 Planarity : 0.004 0.044 3826 Dihedral : 17.113 179.714 4007 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.24 % Allowed : 17.39 % 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 aren not related in a simple way. whole: 2.16 (0.18), residues: 2193 helix: 3.16 (0.13), residues: 1352 sheet: None (None), residues: 0 loop : -1.69 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 40 TYR 0.014 0.001 TYR G 34 PHE 0.014 0.001 PHE M 519 TRP 0.015 0.001 TRP D 38 HIS 0.005 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00367 (23233) covalent geometry : angle 0.83530 (32512) hydrogen bonds : bond 0.05564 ( 1114) hydrogen bonds : angle 3.38440 ( 3276) Misc. bond : bond 0.05667 ( 65) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5098.88 seconds wall clock time: 87 minutes 41.81 seconds (5261.81 seconds total)