Starting phenix.real_space_refine on Sun Jul 5 01:27:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8j5o_35988/07_2026/8j5o_35988.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5o_35988/07_2026/8j5o_35988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8j5o_35988/07_2026/8j5o_35988.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8j5o_35988/07_2026/8j5o_35988.cif" model { file = "/net/cci-nas-00/data/ceres_data/8j5o_35988/07_2026/8j5o_35988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5o_35988/07_2026/8j5o_35988.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j5o_35988/07_2026/8j5o_35988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5o_35988/07_2026/8j5o_35988.map" } resolution = 2.9 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= 0.009 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 4 5.49 5 Mg 48 5.21 5 S 75 5.16 5 C 16852 2.51 5 N 3297 2.21 5 O 3411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23692 Number of models: 1 Model: "" Number of chains: 69 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: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 266 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} 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: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} 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: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} 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: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} 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: "C" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2404 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 24, 'TRANS': 290} 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: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} 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: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} 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: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2364 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} 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: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} 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: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} 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: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} 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: "X" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 206 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} 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: "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: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 214 Unusual residues: {'BCL': 2, 'KGD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "1" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" 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: "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: 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: "5" 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: "6" 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: "7" 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: "8" 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: "9" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "A" 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: "B" 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: "C" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 299 Unusual residues: {'HEM': 4, 'KGD': 2, 'PGV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "D" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" 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: "F" 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: "G" 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: "H" 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: "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: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" 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: "L" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 438 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 2, 'MQE': 1, 'PGV': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 223 Unusual residues: {'BCL': 1, 'BPH': 1, 'MQE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 32 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} Unresolved non-hydrogen planarities: 44 Chain: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" 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: "P" 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: "Q" 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: "R" 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: "S" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 214 Unusual residues: {'BCL': 2, 'KGD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 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: "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} Time building chain proxies: 4.42, per 1000 atoms: 0.19 Number of scatterers: 23692 At special positions: 0 Unit cell: (142.88, 131.271, 126.806, 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 75 16.00 P 4 15.00 Mg 48 11.99 O 3411 8.00 N 3297 7.00 C 16852 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=58, symmetry=0 Number of additional bonds: simple=58, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 915.9 milliseconds 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4346 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 4 sheets defined 68.5% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain '0' and resid 19 through 51 removed outlier: 4.225A pdb=" N LEU 0 24 " --> pdb=" O ASN 0 20 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL 0 25 " --> pdb=" O ALA 0 21 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 34 removed outlier: 3.727A pdb=" N GLY 1 34 " --> pdb=" O VAL 1 30 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 51 removed outlier: 3.819A pdb=" N LEU 2 24 " --> pdb=" O ASN 2 20 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 34 removed outlier: 3.934A pdb=" N GLY 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 51 removed outlier: 4.274A pdb=" N LEU 4 24 " --> pdb=" O ASN 4 20 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL 4 25 " --> pdb=" O ALA 4 21 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 34 removed outlier: 3.850A pdb=" N GLY 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) Processing helix chain '6' and resid 19 through 51 removed outlier: 4.356A pdb=" N LEU 6 24 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL 6 25 " --> pdb=" O ALA 6 21 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 34 removed outlier: 3.944A pdb=" N GLY 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '8' and resid 19 through 51 removed outlier: 4.156A pdb=" N LEU 8 24 " --> pdb=" O ASN 8 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL 8 25 " --> pdb=" O ALA 8 21 " (cutoff:3.500A) Processing helix chain '9' and resid 7 through 34 removed outlier: 3.911A pdb=" N GLY 9 34 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 34 removed outlier: 3.703A pdb=" N GLY A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.624A pdb=" N PHE B 18 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 51 removed outlier: 3.733A pdb=" N TRP B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 14 Processing helix chain 'C' and resid 15 through 46 removed outlier: 3.941A pdb=" N TYR C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 removed outlier: 3.664A pdb=" N ASN C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 109 through 115 removed outlier: 3.562A pdb=" N LEU C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.731A pdb=" N CYS C 121 " --> pdb=" O CYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 156 removed outlier: 3.530A pdb=" N LYS C 139 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 160 Processing helix chain 'C' and resid 170 through 175 removed outlier: 4.100A pdb=" N CYS C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 190 Processing helix chain 'C' and resid 218 through 235 Processing helix chain 'C' and resid 256 through 274 Processing helix chain 'C' and resid 284 through 288 removed outlier: 4.334A pdb=" N ALA C 287 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY C 288 " --> pdb=" O ILE C 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 288' Processing helix chain 'C' and resid 292 through 298 removed outlier: 4.046A pdb=" N CYS C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 33 Processing helix chain 'E' and resid 19 through 51 removed outlier: 4.085A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 34 removed outlier: 3.775A pdb=" N GLY F 34 " --> pdb=" O VAL F 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 51 removed outlier: 4.076A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 33 removed outlier: 3.526A pdb=" N SER H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 51 removed outlier: 4.225A pdb=" N LEU I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 34 removed outlier: 3.853A pdb=" N GLY J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 51 removed outlier: 4.055A pdb=" N VAL K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 43 removed outlier: 4.002A pdb=" N ILE L 39 " --> pdb=" O PRO L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 56 removed outlier: 3.566A pdb=" N ARG L 53 " --> pdb=" O THR L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 93 removed outlier: 3.582A pdb=" N ALA L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY L 91 " --> pdb=" O TYR L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 113 Processing helix chain 'L' and resid 122 through 150 removed outlier: 3.541A pdb=" N PHE L 126 " --> pdb=" O GLY L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 172 Processing helix chain 'L' and resid 172 through 179 Processing helix chain 'L' and resid 191 through 203 removed outlier: 3.609A pdb=" N TRP L 195 " --> pdb=" O HIS L 191 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR L 203 " --> pdb=" O ILE L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 235 Processing helix chain 'L' and resid 244 through 253 Processing helix chain 'L' and resid 259 through 288 removed outlier: 3.844A pdb=" N ILE L 263 " --> pdb=" O GLY L 259 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS L 264 " --> pdb=" O GLU L 260 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG L 265 " --> pdb=" O ILE L 261 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR L 287 " --> pdb=" O PHE L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 299 removed outlier: 4.332A pdb=" N PHE L 298 " --> pdb=" O PHE L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 314 Processing helix chain 'M' and resid 337 through 343 Processing helix chain 'M' and resid 359 through 366 Processing helix chain 'M' and resid 379 through 401 removed outlier: 3.580A pdb=" N VAL M 401 " --> pdb=" O TYR M 397 " (cutoff:3.500A) Processing helix chain 'M' and resid 404 through 411 Processing helix chain 'M' and resid 412 through 415 Processing helix chain 'M' and resid 431 through 434 Processing helix chain 'M' and resid 435 through 464 removed outlier: 3.630A pdb=" N LEU M 439 " --> pdb=" O GLY M 435 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA M 440 " --> pdb=" O GLY M 436 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY M 464 " --> pdb=" O ALA M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 467 through 485 removed outlier: 3.668A pdb=" N TRP M 471 " --> pdb=" O THR M 467 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU M 479 " --> pdb=" O SER M 475 " (cutoff:3.500A) Processing helix chain 'M' and resid 493 through 497 removed outlier: 4.118A pdb=" N ALA M 496 " --> pdb=" O ASN M 493 " (cutoff:3.500A) Processing helix chain 'M' and resid 503 through 516 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 561 Processing helix chain 'M' and resid 565 through 580 Processing helix chain 'M' and resid 586 through 613 removed outlier: 3.963A pdb=" N ILE M 590 " --> pdb=" O TYR M 586 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY M 611 " --> pdb=" O LEU M 607 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR M 612 " --> pdb=" O PHE M 608 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU M 613 " --> pdb=" O LEU M 609 " (cutoff:3.500A) Processing helix chain 'M' and resid 616 through 624 Processing helix chain 'M' and resid 634 through 639 removed outlier: 4.112A pdb=" N GLN M 637 " --> pdb=" O ASP M 634 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL M 639 " --> pdb=" O ALA M 636 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 34 removed outlier: 3.999A pdb=" N GLY N 34 " --> pdb=" O VAL N 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 51 removed outlier: 3.704A pdb=" N TRP O 23 " --> pdb=" O ASN O 19 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU O 24 " --> pdb=" O ASN O 20 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 34 removed outlier: 3.873A pdb=" N GLY P 34 " --> pdb=" O VAL P 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 18 Processing helix chain 'Q' and resid 19 through 51 removed outlier: 4.428A pdb=" N LEU Q 24 " --> pdb=" O ASN Q 20 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL Q 25 " --> pdb=" O ALA Q 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 34 removed outlier: 3.826A pdb=" N GLY R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 51 removed outlier: 4.447A pdb=" N LEU S 24 " --> pdb=" O ASN S 20 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 34 removed outlier: 3.666A pdb=" N GLY T 34 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 15 removed outlier: 3.620A pdb=" N LYS U 15 " --> pdb=" O ASP U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 51 removed outlier: 4.387A pdb=" N LEU U 24 " --> pdb=" O ASN U 20 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 33 Processing helix chain 'W' and resid 19 through 51 removed outlier: 4.412A pdb=" N LEU W 24 " --> pdb=" O ASN W 20 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL W 25 " --> pdb=" O ALA W 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 25 Processing helix chain 'Y' and resid 2 through 17 removed outlier: 3.542A pdb=" N ALA Y 6 " --> pdb=" O ASN Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 30 removed outlier: 3.878A pdb=" N VAL Y 21 " --> pdb=" O PHE Y 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 47 Proline residue: Z 26 - end of helix Processing sheet with id=AA1, first strand: chain 'L' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'L' and resid 32 through 34 removed outlier: 4.104A pdb=" N TYR Z 49 " --> pdb=" O ILE L 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 62 through 64 removed outlier: 3.705A pdb=" N PHE L 62 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE L 67 " --> pdb=" O ILE L 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 349 through 351 1198 hydrogen bonds defined for protein. 3519 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 6834 1.37 - 1.57: 17569 1.57 - 1.77: 8 1.77 - 1.98: 125 1.98 - 2.18: 208 Bond restraints: 24744 Sorted by residual: bond pdb=" NA BCL K 102 " pdb="MG BCL K 102 " ideal model delta sigma weight residual 2.170 1.997 0.173 2.40e-02 1.74e+03 5.19e+01 bond pdb=" NA BCL W 102 " pdb="MG BCL W 102 " ideal model delta sigma weight residual 2.170 2.000 0.170 2.40e-02 1.74e+03 5.00e+01 bond pdb=" CGD BCL W 102 " pdb=" O2D BCL W 102 " ideal model delta sigma weight residual 1.324 1.450 -0.126 2.10e-02 2.27e+03 3.60e+01 bond pdb=" CAY KGD J 103 " pdb=" CBD KGD J 103 " ideal model delta sigma weight residual 1.500 1.381 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C1A BCL K 102 " pdb=" CHA BCL K 102 " ideal model delta sigma weight residual 1.368 1.487 -0.119 2.00e-02 2.50e+03 3.52e+01 ... (remaining 24739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 33792 3.36 - 6.73: 618 6.73 - 10.09: 72 10.09 - 13.46: 8 13.46 - 16.82: 3 Bond angle restraints: 34493 Sorted by residual: angle pdb=" N PHE L 185 " pdb=" CA PHE L 185 " pdb=" C PHE L 185 " ideal model delta sigma weight residual 109.93 121.06 -11.13 1.24e+00 6.50e-01 8.06e+01 angle pdb=" C1D BCL K 102 " pdb=" C2D BCL K 102 " pdb=" CMD BCL K 102 " ideal model delta sigma weight residual 125.57 139.17 -13.59 1.83e+00 2.99e-01 5.53e+01 angle pdb=" C1D BCL W 102 " pdb=" C2D BCL W 102 " pdb=" CMD BCL W 102 " ideal model delta sigma weight residual 125.57 138.52 -12.94 1.83e+00 2.99e-01 5.01e+01 angle pdb=" NA BCL W 102 " pdb="MG BCL W 102 " pdb=" NC BCL W 102 " ideal model delta sigma weight residual 160.52 177.34 -16.82 2.84e+00 1.24e-01 3.51e+01 angle pdb=" N HIS L 183 " pdb=" CA HIS L 183 " pdb=" CB HIS L 183 " ideal model delta sigma weight residual 110.91 102.27 8.64 1.58e+00 4.01e-01 2.99e+01 ... (remaining 34488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 12309 36.00 - 71.99: 291 71.99 - 107.99: 54 107.99 - 143.99: 7 143.99 - 179.98: 1 Dihedral angle restraints: 12662 sinusoidal: 5975 harmonic: 6687 Sorted by residual: dihedral pdb=" C1 BCL L1002 " pdb=" C2 BCL L1002 " pdb=" C3 BCL L1002 " pdb=" C5 BCL L1002 " ideal model delta sinusoidal sigma weight residual 180.00 0.02 179.98 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL W 102 " pdb=" CGA BCL W 102 " pdb=" O2A BCL W 102 " pdb=" CBA BCL W 102 " ideal model delta sinusoidal sigma weight residual 180.00 122.95 57.05 1 6.00e+00 2.78e-02 1.22e+02 dihedral pdb=" C2C HEM C 501 " pdb=" C3C HEM C 501 " pdb=" CAC HEM C 501 " pdb=" CBC HEM C 501 " ideal model delta sinusoidal sigma weight residual 0.00 89.17 -89.17 2 1.00e+01 1.00e-02 4.80e+01 ... (remaining 12659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3377 0.121 - 0.241: 23 0.241 - 0.362: 4 0.362 - 0.483: 0 0.483 - 0.603: 1 Chirality restraints: 3405 Sorted by residual: chirality pdb=" CA PHE L 185 " pdb=" N PHE L 185 " pdb=" C PHE L 185 " pdb=" CB PHE L 185 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.10e+00 chirality pdb=" CA ALA L 315 " pdb=" N ALA L 315 " pdb=" C ALA L 315 " pdb=" CB ALA L 315 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA TYR E 34 " pdb=" N TYR E 34 " pdb=" C TYR E 34 " pdb=" CB TYR E 34 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3402 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL W 102 " 0.328 3.00e-02 1.11e+03 2.65e-01 3.90e+02 pdb=" CBA BCL W 102 " 0.192 3.00e-02 1.11e+03 pdb=" CGA BCL W 102 " -0.079 3.00e-02 1.11e+03 pdb=" O1A BCL W 102 " 0.006 3.00e-02 1.11e+03 pdb=" O2A BCL W 102 " -0.447 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1A BCL K 102 " 0.035 3.20e-02 9.77e+02 1.72e-01 1.45e+02 pdb=" C4A BCL K 102 " 0.094 3.20e-02 9.77e+02 pdb=" CHA BCL K 102 " -0.173 3.20e-02 9.77e+02 pdb=" CHB BCL K 102 " -0.210 3.20e-02 9.77e+02 pdb=" NA BCL K 102 " 0.254 3.20e-02 9.77e+02 delta sigma weight rms_deltas residual plane pdb=" C1A BCL W 102 " 0.032 3.20e-02 9.77e+02 1.55e-01 1.18e+02 pdb=" C4A BCL W 102 " 0.113 3.20e-02 9.77e+02 pdb=" CHA BCL W 102 " -0.154 3.20e-02 9.77e+02 pdb=" CHB BCL W 102 " -0.200 3.20e-02 9.77e+02 pdb=" NA BCL W 102 " 0.208 3.20e-02 9.77e+02 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 48 2.46 - 3.07: 14648 3.07 - 3.68: 32362 3.68 - 4.29: 53062 4.29 - 4.90: 89583 Nonbonded interactions: 189703 Sorted by model distance: nonbonded pdb=" CE1 HIS 3 27 " pdb="MG BCL 3 101 " model vdw 1.849 3.130 nonbonded pdb=" CE1 HIS P 27 " pdb="MG BCL P 101 " model vdw 2.084 3.130 nonbonded pdb=" OE2 GLU M 557 " pdb="FE FE L1004 " model vdw 2.086 2.260 nonbonded pdb=" SD MET C 229 " pdb="FE HEM C 503 " model vdw 2.127 3.360 nonbonded pdb=" SD MET C 145 " pdb="FE HEM C 502 " model vdw 2.132 3.360 ... (remaining 189698 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' and resid 7 through 101) selection = (chain '2' and resid 7 through 101) selection = (chain '4' and resid 7 through 101) selection = (chain '6' and resid 7 through 101) selection = (chain '8' and resid 7 through 101) selection = (chain 'B' and resid 7 through 101) selection = (chain 'E' and resid 7 through 101) selection = (chain 'G' and resid 7 through 101) selection = (chain 'I' and resid 7 through 101) selection = (chain 'K' and resid 7 through 101) selection = (chain 'O' and resid 7 through 101) selection = (chain 'Q' and resid 7 through 101) selection = (chain 'S' and resid 7 through 101) selection = (chain 'U' and resid 7 through 101) selection = (chain 'W' and resid 7 through 101) } ncs_group { reference = (chain '1' and resid 7 through 40) selection = (chain '3' and resid 7 through 40) selection = (chain '5' and resid 7 through 40) selection = (chain '7' and resid 7 through 40) selection = (chain '9' and resid 7 through 40) selection = (chain 'A' and resid 7 through 40) selection = (chain 'D' and resid 7 through 40) selection = (chain 'F' and resid 7 through 40) selection = (chain 'H' and resid 7 through 40) selection = (chain 'J' and resid 7 through 40) selection = (chain 'N' and resid 7 through 40) selection = (chain 'P' and resid 7 through 40) selection = (chain 'R' and resid 7 through 40) selection = (chain 'T' and resid 7 through 40) selection = (chain 'V' and resid 7 through 40) } 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.370 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 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 : 0.010 0.403 24802 Z= 0.727 Angle : 0.980 16.821 34493 Z= 0.403 Chirality : 0.043 0.603 3405 Planarity : 0.008 0.265 4200 Dihedral : 16.446 179.983 8316 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.18), residues: 2244 helix: 3.62 (0.13), residues: 1398 sheet: None (None), residues: 0 loop : -1.59 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 251 TYR 0.030 0.002 TYR L 204 PHE 0.040 0.002 PHE L 185 TRP 0.058 0.002 TRP L 305 HIS 0.022 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.34 (24744) covalent geometry : angle 0.98010 / 0.40 (34493) hydrogen bonds : bond 0.12015 / 8.33 ( 1198) hydrogen bonds : angle 4.07481 / 3.13 ( 3519) Misc. bond : bond 0.13283 / 9.26 ( 58) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.830 Fit side-chains REVERT: 5 22 MET cc_start: 0.9206 (mmp) cc_final: 0.8989 (mmp) REVERT: 7 16 THR cc_start: 0.8956 (m) cc_final: 0.8693 (m) REVERT: N 14 VAL cc_start: 0.8349 (t) cc_final: 0.8131 (t) outliers start: 0 outliers final: 1 residues processed: 301 average time/residue: 0.5576 time to fit residues: 194.8137 Evaluate side-chains 236 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 240 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN C 61 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 ASN C 301 ASN G 13 GLN H 37 ASN I 22 GLN L 183 HIS L 209 ASN L 252 ASN L 264 HIS M 637 GLN O 13 GLN Q 13 GLN U 13 GLN U 22 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.104767 restraints weight = 28418.620| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.13 r_work: 0.2812 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 24802 Z= 0.179 Angle : 0.810 12.204 34493 Z= 0.323 Chirality : 0.043 0.185 3405 Planarity : 0.005 0.060 4200 Dihedral : 16.594 179.920 4319 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.53 % Allowed : 6.66 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.18), residues: 2244 helix: 3.35 (0.13), residues: 1423 sheet: None (None), residues: 0 loop : -1.65 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 4 TYR 0.014 0.002 TYR C 205 PHE 0.019 0.002 PHE L 123 TRP 0.031 0.002 TRP L 305 HIS 0.015 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (24744) covalent geometry : angle 0.81014 / 0.32 (34493) hydrogen bonds : bond 0.07298 / 4.89 ( 1198) hydrogen bonds : angle 3.61421 / 2.76 ( 3519) Misc. bond : bond 0.02210 / 1.70 ( 58) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.638 Fit side-chains REVERT: 5 22 MET cc_start: 0.9214 (mmp) cc_final: 0.8982 (mmp) REVERT: 7 16 THR cc_start: 0.8998 (m) cc_final: 0.8743 (m) REVERT: C 78 MET cc_start: 0.5867 (tmm) cc_final: 0.5586 (ttm) REVERT: C 247 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7987 (ptm160) REVERT: C 272 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: L 94 ASN cc_start: 0.7299 (m110) cc_final: 0.6925 (m-40) REVERT: M 341 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7973 (mm-30) REVERT: N 14 VAL cc_start: 0.8433 (t) cc_final: 0.8228 (t) REVERT: Q 15 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7647 (mttp) REVERT: Z 42 ASP cc_start: 0.8525 (t70) cc_final: 0.8155 (t0) REVERT: Z 53 ASP cc_start: 0.7476 (t0) cc_final: 0.7258 (t0) outliers start: 30 outliers final: 14 residues processed: 249 average time/residue: 0.5408 time to fit residues: 156.3924 Evaluate side-chains 238 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain M residue 607 LEU Chi-restraints excluded: chain O residue 31 LYS Chi-restraints excluded: chain Q residue 15 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 172 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS C 225 ASN C 226 GLN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN M 572 GLN M 637 GLN O 13 GLN P 37 ASN U 13 GLN U 22 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.119843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.100713 restraints weight = 28555.803| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.14 r_work: 0.2742 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 24802 Z= 0.207 Angle : 0.843 13.432 34493 Z= 0.337 Chirality : 0.044 0.204 3405 Planarity : 0.005 0.058 4200 Dihedral : 16.209 179.836 4319 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.93 % Allowed : 9.35 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.18), residues: 2244 helix: 3.09 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.86 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 3 4 TYR 0.020 0.002 TYR C 205 PHE 0.025 0.002 PHE 9 36 TRP 0.022 0.002 TRP L 305 HIS 0.010 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.21 (24744) covalent geometry : angle 0.84347 / 0.34 (34493) hydrogen bonds : bond 0.08051 / 5.39 ( 1198) hydrogen bonds : angle 3.65860 / 2.79 ( 3519) Misc. bond : bond 0.02008 / 1.52 ( 58) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 0.714 Fit side-chains REVERT: 5 22 MET cc_start: 0.9248 (mmp) cc_final: 0.8998 (mmp) REVERT: 7 16 THR cc_start: 0.8997 (m) cc_final: 0.8760 (m) REVERT: 7 17 LEU cc_start: 0.8528 (mm) cc_final: 0.8208 (tp) REVERT: C 78 MET cc_start: 0.6012 (tmm) cc_final: 0.5590 (ttm) REVERT: C 247 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7904 (ptm160) REVERT: C 253 GLU cc_start: 0.7845 (pt0) cc_final: 0.7609 (pt0) REVERT: C 272 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: L 94 ASN cc_start: 0.7606 (m110) cc_final: 0.7226 (m-40) REVERT: L 106 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8105 (mm-30) REVERT: L 310 GLN cc_start: 0.6111 (OUTLIER) cc_final: 0.5897 (tp40) REVERT: M 341 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8200 (mp0) REVERT: M 343 TYR cc_start: 0.8280 (m-80) cc_final: 0.8067 (m-80) REVERT: M 367 GLU cc_start: 0.8507 (tp30) cc_final: 0.8176 (tm-30) REVERT: N 14 VAL cc_start: 0.8447 (t) cc_final: 0.8247 (t) REVERT: V 16 THR cc_start: 0.9015 (m) cc_final: 0.8784 (m) REVERT: Z 53 ASP cc_start: 0.7447 (t0) cc_final: 0.7224 (t0) outliers start: 38 outliers final: 23 residues processed: 261 average time/residue: 0.5356 time to fit residues: 162.2584 Evaluate side-chains 253 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 6 residue 15 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 310 GLN Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 607 LEU Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain Z residue 35 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 84 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 75 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 72 optimal weight: 0.0870 chunk 65 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 0.2980 overall best weight: 1.4920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 20 ASN 6 20 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN O 13 GLN U 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.124542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.105404 restraints weight = 28464.371| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.11 r_work: 0.2837 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 24802 Z= 0.127 Angle : 0.691 11.358 34493 Z= 0.273 Chirality : 0.039 0.157 3405 Planarity : 0.004 0.052 4200 Dihedral : 15.531 179.986 4317 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.27 % Allowed : 10.63 % Favored : 88.10 % 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 are not related in a simple way. whole: 2.61 (0.18), residues: 2244 helix: 3.58 (0.13), residues: 1410 sheet: None (None), residues: 0 loop : -1.80 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 4 TYR 0.015 0.001 TYR M 424 PHE 0.016 0.001 PHE M 387 TRP 0.012 0.001 TRP M 594 HIS 0.007 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (24744) covalent geometry : angle 0.69086 / 0.27 (34493) hydrogen bonds : bond 0.05934 / 3.98 ( 1198) hydrogen bonds : angle 3.37231 / 2.57 ( 3519) Misc. bond : bond 0.01465 / 1.04 ( 58) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.814 Fit side-chains REVERT: 7 16 THR cc_start: 0.8987 (m) cc_final: 0.8722 (m) REVERT: 7 17 LEU cc_start: 0.8477 (mm) cc_final: 0.8128 (tp) REVERT: C 78 MET cc_start: 0.6121 (tmm) cc_final: 0.5673 (ttm) REVERT: C 236 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7610 (mtt) REVERT: C 272 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: L 94 ASN cc_start: 0.7260 (m110) cc_final: 0.6914 (m-40) REVERT: L 145 ASP cc_start: 0.8074 (m-30) cc_final: 0.7820 (m-30) REVERT: M 367 GLU cc_start: 0.8432 (tp30) cc_final: 0.8087 (tm-30) REVERT: N 14 VAL cc_start: 0.8397 (t) cc_final: 0.8166 (t) REVERT: Z 42 ASP cc_start: 0.8522 (t70) cc_final: 0.8273 (t0) REVERT: Z 53 ASP cc_start: 0.7547 (t0) cc_final: 0.7311 (t0) outliers start: 25 outliers final: 14 residues processed: 245 average time/residue: 0.5360 time to fit residues: 153.3125 Evaluate side-chains 238 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain Z residue 35 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 201 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 20 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN O 13 GLN U 13 GLN Z 44 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.122587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.103367 restraints weight = 28304.864| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.10 r_work: 0.2804 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 24802 Z= 0.151 Angle : 0.729 12.267 34493 Z= 0.289 Chirality : 0.040 0.180 3405 Planarity : 0.005 0.056 4200 Dihedral : 15.317 179.937 4317 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.88 % Allowed : 11.13 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.18), residues: 2244 helix: 3.43 (0.13), residues: 1417 sheet: None (None), residues: 0 loop : -1.81 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 4 TYR 0.015 0.001 TYR M 424 PHE 0.017 0.001 PHE M 387 TRP 0.010 0.001 TRP M 594 HIS 0.009 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (24744) covalent geometry : angle 0.72898 / 0.29 (34493) hydrogen bonds : bond 0.06566 / 4.40 ( 1198) hydrogen bonds : angle 3.42889 / 2.61 ( 3519) Misc. bond : bond 0.01490 / 1.07 ( 58) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 0.636 Fit side-chains REVERT: 7 16 THR cc_start: 0.8997 (m) cc_final: 0.8740 (m) REVERT: 7 17 LEU cc_start: 0.8482 (mm) cc_final: 0.8143 (tp) REVERT: A 4 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.5054 (ppt-90) REVERT: C 78 MET cc_start: 0.6233 (tmm) cc_final: 0.5724 (ttm) REVERT: C 247 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7779 (ptm160) REVERT: C 272 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: L 94 ASN cc_start: 0.7287 (m110) cc_final: 0.6934 (m-40) REVERT: L 145 ASP cc_start: 0.8031 (m-30) cc_final: 0.7773 (m-30) REVERT: M 341 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: M 367 GLU cc_start: 0.8468 (tp30) cc_final: 0.8127 (tm-30) REVERT: N 14 VAL cc_start: 0.8391 (t) cc_final: 0.8153 (t) REVERT: V 16 THR cc_start: 0.8991 (m) cc_final: 0.8783 (m) REVERT: Z 42 ASP cc_start: 0.8557 (t70) cc_final: 0.8295 (t0) REVERT: Z 53 ASP cc_start: 0.7462 (t0) cc_final: 0.7229 (t0) outliers start: 37 outliers final: 20 residues processed: 256 average time/residue: 0.5216 time to fit residues: 155.6409 Evaluate side-chains 250 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain Z residue 35 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 141 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 6 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 HIS C 61 ASN C 191 ASN C 220 HIS ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN U 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.117988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.098827 restraints weight = 28594.151| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.09 r_work: 0.2718 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.193 24802 Z= 0.297 Angle : 0.937 14.250 34493 Z= 0.374 Chirality : 0.048 0.251 3405 Planarity : 0.006 0.061 4200 Dihedral : 15.988 179.683 4317 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.39 % Allowed : 10.88 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.17), residues: 2244 helix: 2.94 (0.13), residues: 1407 sheet: None (None), residues: 0 loop : -1.99 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 4 TYR 0.021 0.003 TYR C 205 PHE 0.021 0.002 PHE Z 40 TRP 0.015 0.002 TRP L 181 HIS 0.008 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.27 (24744) covalent geometry : angle 0.93741 / 0.37 (34493) hydrogen bonds : bond 0.09138 / 6.11 ( 1198) hydrogen bonds : angle 3.76242 / 2.87 ( 3519) Misc. bond : bond 0.03048 / 1.83 ( 58) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 0.586 Fit side-chains REVERT: 7 17 LEU cc_start: 0.8579 (mm) cc_final: 0.8250 (tp) REVERT: A 4 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.5145 (ppt-90) REVERT: C 78 MET cc_start: 0.6270 (tmm) cc_final: 0.5838 (ttm) REVERT: C 247 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8112 (ptm160) REVERT: C 272 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: I 7 ASN cc_start: 0.6981 (p0) cc_final: 0.6734 (p0) REVERT: J 4 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7037 (ptt90) REVERT: L 94 ASN cc_start: 0.7817 (m110) cc_final: 0.7484 (m-40) REVERT: L 145 ASP cc_start: 0.8180 (m-30) cc_final: 0.7904 (m-30) REVERT: L 205 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7889 (m-40) REVERT: M 341 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: M 343 TYR cc_start: 0.8265 (m-80) cc_final: 0.8007 (m-80) REVERT: M 367 GLU cc_start: 0.8550 (tp30) cc_final: 0.8226 (tm-30) REVERT: V 16 THR cc_start: 0.9024 (m) cc_final: 0.8811 (m) outliers start: 47 outliers final: 22 residues processed: 268 average time/residue: 0.5338 time to fit residues: 166.3180 Evaluate side-chains 254 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 205 ASN Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 607 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain U residue 31 LYS Chi-restraints excluded: chain W residue 12 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 197 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 37 ASN 6 20 ASN C 61 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN G 13 GLN H 37 ASN I 22 GLN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN U 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.121232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.101971 restraints weight = 28427.275| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.10 r_work: 0.2800 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24802 Z= 0.139 Angle : 0.724 12.363 34493 Z= 0.289 Chirality : 0.040 0.179 3405 Planarity : 0.005 0.052 4200 Dihedral : 15.357 179.983 4317 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.78 % Allowed : 11.69 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.18), residues: 2244 helix: 3.36 (0.13), residues: 1411 sheet: None (None), residues: 0 loop : -1.96 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 4 TYR 0.020 0.001 TYR M 424 PHE 0.017 0.001 PHE M 387 TRP 0.012 0.001 TRP M 594 HIS 0.009 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (24744) covalent geometry : angle 0.72387 / 0.29 (34493) hydrogen bonds : bond 0.06491 / 4.35 ( 1198) hydrogen bonds : angle 3.46195 / 2.64 ( 3519) Misc. bond : bond 0.01184 / 0.75 ( 58) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 0.776 Fit side-chains REVERT: 7 16 THR cc_start: 0.8940 (m) cc_final: 0.8683 (m) REVERT: 7 17 LEU cc_start: 0.8464 (mm) cc_final: 0.8115 (tp) REVERT: A 4 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.5030 (ppt-90) REVERT: C 78 MET cc_start: 0.6207 (tmm) cc_final: 0.5624 (ttm) REVERT: C 247 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.7707 (ptm160) REVERT: C 272 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: I 7 ASN cc_start: 0.6845 (p0) cc_final: 0.6541 (p0) REVERT: L 94 ASN cc_start: 0.7417 (m110) cc_final: 0.7052 (m-40) REVERT: L 145 ASP cc_start: 0.7990 (m-30) cc_final: 0.7665 (m-30) REVERT: M 341 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: M 367 GLU cc_start: 0.8461 (tp30) cc_final: 0.8136 (tm-30) REVERT: M 609 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7561 (mp) REVERT: V 16 THR cc_start: 0.8982 (m) cc_final: 0.8772 (m) outliers start: 35 outliers final: 19 residues processed: 252 average time/residue: 0.5086 time to fit residues: 149.7249 Evaluate side-chains 248 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain W residue 12 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 178 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 191 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 37 ASN C 61 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 205 ASN O 13 GLN U 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.122219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.103032 restraints weight = 28406.700| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.09 r_work: 0.2795 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24802 Z= 0.147 Angle : 0.729 12.723 34493 Z= 0.292 Chirality : 0.040 0.185 3405 Planarity : 0.005 0.054 4200 Dihedral : 15.211 179.947 4317 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.88 % Allowed : 12.25 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.18), residues: 2244 helix: 3.38 (0.13), residues: 1417 sheet: None (None), residues: 0 loop : -1.92 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 4 TYR 0.020 0.001 TYR M 424 PHE 0.014 0.001 PHE M 387 TRP 0.012 0.001 TRP M 594 HIS 0.009 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (24744) covalent geometry : angle 0.72902 / 0.29 (34493) hydrogen bonds : bond 0.06510 / 4.36 ( 1198) hydrogen bonds : angle 3.44072 / 2.62 ( 3519) Misc. bond : bond 0.01103 / 0.73 ( 58) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 0.812 Fit side-chains REVERT: 7 16 THR cc_start: 0.8982 (m) cc_final: 0.8736 (m) REVERT: 7 17 LEU cc_start: 0.8502 (mm) cc_final: 0.8137 (tp) REVERT: A 4 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.5075 (ppt-90) REVERT: C 78 MET cc_start: 0.6317 (tmm) cc_final: 0.5525 (ttm) REVERT: C 82 ILE cc_start: 0.7466 (mt) cc_final: 0.7256 (mt) REVERT: C 247 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7765 (ptm160) REVERT: C 272 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: I 7 ASN cc_start: 0.6949 (p0) cc_final: 0.6696 (p0) REVERT: L 94 ASN cc_start: 0.7353 (m110) cc_final: 0.7024 (m-40) REVERT: L 145 ASP cc_start: 0.8034 (m-30) cc_final: 0.7734 (m-30) REVERT: M 341 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: M 367 GLU cc_start: 0.8500 (tp30) cc_final: 0.8170 (tm-30) REVERT: M 557 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8182 (mm-30) REVERT: V 16 THR cc_start: 0.8999 (m) cc_final: 0.8793 (m) outliers start: 37 outliers final: 21 residues processed: 253 average time/residue: 0.4960 time to fit residues: 146.8697 Evaluate side-chains 252 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 37 ASN Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 557 GLU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain W residue 12 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 63 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 172 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 37 ASN C 61 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN U 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.119217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.100262 restraints weight = 28444.483| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.06 r_work: 0.2740 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 24802 Z= 0.225 Angle : 0.872 13.842 34493 Z= 0.351 Chirality : 0.046 0.251 3405 Planarity : 0.006 0.057 4200 Dihedral : 15.617 179.871 4317 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.78 % Allowed : 12.76 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.18), residues: 2244 helix: 3.06 (0.13), residues: 1409 sheet: None (None), residues: 0 loop : -1.99 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 4 TYR 0.020 0.002 TYR C 205 PHE 0.019 0.002 PHE Z 40 TRP 0.017 0.002 TRP L 181 HIS 0.008 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.23 (24744) covalent geometry : angle 0.87226 / 0.35 (34493) hydrogen bonds : bond 0.08311 / 5.57 ( 1198) hydrogen bonds : angle 3.66309 / 2.79 ( 3519) Misc. bond : bond 0.01509 / 1.10 ( 58) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 0.807 Fit side-chains REVERT: 7 17 LEU cc_start: 0.8568 (mm) cc_final: 0.8226 (tp) REVERT: A 4 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.5149 (ppt-90) REVERT: C 78 MET cc_start: 0.6265 (tmm) cc_final: 0.5753 (ttm) REVERT: C 247 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.7948 (ptm160) REVERT: J 4 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6999 (ptt90) REVERT: L 94 ASN cc_start: 0.7724 (m110) cc_final: 0.7371 (m-40) REVERT: L 145 ASP cc_start: 0.8152 (m-30) cc_final: 0.7846 (m-30) REVERT: M 341 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: M 343 TYR cc_start: 0.8313 (m-80) cc_final: 0.8085 (m-80) REVERT: M 367 GLU cc_start: 0.8595 (tp30) cc_final: 0.8267 (tm-30) REVERT: M 557 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8169 (mm-30) REVERT: M 609 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7941 (mp) REVERT: V 16 THR cc_start: 0.9020 (m) cc_final: 0.8801 (m) outliers start: 35 outliers final: 20 residues processed: 255 average time/residue: 0.5518 time to fit residues: 163.7458 Evaluate side-chains 251 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 37 ASN Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 557 GLU Chi-restraints excluded: chain M residue 607 LEU Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain W residue 12 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 37 ASN C 61 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN L 183 HIS O 13 GLN U 13 GLN Z 44 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.126262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.108228 restraints weight = 28424.845| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.05 r_work: 0.2884 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24802 Z= 0.119 Angle : 0.662 12.569 34493 Z= 0.268 Chirality : 0.038 0.138 3405 Planarity : 0.004 0.049 4200 Dihedral : 15.005 179.988 4317 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.61 % Allowed : 13.93 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.18), residues: 2244 helix: 3.62 (0.13), residues: 1411 sheet: None (None), residues: 0 loop : -1.84 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 9 40 TYR 0.022 0.001 TYR M 424 PHE 0.014 0.001 PHE L 283 TRP 0.014 0.001 TRP M 594 HIS 0.006 0.000 HIS M 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (24744) covalent geometry : angle 0.66172 / 0.27 (34493) hydrogen bonds : bond 0.05233 / 3.51 ( 1198) hydrogen bonds : angle 3.31404 / 2.52 ( 3519) Misc. bond : bond 0.00977 / 0.59 ( 58) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 227 time to evaluate : 0.574 Fit side-chains REVERT: 7 17 LEU cc_start: 0.8432 (mm) cc_final: 0.8103 (tp) REVERT: 9 40 ARG cc_start: 0.7037 (tpp80) cc_final: 0.6661 (mtt-85) REVERT: C 78 MET cc_start: 0.6363 (tmm) cc_final: 0.5515 (ttm) REVERT: L 94 ASN cc_start: 0.7135 (m110) cc_final: 0.6809 (m-40) REVERT: L 145 ASP cc_start: 0.7880 (m-30) cc_final: 0.7562 (m-30) REVERT: M 341 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: M 367 GLU cc_start: 0.8413 (tp30) cc_final: 0.8095 (tm-30) REVERT: X 18 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6857 (mm) outliers start: 12 outliers final: 9 residues processed: 236 average time/residue: 0.5178 time to fit residues: 142.6073 Evaluate side-chains 230 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 219 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 37 ASN Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 6 residue 9 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain X residue 18 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 109 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 37 ASN 7 37 ASN C 61 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN O 13 GLN U 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.121757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.102790 restraints weight = 28354.037| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.07 r_work: 0.2779 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24802 Z= 0.174 Angle : 0.773 13.132 34493 Z= 0.313 Chirality : 0.042 0.210 3405 Planarity : 0.005 0.055 4200 Dihedral : 15.192 179.863 4317 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.07 % Allowed : 13.93 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.18), residues: 2244 helix: 3.34 (0.13), residues: 1417 sheet: None (None), residues: 0 loop : -1.93 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 9 40 TYR 0.018 0.002 TYR M 424 PHE 0.016 0.002 PHE L 185 TRP 0.018 0.002 TRP 1 38 HIS 0.008 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.17 (24744) covalent geometry : angle 0.77279 / 0.31 (34493) hydrogen bonds : bond 0.07047 / 4.72 ( 1198) hydrogen bonds : angle 3.48634 / 2.65 ( 3519) Misc. bond : bond 0.01311 / 0.91 ( 58) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6221.93 seconds wall clock time: 106 minutes 33.56 seconds (6393.56 seconds total)