Starting phenix.real_space_refine on Fri May 23 22:15:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5o_35988/05_2025/8j5o_35988.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5o_35988/05_2025/8j5o_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j5o_35988/05_2025/8j5o_35988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5o_35988/05_2025/8j5o_35988.map" model { file = "/net/cci-nas-00/data/ceres_data/8j5o_35988/05_2025/8j5o_35988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5o_35988/05_2025/8j5o_35988.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 38 Planarities with less than four sites: {'MQE:plan-12': 1, 'MQE:plan-11': 1, 'MQE:plan-10': 1, 'MQE:plan-9': 1, 'MQE:plan-6': 1, 'MQE:plan-5': 1, 'MQE:plan-4': 1, 'MQE:plan-3': 1, 'MQE:plan-2': 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: 14.46, per 1000 atoms: 0.61 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: 7.65 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.71 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: 5.79 Time building geometry restraints manager: 8.60 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: 12546 36.00 - 71.99: 364 71.99 - 107.99: 55 107.99 - 143.99: 11 143.99 - 179.98: 2 Dihedral angle restraints: 12978 sinusoidal: 6291 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 12975 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 55 or resid 101)) selection = (chain '2' and (resid 7 through 55 or resid 101)) selection = (chain '4' and (resid 7 through 55 or resid 101)) selection = (chain '6' and (resid 7 through 55 or resid 101)) selection = (chain '8' and (resid 7 through 55 or resid 101)) selection = (chain 'B' and (resid 7 through 55 or resid 101)) selection = (chain 'E' and (resid 7 through 55 or resid 101)) selection = (chain 'G' and (resid 7 through 55 or resid 101)) selection = (chain 'I' and (resid 7 through 55 or resid 101)) selection = (chain 'K' and (resid 7 through 55 or resid 101)) selection = (chain 'O' and (resid 7 through 55 or resid 101)) selection = (chain 'Q' and (resid 7 through 55 or resid 101)) selection = (chain 'S' and (resid 7 through 55 or resid 101)) selection = (chain 'U' and (resid 7 through 55 or resid 101)) selection = (chain 'W' and (resid 7 through 55 or resid 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: 1.120 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: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 49.260 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 17.270 179.983 8632 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 18.76 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (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 TRP 0.058 0.002 TRP L 305 HIS 0.022 0.001 HIS L 192 PHE 0.040 0.002 PHE L 185 TYR 0.030 0.002 TYR L 204 ARG 0.007 0.000 ARG L 251 Details of bonding type rmsd hydrogen bonds : bond 0.12015 ( 1198) hydrogen bonds : angle 4.07481 ( 3519) covalent geometry : bond 0.00742 (24744) covalent geometry : angle 0.98010 (34493) Misc. bond : bond 0.13283 ( 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 : 2.234 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: 1.2372 time to fit residues: 431.6790 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 : 2.049 ------------------------------------------------------------------------------- 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 172 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN L 183 HIS L 209 ASN L 252 ASN M 637 GLN O 13 GLN Q 13 GLN U 13 GLN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.127620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.108443 restraints weight = 28509.312| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.16 r_work: 0.2894 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.170 24802 Z= 0.136 Angle : 0.727 11.220 34493 Z= 0.288 Chirality : 0.039 0.157 3405 Planarity : 0.005 0.059 4200 Dihedral : 17.192 179.964 4635 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.32 % Allowed : 6.51 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.18), residues: 2244 helix: 3.67 (0.13), residues: 1418 sheet: None (None), residues: 0 loop : -1.57 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 305 HIS 0.011 0.001 HIS L 192 PHE 0.016 0.001 PHE L 185 TYR 0.012 0.001 TYR C 205 ARG 0.003 0.000 ARG M 344 Details of bonding type rmsd hydrogen bonds : bond 0.05864 ( 1198) hydrogen bonds : angle 3.48492 ( 3519) covalent geometry : bond 0.00313 (24744) covalent geometry : angle 0.72716 (34493) Misc. bond : bond 0.03024 ( 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 256 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 2.400 Fit side-chains REVERT: 5 22 MET cc_start: 0.9153 (mmp) cc_final: 0.8914 (mmp) REVERT: 7 16 THR cc_start: 0.8967 (m) cc_final: 0.8685 (m) REVERT: C 78 MET cc_start: 0.5719 (tmm) cc_final: 0.5478 (ttm) REVERT: C 236 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7437 (mtt) REVERT: C 272 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: L 48 LYS cc_start: 0.7765 (mppt) cc_final: 0.7519 (mtpt) REVERT: L 95 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7384 (mt-10) REVERT: M 341 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8009 (mm-30) REVERT: N 14 VAL cc_start: 0.8365 (t) cc_final: 0.8159 (t) REVERT: Z 42 ASP cc_start: 0.8504 (t70) cc_final: 0.8185 (t0) REVERT: Z 53 ASP cc_start: 0.7463 (t0) cc_final: 0.7236 (t0) outliers start: 26 outliers final: 10 residues processed: 242 average time/residue: 1.2057 time to fit residues: 340.4394 Evaluate side-chains 229 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 217 time to evaluate : 3.690 ------------------------------------------------------------------------------- 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 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 I residue 38 ILE Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain M residue 607 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 167 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN G 13 GLN H 37 ASN I 22 GLN O 13 GLN U 13 GLN U 22 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.127406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.108664 restraints weight = 28344.675| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.20 r_work: 0.2872 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 24802 Z= 0.127 Angle : 0.688 11.654 34493 Z= 0.269 Chirality : 0.039 0.153 3405 Planarity : 0.004 0.055 4200 Dihedral : 16.109 179.973 4635 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.22 % Allowed : 8.85 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.18), residues: 2244 helix: 3.73 (0.13), residues: 1412 sheet: None (None), residues: 0 loop : -1.62 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 305 HIS 0.010 0.001 HIS L 192 PHE 0.015 0.001 PHE L 185 TYR 0.011 0.001 TYR C 156 ARG 0.003 0.000 ARG D 4 Details of bonding type rmsd hydrogen bonds : bond 0.05680 ( 1198) hydrogen bonds : angle 3.33984 ( 3519) covalent geometry : bond 0.00291 (24744) covalent geometry : angle 0.68784 (34493) Misc. bond : bond 0.01637 ( 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 259 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 2.119 Fit side-chains REVERT: 5 22 MET cc_start: 0.9182 (mmp) cc_final: 0.8881 (mmp) REVERT: 7 16 THR cc_start: 0.8983 (m) cc_final: 0.8723 (m) REVERT: C 78 MET cc_start: 0.5957 (tmm) cc_final: 0.5568 (ttm) REVERT: C 236 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7471 (mtt) REVERT: C 247 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7647 (ptm160) REVERT: C 272 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: L 48 LYS cc_start: 0.7718 (mppt) cc_final: 0.7434 (mtpt) REVERT: M 367 GLU cc_start: 0.8397 (tp30) cc_final: 0.7883 (tt0) REVERT: N 14 VAL cc_start: 0.8366 (t) cc_final: 0.8138 (t) REVERT: X 20 PHE cc_start: 0.7158 (m-80) cc_final: 0.6927 (m-80) REVERT: Z 53 ASP cc_start: 0.7510 (t0) cc_final: 0.7291 (t0) outliers start: 24 outliers final: 10 residues processed: 248 average time/residue: 1.3083 time to fit residues: 377.9785 Evaluate side-chains 234 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 221 time to evaluate : 2.161 ------------------------------------------------------------------------------- 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 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 I residue 38 ILE Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 241 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 88 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 69 optimal weight: 0.4980 chunk 193 optimal weight: 9.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 37 ASN 6 20 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** G 13 GLN H 37 ASN I 22 GLN L 264 HIS M 572 GLN 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 = 0.3298 r_free = 0.3298 target = 0.122121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.102764 restraints weight = 28571.793| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.10 r_work: 0.2796 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 24802 Z= 0.170 Angle : 0.766 12.716 34493 Z= 0.304 Chirality : 0.042 0.189 3405 Planarity : 0.005 0.058 4200 Dihedral : 16.117 179.926 4633 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.73 % Allowed : 9.91 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.18), residues: 2244 helix: 3.39 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.73 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 305 HIS 0.011 0.001 HIS L 192 PHE 0.019 0.002 PHE 9 36 TYR 0.014 0.002 TYR C 205 ARG 0.004 0.000 ARG D 4 Details of bonding type rmsd hydrogen bonds : bond 0.07067 ( 1198) hydrogen bonds : angle 3.48690 ( 3519) covalent geometry : bond 0.00415 (24744) covalent geometry : angle 0.76613 (34493) Misc. bond : bond 0.01682 ( 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 267 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 2.485 Fit side-chains REVERT: 5 22 MET cc_start: 0.9214 (mmp) cc_final: 0.8968 (mmp) REVERT: 7 16 THR cc_start: 0.8992 (m) cc_final: 0.8742 (m) REVERT: 7 17 LEU cc_start: 0.8495 (mm) cc_final: 0.8169 (tp) REVERT: C 78 MET cc_start: 0.6010 (tmm) cc_final: 0.5658 (ttm) REVERT: C 247 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7797 (ptm160) REVERT: C 272 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: L 48 LYS cc_start: 0.7816 (mppt) cc_final: 0.7510 (mtpt) REVERT: L 94 ASN cc_start: 0.7390 (m110) cc_final: 0.7048 (m-40) REVERT: L 106 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: L 304 ILE cc_start: 0.8578 (mp) cc_final: 0.8340 (pt) REVERT: M 367 GLU cc_start: 0.8501 (tp30) cc_final: 0.8150 (tm-30) REVERT: N 14 VAL cc_start: 0.8410 (t) cc_final: 0.8179 (t) REVERT: Z 53 ASP cc_start: 0.7452 (t0) cc_final: 0.7226 (t0) outliers start: 34 outliers final: 20 residues processed: 251 average time/residue: 1.2253 time to fit residues: 357.7907 Evaluate side-chains 249 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 2.359 ------------------------------------------------------------------------------- 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 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 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 240 ASN Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain M residue 375 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 88 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 37 ASN 6 20 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS ** 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** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.121558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.102307 restraints weight = 28456.790| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.09 r_work: 0.2782 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 24802 Z= 0.171 Angle : 0.765 13.056 34493 Z= 0.305 Chirality : 0.042 0.191 3405 Planarity : 0.005 0.055 4200 Dihedral : 15.882 179.910 4633 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.83 % Allowed : 10.37 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.18), residues: 2244 helix: 3.31 (0.13), residues: 1417 sheet: None (None), residues: 0 loop : -1.83 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 630 HIS 0.010 0.001 HIS L 192 PHE 0.018 0.001 PHE 9 36 TYR 0.017 0.002 TYR C 205 ARG 0.004 0.000 ARG 3 4 Details of bonding type rmsd hydrogen bonds : bond 0.07152 ( 1198) hydrogen bonds : angle 3.50753 ( 3519) covalent geometry : bond 0.00416 (24744) covalent geometry : angle 0.76504 (34493) Misc. bond : bond 0.01411 ( 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 273 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 2.328 Fit side-chains REVERT: 5 22 MET cc_start: 0.9208 (mmp) cc_final: 0.8982 (mmp) REVERT: 7 16 THR cc_start: 0.9003 (m) cc_final: 0.8769 (m) REVERT: 7 17 LEU cc_start: 0.8490 (mm) cc_final: 0.8174 (tp) REVERT: A 4 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.5033 (ppt-90) REVERT: C 78 MET cc_start: 0.6235 (tmm) cc_final: 0.5792 (ttm) REVERT: C 247 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7802 (ptm160) REVERT: C 253 GLU cc_start: 0.7755 (pt0) cc_final: 0.7508 (pt0) REVERT: C 272 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: L 94 ASN cc_start: 0.7592 (m110) cc_final: 0.7251 (m-40) REVERT: L 106 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8136 (mm-30) REVERT: L 145 ASP cc_start: 0.8054 (m-30) cc_final: 0.7828 (m-30) REVERT: L 304 ILE cc_start: 0.8590 (mp) cc_final: 0.8384 (pt) REVERT: M 341 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: M 367 GLU cc_start: 0.8479 (tp30) cc_final: 0.8152 (tm-30) REVERT: N 14 VAL cc_start: 0.8431 (t) cc_final: 0.8199 (t) REVERT: O 20 ASN cc_start: 0.9008 (t0) cc_final: 0.8783 (t0) REVERT: V 16 THR cc_start: 0.9015 (m) cc_final: 0.8781 (m) REVERT: Z 42 ASP cc_start: 0.8588 (t70) cc_final: 0.8198 (t0) REVERT: Z 53 ASP cc_start: 0.7508 (t0) cc_final: 0.7269 (t0) outliers start: 36 outliers final: 18 residues processed: 258 average time/residue: 1.2063 time to fit residues: 364.8008 Evaluate side-chains 255 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 232 time to evaluate : 2.077 ------------------------------------------------------------------------------- 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 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 M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 195 optimal weight: 20.0000 chunk 128 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 37 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 191 ASN C 220 HIS ** 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** G 13 GLN H 37 ASN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 205 ASN M 637 GLN O 13 GLN U 13 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.119815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.100566 restraints weight = 28361.166| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.19 r_work: 0.2731 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 24802 Z= 0.198 Angle : 0.821 13.654 34493 Z= 0.327 Chirality : 0.044 0.208 3405 Planarity : 0.005 0.057 4200 Dihedral : 16.115 179.841 4633 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.19 % Allowed : 10.47 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.18), residues: 2244 helix: 3.14 (0.13), residues: 1418 sheet: None (None), residues: 0 loop : -1.94 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 630 HIS 0.008 0.001 HIS L 192 PHE 0.018 0.002 PHE 9 36 TYR 0.019 0.002 TYR C 205 ARG 0.006 0.001 ARG F 4 Details of bonding type rmsd hydrogen bonds : bond 0.07839 ( 1198) hydrogen bonds : angle 3.59735 ( 3519) covalent geometry : bond 0.00494 (24744) covalent geometry : angle 0.82076 (34493) Misc. bond : bond 0.01621 ( 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 278 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 2.177 Fit side-chains REVERT: 5 22 MET cc_start: 0.9147 (mmp) cc_final: 0.8909 (mmp) REVERT: 7 16 THR cc_start: 0.8944 (m) cc_final: 0.8688 (m) REVERT: 7 17 LEU cc_start: 0.8444 (mm) cc_final: 0.8109 (tp) REVERT: A 4 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.4873 (ppt-90) REVERT: C 78 MET cc_start: 0.6240 (tmm) cc_final: 0.5772 (ttm) REVERT: C 247 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7983 (ptm160) REVERT: C 272 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: I 7 ASN cc_start: 0.6763 (p0) cc_final: 0.6522 (p0) REVERT: L 94 ASN cc_start: 0.7522 (m110) cc_final: 0.7212 (m-40) REVERT: L 106 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7925 (mm-30) REVERT: L 145 ASP cc_start: 0.7885 (m-30) cc_final: 0.7568 (m-30) REVERT: M 341 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: M 367 GLU cc_start: 0.8370 (tp30) cc_final: 0.8074 (tm-30) REVERT: N 14 VAL cc_start: 0.8392 (t) cc_final: 0.8175 (t) REVERT: O 20 ASN cc_start: 0.8992 (t0) cc_final: 0.8728 (t0) REVERT: V 16 THR cc_start: 0.8957 (m) cc_final: 0.8731 (m) REVERT: Z 42 ASP cc_start: 0.8403 (t70) cc_final: 0.7971 (t0) REVERT: Z 53 ASP cc_start: 0.7516 (t0) cc_final: 0.7268 (t0) outliers start: 43 outliers final: 23 residues processed: 261 average time/residue: 1.1767 time to fit residues: 358.3199 Evaluate side-chains 256 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 2.046 ------------------------------------------------------------------------------- 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 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 69 VAL Chi-restraints excluded: chain L residue 106 GLU 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 P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain S residue 20 ASN Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain Z residue 35 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 104 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 20 ASN 1 37 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** E 22 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.121288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.102148 restraints weight = 28397.453| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.08 r_work: 0.2772 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 24802 Z= 0.170 Angle : 0.770 13.053 34493 Z= 0.308 Chirality : 0.042 0.200 3405 Planarity : 0.005 0.054 4200 Dihedral : 15.830 179.923 4633 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.08 % Allowed : 11.03 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.18), residues: 2244 helix: 3.23 (0.13), residues: 1417 sheet: None (None), residues: 0 loop : -1.94 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 360 HIS 0.008 0.001 HIS L 192 PHE 0.015 0.001 PHE L 185 TYR 0.017 0.002 TYR C 205 ARG 0.004 0.000 ARG 3 4 Details of bonding type rmsd hydrogen bonds : bond 0.07173 ( 1198) hydrogen bonds : angle 3.52168 ( 3519) covalent geometry : bond 0.00416 (24744) covalent geometry : angle 0.76954 (34493) Misc. bond : bond 0.01390 ( 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 271 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 2.087 Fit side-chains REVERT: 7 16 THR cc_start: 0.8991 (m) cc_final: 0.8754 (m) REVERT: 7 17 LEU cc_start: 0.8499 (mm) cc_final: 0.8168 (tp) REVERT: A 4 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.5065 (ppt-90) REVERT: C 78 MET cc_start: 0.6332 (tmm) cc_final: 0.5688 (ttm) REVERT: C 247 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.7809 (ptm160) REVERT: C 272 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: I 7 ASN cc_start: 0.6909 (p0) cc_final: 0.6648 (p0) REVERT: L 94 ASN cc_start: 0.7591 (m110) cc_final: 0.7247 (m-40) REVERT: L 145 ASP cc_start: 0.8077 (m-30) cc_final: 0.7822 (m-30) REVERT: M 341 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: M 367 GLU cc_start: 0.8545 (tp30) cc_final: 0.8227 (tm-30) REVERT: N 14 VAL cc_start: 0.8418 (t) cc_final: 0.8189 (t) REVERT: O 20 ASN cc_start: 0.9013 (t0) cc_final: 0.8758 (t0) REVERT: V 16 THR cc_start: 0.9006 (m) cc_final: 0.8765 (m) REVERT: X 18 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6873 (mm) outliers start: 41 outliers final: 26 residues processed: 256 average time/residue: 1.1590 time to fit residues: 346.7991 Evaluate side-chains 255 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 37 ASN 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 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 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 348 GLU Chi-restraints excluded: chain M residue 375 VAL 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 S residue 20 ASN Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain X residue 18 LEU Chi-restraints excluded: chain Z residue 35 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 65 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** E 22 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.123967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.104604 restraints weight = 28287.727| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.14 r_work: 0.2840 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24802 Z= 0.126 Angle : 0.680 12.606 34493 Z= 0.273 Chirality : 0.039 0.155 3405 Planarity : 0.005 0.050 4200 Dihedral : 15.312 179.970 4633 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.58 % Allowed : 11.39 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.18), residues: 2244 helix: 3.58 (0.13), residues: 1411 sheet: None (None), residues: 0 loop : -1.83 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 594 HIS 0.007 0.001 HIS L 192 PHE 0.021 0.001 PHE 1 36 TYR 0.019 0.001 TYR M 424 ARG 0.002 0.000 ARG M 399 Details of bonding type rmsd hydrogen bonds : bond 0.05747 ( 1198) hydrogen bonds : angle 3.34938 ( 3519) covalent geometry : bond 0.00284 (24744) covalent geometry : angle 0.68021 (34493) Misc. bond : bond 0.01127 ( 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 261 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 2.236 Fit side-chains REVERT: 7 16 THR cc_start: 0.8985 (m) cc_final: 0.8717 (m) REVERT: 7 17 LEU cc_start: 0.8466 (mm) cc_final: 0.8105 (tp) REVERT: A 4 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.5266 (ppt-90) REVERT: C 78 MET cc_start: 0.6372 (tmm) cc_final: 0.5504 (ttm) REVERT: C 236 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7509 (mtt) REVERT: C 247 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.7651 (ptm160) REVERT: C 272 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: I 7 ASN cc_start: 0.6888 (p0) cc_final: 0.6628 (p0) REVERT: L 94 ASN cc_start: 0.7210 (m110) cc_final: 0.6888 (m-40) REVERT: L 145 ASP cc_start: 0.8042 (m-30) cc_final: 0.7732 (m-30) REVERT: M 341 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: M 367 GLU cc_start: 0.8465 (tp30) cc_final: 0.8142 (tm-30) REVERT: N 14 VAL cc_start: 0.8342 (t) cc_final: 0.8100 (t) REVERT: V 16 THR cc_start: 0.9017 (m) cc_final: 0.8801 (m) outliers start: 31 outliers final: 17 residues processed: 249 average time/residue: 1.1728 time to fit residues: 344.8081 Evaluate side-chains 246 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 2.136 ------------------------------------------------------------------------------- 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 H residue 32 SER Chi-restraints excluded: chain H residue 37 ASN 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 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain Z residue 35 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 158 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 54 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 37 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** E 22 GLN ** 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 Z 44 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.118831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.099044 restraints weight = 28296.068| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.03 r_work: 0.2837 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 24802 Z= 0.193 Angle : 0.812 13.652 34493 Z= 0.327 Chirality : 0.043 0.217 3405 Planarity : 0.005 0.056 4200 Dihedral : 15.795 179.908 4633 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.68 % Allowed : 12.15 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.18), residues: 2244 helix: 3.22 (0.13), residues: 1417 sheet: None (None), residues: 0 loop : -1.95 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 360 HIS 0.008 0.001 HIS L 192 PHE 0.017 0.002 PHE L 185 TYR 0.017 0.002 TYR C 205 ARG 0.005 0.000 ARG F 4 Details of bonding type rmsd hydrogen bonds : bond 0.07610 ( 1198) hydrogen bonds : angle 3.56304 ( 3519) covalent geometry : bond 0.00479 (24744) covalent geometry : angle 0.81200 (34493) Misc. bond : bond 0.01479 ( 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 261 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 2.389 Fit side-chains REVERT: 7 16 THR cc_start: 0.8969 (m) cc_final: 0.8715 (m) REVERT: 7 17 LEU cc_start: 0.8492 (mm) cc_final: 0.8141 (tp) REVERT: A 4 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.5025 (ppt-90) REVERT: C 78 MET cc_start: 0.6279 (tmm) cc_final: 0.5638 (ttm) REVERT: C 247 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.7878 (ptm160) REVERT: I 7 ASN cc_start: 0.6911 (p0) cc_final: 0.6690 (p0) REVERT: L 94 ASN cc_start: 0.7498 (m110) cc_final: 0.7193 (m-40) REVERT: L 145 ASP cc_start: 0.7947 (m-30) cc_final: 0.7656 (m-30) REVERT: M 341 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: M 367 GLU cc_start: 0.8464 (tp30) cc_final: 0.8153 (tm-30) REVERT: N 14 VAL cc_start: 0.8400 (t) cc_final: 0.8180 (t) REVERT: O 20 ASN cc_start: 0.9034 (t0) cc_final: 0.8780 (t0) REVERT: V 16 THR cc_start: 0.9002 (m) cc_final: 0.8786 (m) outliers start: 33 outliers final: 23 residues processed: 252 average time/residue: 1.2315 time to fit residues: 361.2950 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 : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 7 residue 37 ASN Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 63 THR 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 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 37 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain L residue 314 VAL 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 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 26 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 177 optimal weight: 0.0980 chunk 102 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 37 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** E 22 GLN ** 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 = 0.3271 r_free = 0.3271 target = 0.120517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.100974 restraints weight = 28225.048| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.01 r_work: 0.2842 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24802 Z= 0.156 Angle : 0.748 13.083 34493 Z= 0.301 Chirality : 0.041 0.194 3405 Planarity : 0.005 0.053 4200 Dihedral : 15.613 179.929 4633 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.58 % Allowed : 12.40 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.18), residues: 2244 helix: 3.32 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.91 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 594 HIS 0.010 0.001 HIS L 192 PHE 0.015 0.001 PHE M 387 TYR 0.018 0.002 TYR M 424 ARG 0.003 0.000 ARG F 4 Details of bonding type rmsd hydrogen bonds : bond 0.06885 ( 1198) hydrogen bonds : angle 3.48683 ( 3519) covalent geometry : bond 0.00373 (24744) covalent geometry : angle 0.74814 (34493) Misc. bond : bond 0.01350 ( 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 257 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 2.159 Fit side-chains REVERT: 7 16 THR cc_start: 0.8992 (m) cc_final: 0.8741 (m) REVERT: 7 17 LEU cc_start: 0.8462 (mm) cc_final: 0.8128 (tp) REVERT: A 4 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.5132 (ppt-90) REVERT: C 78 MET cc_start: 0.6319 (tmm) cc_final: 0.5681 (ttm) REVERT: C 247 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7809 (ptm160) REVERT: I 7 ASN cc_start: 0.6954 (p0) cc_final: 0.6742 (p0) REVERT: L 94 ASN cc_start: 0.7408 (m110) cc_final: 0.7089 (m-40) REVERT: L 145 ASP cc_start: 0.7958 (m-30) cc_final: 0.7662 (m-30) REVERT: M 341 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: M 367 GLU cc_start: 0.8473 (tp30) cc_final: 0.8159 (tm-30) REVERT: N 14 VAL cc_start: 0.8391 (t) cc_final: 0.8155 (t) REVERT: O 20 ASN cc_start: 0.9037 (t0) cc_final: 0.8832 (t0) REVERT: V 16 THR cc_start: 0.9024 (m) cc_final: 0.8808 (m) outliers start: 31 outliers final: 24 residues processed: 246 average time/residue: 1.1882 time to fit residues: 341.2046 Evaluate side-chains 252 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 7 residue 37 ASN 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 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 69 VAL Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain L residue 314 VAL Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 564 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 S residue 20 ASN 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 31 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 37 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.118293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.099220 restraints weight = 28130.788| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 0.98 r_work: 0.2832 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 24802 Z= 0.204 Angle : 0.831 13.759 34493 Z= 0.335 Chirality : 0.044 0.229 3405 Planarity : 0.005 0.057 4200 Dihedral : 15.907 179.944 4633 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.68 % Allowed : 12.51 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.18), residues: 2244 helix: 3.09 (0.13), residues: 1417 sheet: None (None), residues: 0 loop : -1.98 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 181 HIS 0.008 0.001 HIS L 192 PHE 0.017 0.002 PHE L 185 TYR 0.018 0.002 TYR C 205 ARG 0.005 0.001 ARG F 4 Details of bonding type rmsd hydrogen bonds : bond 0.07844 ( 1198) hydrogen bonds : angle 3.59710 ( 3519) covalent geometry : bond 0.00511 (24744) covalent geometry : angle 0.83076 (34493) Misc. bond : bond 0.01453 ( 58) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14154.14 seconds wall clock time: 244 minutes 19.48 seconds (14659.48 seconds total)