Starting phenix.real_space_refine on Sat Jun 21 09:37:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5o_35988/06_2025/8j5o_35988.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5o_35988/06_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_35988/06_2025/8j5o_35988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5o_35988/06_2025/8j5o_35988.map" model { file = "/net/cci-nas-00/data/ceres_data/8j5o_35988/06_2025/8j5o_35988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5o_35988/06_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-5710/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: 14.38, 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: 8.74 Conformation dependent library (CDL) restraints added in 2.5 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: 6.03 Time building geometry restraints manager: 9.44 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: 1.510 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: 0.990 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 52.050 Find NCS groups from input model: 1.320 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: 0.010 Load rotamer database and sin/cos tables:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.560 ------------------------------------------------------------------------------- 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 : 2.245 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: 1.2575 time to fit residues: 439.9667 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 : 2.547 ------------------------------------------------------------------------------- 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** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.127615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.108446 restraints weight = 28510.252| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.16 r_work: 0.2898 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1014 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 : 0.728 11.228 34493 Z= 0.288 Chirality : 0.039 0.158 3405 Planarity : 0.005 0.059 4200 Dihedral : 17.193 179.958 4635 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.27 % Allowed : 6.56 % 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 : -1.56 (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 0.015 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 0.05865 ( 1198) hydrogen bonds : angle 3.48523 ( 3519) covalent geometry : bond 0.00314 (24744) covalent geometry : angle 0.72750 (34493) Misc. bond : bond 0.03032 ( 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 255 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 2.505 Fit side-chains REVERT: 5 22 MET cc_start: 0.9147 (mmp) cc_final: 0.8903 (mmp) REVERT: 7 16 THR cc_start: 0.8960 (m) cc_final: 0.8679 (m) REVERT: C 78 MET cc_start: 0.5742 (tmm) cc_final: 0.5500 (ttm) REVERT: C 236 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7416 (mtt) REVERT: C 272 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: L 48 LYS cc_start: 0.7766 (mppt) cc_final: 0.7517 (mtpt) REVERT: L 95 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7383 (mt-10) REVERT: M 341 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8004 (mm-30) REVERT: N 14 VAL cc_start: 0.8358 (t) cc_final: 0.8153 (t) REVERT: Z 42 ASP cc_start: 0.8496 (t70) cc_final: 0.8174 (t0) REVERT: Z 53 ASP cc_start: 0.7463 (t0) cc_final: 0.7237 (t0) outliers start: 25 outliers final: 10 residues processed: 242 average time/residue: 1.3418 time to fit residues: 379.1561 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 : 2.194 ------------------------------------------------------------------------------- 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: 1.9990 chunk 138 optimal weight: 0.0050 chunk 3 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 195 optimal weight: 7.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- 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 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 301 ASN G 13 GLN H 37 ASN I 22 GLN L 264 HIS O 13 GLN U 13 GLN U 22 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.124841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.105763 restraints weight = 28370.200| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.18 r_work: 0.2807 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 24802 Z= 0.150 Angle : 0.736 12.059 34493 Z= 0.290 Chirality : 0.040 0.173 3405 Planarity : 0.005 0.057 4200 Dihedral : 16.464 179.923 4635 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.37 % Allowed : 8.69 % 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: 2.66 (0.18), residues: 2244 helix: 3.53 (0.13), residues: 1418 sheet: None (None), residues: 0 loop : -1.65 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 305 HIS 0.011 0.001 HIS L 192 PHE 0.016 0.001 PHE L 185 TYR 0.013 0.001 TYR C 205 ARG 0.003 0.000 ARG D 4 Details of bonding type rmsd hydrogen bonds : bond 0.06521 ( 1198) hydrogen bonds : angle 3.45524 ( 3519) covalent geometry : bond 0.00360 (24744) covalent geometry : angle 0.73570 (34493) Misc. bond : bond 0.02036 ( 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 264 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 3.706 Fit side-chains REVERT: 5 22 MET cc_start: 0.9175 (mmp) cc_final: 0.8873 (mmp) REVERT: 7 16 THR cc_start: 0.8954 (m) cc_final: 0.8707 (m) REVERT: C 78 MET cc_start: 0.6166 (tmm) cc_final: 0.5805 (ttm) REVERT: C 247 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.7777 (ptm160) REVERT: C 272 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: L 48 LYS cc_start: 0.7799 (mppt) cc_final: 0.7461 (mtpt) REVERT: L 94 ASN cc_start: 0.7131 (m110) cc_final: 0.6822 (m-40) REVERT: M 367 GLU cc_start: 0.8303 (tp30) cc_final: 0.7914 (tm-30) REVERT: N 14 VAL cc_start: 0.8345 (t) cc_final: 0.8128 (t) REVERT: Z 53 ASP cc_start: 0.7509 (t0) cc_final: 0.7288 (t0) outliers start: 27 outliers final: 14 residues processed: 250 average time/residue: 1.3919 time to fit residues: 403.9476 Evaluate side-chains 243 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 227 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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 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 G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain V residue 32 SER 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: 7.9990 chunk 145 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 M 572 GLN M 637 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 = 0.3275 r_free = 0.3275 target = 0.120370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.101029 restraints weight = 28569.738| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.11 r_work: 0.2767 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 24802 Z= 0.192 Angle : 0.818 13.338 34493 Z= 0.326 Chirality : 0.043 0.200 3405 Planarity : 0.005 0.059 4200 Dihedral : 16.487 179.880 4633 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.83 % Allowed : 9.71 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.24 (0.18), residues: 2244 helix: 3.20 (0.13), residues: 1423 sheet: None (None), residues: 0 loop : -1.84 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 630 HIS 0.010 0.001 HIS L 192 PHE 0.024 0.002 PHE 9 36 TYR 0.018 0.002 TYR C 205 ARG 0.005 0.001 ARG 3 4 Details of bonding type rmsd hydrogen bonds : bond 0.07817 ( 1198) hydrogen bonds : angle 3.60454 ( 3519) covalent geometry : bond 0.00472 (24744) covalent geometry : angle 0.81814 (34493) Misc. bond : bond 0.01801 ( 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 273 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 5.316 Fit side-chains REVERT: 5 22 MET cc_start: 0.9214 (mmp) cc_final: 0.8954 (mmp) REVERT: 7 16 THR cc_start: 0.8975 (m) cc_final: 0.8736 (m) REVERT: 7 17 LEU cc_start: 0.8494 (mm) cc_final: 0.8169 (tp) REVERT: 8 7 ASN cc_start: 0.7355 (p0) cc_final: 0.7149 (p0) REVERT: C 78 MET cc_start: 0.6153 (tmm) cc_final: 0.5687 (ttm) REVERT: C 247 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7974 (ptm160) REVERT: C 272 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: L 94 ASN cc_start: 0.7607 (m110) cc_final: 0.7254 (m-40) REVERT: M 341 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8204 (mp0) REVERT: M 343 TYR cc_start: 0.8266 (m-80) cc_final: 0.8062 (m-80) REVERT: M 367 GLU cc_start: 0.8462 (tp30) cc_final: 0.8127 (tm-30) REVERT: N 14 VAL cc_start: 0.8423 (t) cc_final: 0.8207 (t) REVERT: O 20 ASN cc_start: 0.8987 (t0) cc_final: 0.8775 (t0) REVERT: V 16 THR cc_start: 0.9007 (m) cc_final: 0.8771 (m) REVERT: Z 42 ASP cc_start: 0.8516 (t70) cc_final: 0.8256 (t0) REVERT: Z 53 ASP cc_start: 0.7450 (t0) cc_final: 0.7220 (t0) outliers start: 36 outliers final: 18 residues processed: 257 average time/residue: 1.5786 time to fit residues: 467.9337 Evaluate side-chains 249 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 229 time to evaluate : 2.328 ------------------------------------------------------------------------------- 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 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 M residue 375 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 88 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 141 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.122023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.102739 restraints weight = 28397.034| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.10 r_work: 0.2787 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 24802 Z= 0.159 Angle : 0.747 12.592 34493 Z= 0.297 Chirality : 0.041 0.180 3405 Planarity : 0.005 0.054 4200 Dihedral : 16.039 179.928 4633 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.68 % Allowed : 10.52 % 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: 2.37 (0.18), residues: 2244 helix: 3.34 (0.13), residues: 1417 sheet: None (None), residues: 0 loop : -1.85 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 630 HIS 0.010 0.001 HIS L 192 PHE 0.016 0.001 PHE M 387 TYR 0.017 0.002 TYR C 205 ARG 0.004 0.000 ARG 3 4 Details of bonding type rmsd hydrogen bonds : bond 0.06852 ( 1198) hydrogen bonds : angle 3.48298 ( 3519) covalent geometry : bond 0.00382 (24744) covalent geometry : angle 0.74733 (34493) Misc. bond : bond 0.01348 ( 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 268 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 2.103 Fit side-chains REVERT: 5 22 MET cc_start: 0.9194 (mmp) cc_final: 0.8978 (mmp) REVERT: 7 16 THR cc_start: 0.9002 (m) cc_final: 0.8750 (m) REVERT: 7 17 LEU cc_start: 0.8493 (mm) cc_final: 0.8145 (tp) REVERT: A 4 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.4958 (ppt-90) REVERT: C 78 MET cc_start: 0.6239 (tmm) cc_final: 0.5743 (ttm) REVERT: C 247 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7755 (ptm160) REVERT: C 272 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: L 94 ASN cc_start: 0.7532 (m110) cc_final: 0.7180 (m-40) REVERT: M 341 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8194 (mp0) REVERT: M 343 TYR cc_start: 0.8283 (m-80) cc_final: 0.8065 (m-80) REVERT: M 367 GLU cc_start: 0.8483 (tp30) cc_final: 0.8145 (tm-30) REVERT: N 14 VAL cc_start: 0.8419 (t) cc_final: 0.8191 (t) REVERT: V 16 THR cc_start: 0.9008 (m) cc_final: 0.8776 (m) REVERT: Z 42 ASP cc_start: 0.8593 (t70) cc_final: 0.8208 (t0) REVERT: Z 53 ASP cc_start: 0.7479 (t0) cc_final: 0.7238 (t0) outliers start: 33 outliers final: 22 residues processed: 258 average time/residue: 1.3072 time to fit residues: 394.0867 Evaluate side-chains 255 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 2.173 ------------------------------------------------------------------------------- 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 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 I residue 38 ILE Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain 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: 8.9990 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 195 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- 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 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 O 13 GLN U 13 GLN Z 44 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.119862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.100433 restraints weight = 28339.253| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.10 r_work: 0.2769 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 24802 Z= 0.189 Angle : 0.804 13.402 34493 Z= 0.320 Chirality : 0.043 0.202 3405 Planarity : 0.005 0.056 4200 Dihedral : 16.089 179.871 4633 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.98 % Allowed : 10.83 % Favored : 87.19 % 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: 2.16 (0.18), residues: 2244 helix: 3.17 (0.13), residues: 1418 sheet: None (None), residues: 0 loop : -1.93 (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 0.017 0.002 PHE L 185 TYR 0.019 0.002 TYR C 205 ARG 0.004 0.001 ARG F 4 Details of bonding type rmsd hydrogen bonds : bond 0.07641 ( 1198) hydrogen bonds : angle 3.57174 ( 3519) covalent geometry : bond 0.00469 (24744) covalent geometry : angle 0.80429 (34493) Misc. bond : bond 0.01424 ( 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 271 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 2.932 Fit side-chains REVERT: 7 16 THR cc_start: 0.8971 (m) cc_final: 0.8714 (m) REVERT: 7 17 LEU cc_start: 0.8495 (mm) cc_final: 0.8167 (tp) REVERT: A 4 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.4948 (ppt-90) REVERT: C 78 MET cc_start: 0.6263 (tmm) cc_final: 0.5714 (ttm) REVERT: C 247 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7849 (ptm160) REVERT: C 272 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: I 7 ASN cc_start: 0.6808 (p0) cc_final: 0.6559 (p0) REVERT: L 94 ASN cc_start: 0.7600 (m110) cc_final: 0.7248 (m-40) REVERT: M 341 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8188 (mp0) REVERT: M 343 TYR cc_start: 0.8288 (m-80) cc_final: 0.8059 (m-80) REVERT: M 367 GLU cc_start: 0.8503 (tp30) cc_final: 0.8174 (tm-30) REVERT: N 14 VAL cc_start: 0.8424 (t) cc_final: 0.8204 (t) REVERT: V 16 THR cc_start: 0.9002 (m) cc_final: 0.8764 (m) REVERT: X 18 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6902 (mm) REVERT: Z 42 ASP cc_start: 0.8569 (t70) cc_final: 0.8156 (t0) REVERT: Z 53 ASP cc_start: 0.7524 (t0) cc_final: 0.7282 (t0) outliers start: 39 outliers final: 23 residues processed: 257 average time/residue: 1.8982 time to fit residues: 566.9441 Evaluate side-chains 253 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 4.468 ------------------------------------------------------------------------------- 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 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 U residue 31 LYS Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain X residue 18 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 104 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 225 ASN C 226 GLN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.119283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.100008 restraints weight = 28443.522| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.09 r_work: 0.2741 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 24802 Z= 0.204 Angle : 0.837 13.507 34493 Z= 0.334 Chirality : 0.044 0.223 3405 Planarity : 0.005 0.056 4200 Dihedral : 16.154 179.865 4633 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.93 % Allowed : 11.24 % Favored : 86.83 % 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: 2.08 (0.18), residues: 2244 helix: 3.14 (0.13), residues: 1407 sheet: None (None), residues: 0 loop : -1.96 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 181 HIS 0.008 0.001 HIS L 192 PHE 0.017 0.002 PHE 9 36 TYR 0.020 0.002 TYR C 205 ARG 0.004 0.001 ARG 3 4 Details of bonding type rmsd hydrogen bonds : bond 0.07998 ( 1198) hydrogen bonds : angle 3.64117 ( 3519) covalent geometry : bond 0.00508 (24744) covalent geometry : angle 0.83659 (34493) Misc. bond : bond 0.01312 ( 58) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 3.272 Fit side-chains REVERT: 7 17 LEU cc_start: 0.8530 (mm) cc_final: 0.8194 (tp) REVERT: C 78 MET cc_start: 0.6296 (tmm) cc_final: 0.5727 (ttm) REVERT: C 247 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.7971 (ptm160) REVERT: C 272 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: I 7 ASN cc_start: 0.6989 (p0) cc_final: 0.6753 (p0) REVERT: L 94 ASN cc_start: 0.7680 (m110) cc_final: 0.7312 (m-40) REVERT: M 367 GLU cc_start: 0.8554 (tp30) cc_final: 0.8219 (tm-30) REVERT: M 609 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7821 (mp) REVERT: N 14 VAL cc_start: 0.8441 (t) cc_final: 0.8221 (t) REVERT: V 16 THR cc_start: 0.9029 (m) cc_final: 0.8788 (m) REVERT: Z 53 ASP cc_start: 0.7543 (t0) cc_final: 0.7297 (t0) outliers start: 38 outliers final: 25 residues processed: 253 average time/residue: 1.3300 time to fit residues: 391.9428 Evaluate side-chains 250 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 2.447 ------------------------------------------------------------------------------- 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 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 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 65 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN O 13 GLN U 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.124487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.105437 restraints weight = 28377.612| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.09 r_work: 0.2829 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24802 Z= 0.125 Angle : 0.683 12.527 34493 Z= 0.273 Chirality : 0.039 0.155 3405 Planarity : 0.005 0.050 4200 Dihedral : 15.403 180.000 4633 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.68 % Allowed : 11.85 % Favored : 86.48 % 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: 2.54 (0.18), residues: 2244 helix: 3.54 (0.13), residues: 1411 sheet: None (None), residues: 0 loop : -1.87 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 594 HIS 0.007 0.001 HIS L 192 PHE 0.015 0.001 PHE M 387 TYR 0.020 0.001 TYR M 424 ARG 0.002 0.000 ARG M 399 Details of bonding type rmsd hydrogen bonds : bond 0.05758 ( 1198) hydrogen bonds : angle 3.36599 ( 3519) covalent geometry : bond 0.00281 (24744) covalent geometry : angle 0.68293 (34493) Misc. bond : bond 0.00947 ( 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 262 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 2.593 Fit side-chains REVERT: 7 17 LEU cc_start: 0.8484 (mm) cc_final: 0.8148 (tp) REVERT: A 4 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.5273 (ppt-90) REVERT: C 78 MET cc_start: 0.6381 (tmm) cc_final: 0.5543 (ttm) REVERT: C 247 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7654 (ptm160) REVERT: C 272 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: I 7 ASN cc_start: 0.6899 (p0) cc_final: 0.6689 (p0) REVERT: L 94 ASN cc_start: 0.7184 (m110) cc_final: 0.6845 (m-40) REVERT: M 341 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: M 367 GLU cc_start: 0.8449 (tp30) cc_final: 0.8119 (tm-30) REVERT: N 14 VAL cc_start: 0.8366 (t) cc_final: 0.8125 (t) REVERT: V 16 THR cc_start: 0.9028 (m) cc_final: 0.8805 (m) REVERT: X 18 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6855 (mm) REVERT: Z 53 ASP cc_start: 0.7547 (t0) cc_final: 0.7297 (t0) outliers start: 33 outliers final: 19 residues processed: 250 average time/residue: 1.4570 time to fit residues: 428.9285 Evaluate side-chains 246 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 37 ASN Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 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 P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain X residue 18 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: 5.9990 chunk 7 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 188 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 37 ASN 7 37 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN ** 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 = 0.3285 r_free = 0.3285 target = 0.121197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101820 restraints weight = 28373.369| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.11 r_work: 0.2782 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24802 Z= 0.165 Angle : 0.760 13.020 34493 Z= 0.306 Chirality : 0.041 0.194 3405 Planarity : 0.005 0.053 4200 Dihedral : 15.597 179.890 4633 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.68 % Allowed : 12.66 % Favored : 85.66 % 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: 2.34 (0.18), residues: 2244 helix: 3.34 (0.13), residues: 1417 sheet: None (None), residues: 0 loop : -1.91 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 630 HIS 0.008 0.001 HIS L 192 PHE 0.015 0.001 PHE L 185 TYR 0.017 0.002 TYR M 424 ARG 0.003 0.000 ARG F 4 Details of bonding type rmsd hydrogen bonds : bond 0.06886 ( 1198) hydrogen bonds : angle 3.49001 ( 3519) covalent geometry : bond 0.00400 (24744) covalent geometry : angle 0.75982 (34493) Misc. bond : bond 0.01199 ( 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 260 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 2.231 Fit side-chains REVERT: 7 17 LEU cc_start: 0.8505 (mm) cc_final: 0.8189 (tp) REVERT: A 4 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.5032 (ppt-90) REVERT: C 78 MET cc_start: 0.6185 (tmm) cc_final: 0.5517 (ttm) REVERT: C 247 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7828 (ptm160) REVERT: C 272 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: I 7 ASN cc_start: 0.6975 (p0) cc_final: 0.6715 (p0) REVERT: L 94 ASN cc_start: 0.7413 (m110) cc_final: 0.7073 (m-40) REVERT: M 341 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: M 367 GLU cc_start: 0.8575 (tp30) cc_final: 0.8231 (tm-30) REVERT: N 14 VAL cc_start: 0.8394 (t) cc_final: 0.8157 (t) REVERT: S 37 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7790 (mp) REVERT: V 16 THR cc_start: 0.9004 (m) cc_final: 0.8773 (m) REVERT: X 18 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6905 (mm) REVERT: Z 53 ASP cc_start: 0.7542 (t0) cc_final: 0.7310 (t0) outliers start: 33 outliers final: 25 residues processed: 250 average time/residue: 1.2814 time to fit residues: 372.1302 Evaluate side-chains 254 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 2.305 ------------------------------------------------------------------------------- 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 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 C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain I residue 38 ILE 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 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 37 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 26 optimal weight: 10.0000 chunk 80 optimal weight: 0.1980 chunk 185 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 177 optimal weight: 0.2980 chunk 102 optimal weight: 0.0770 chunk 32 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.2740 ------------------------------------------------------------------------------- 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 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN O 13 GLN U 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.125544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.106715 restraints weight = 28287.302| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.15 r_work: 0.2830 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24802 Z= 0.121 Angle : 0.675 12.655 34493 Z= 0.273 Chirality : 0.038 0.150 3405 Planarity : 0.005 0.050 4200 Dihedral : 15.225 179.969 4633 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.37 % Allowed : 13.07 % Favored : 85.56 % 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: 2.65 (0.18), residues: 2244 helix: 3.61 (0.13), residues: 1412 sheet: None (None), residues: 0 loop : -1.81 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 594 HIS 0.007 0.000 HIS L 192 PHE 0.016 0.001 PHE 1 36 TYR 0.021 0.001 TYR M 424 ARG 0.002 0.000 ARG 1 40 Details of bonding type rmsd hydrogen bonds : bond 0.05612 ( 1198) hydrogen bonds : angle 3.35343 ( 3519) covalent geometry : bond 0.00272 (24744) covalent geometry : angle 0.67452 (34493) Misc. bond : bond 0.01037 ( 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 253 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 2.377 Fit side-chains REVERT: 7 17 LEU cc_start: 0.8471 (mm) cc_final: 0.8152 (tp) REVERT: A 4 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.5376 (ppt-90) REVERT: C 78 MET cc_start: 0.6388 (tmm) cc_final: 0.5631 (ttm) REVERT: C 247 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7639 (ptm160) REVERT: C 272 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: I 7 ASN cc_start: 0.6912 (p0) cc_final: 0.6674 (p0) REVERT: L 37 SER cc_start: 0.7914 (OUTLIER) cc_final: 0.7688 (p) REVERT: L 94 ASN cc_start: 0.7181 (m110) cc_final: 0.6878 (m-40) REVERT: M 367 GLU cc_start: 0.8518 (tp30) cc_final: 0.8179 (tm-30) REVERT: N 14 VAL cc_start: 0.8344 (t) cc_final: 0.8105 (t) REVERT: S 37 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7776 (mp) REVERT: V 16 THR cc_start: 0.9043 (m) cc_final: 0.8823 (m) REVERT: X 18 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6856 (mm) REVERT: Z 53 ASP cc_start: 0.7545 (t0) cc_final: 0.7313 (t0) outliers start: 27 outliers final: 16 residues processed: 246 average time/residue: 1.2648 time to fit residues: 362.8190 Evaluate side-chains 245 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 2.289 ------------------------------------------------------------------------------- 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 170 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain 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 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 37 LEU Chi-restraints excluded: chain X residue 18 LEU Chi-restraints excluded: chain Z residue 35 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 31 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 21 optimal weight: 0.0020 chunk 135 optimal weight: 9.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 37 ASN 7 37 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN ** 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 = 0.3280 r_free = 0.3280 target = 0.120774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101579 restraints weight = 28197.209| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.09 r_work: 0.2761 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 24802 Z= 0.186 Angle : 0.800 13.551 34493 Z= 0.323 Chirality : 0.043 0.213 3405 Planarity : 0.005 0.056 4200 Dihedral : 15.672 179.892 4633 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.83 % Allowed : 12.71 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.25 (0.18), residues: 2244 helix: 3.26 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.92 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 7 38 HIS 0.009 0.001 HIS L 192 PHE 0.017 0.002 PHE L 185 TYR 0.016 0.002 TYR M 424 ARG 0.004 0.000 ARG F 4 Details of bonding type rmsd hydrogen bonds : bond 0.07410 ( 1198) hydrogen bonds : angle 3.54559 ( 3519) covalent geometry : bond 0.00459 (24744) covalent geometry : angle 0.79958 (34493) Misc. bond : bond 0.01317 ( 58) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15739.20 seconds wall clock time: 275 minutes 22.67 seconds (16522.67 seconds total)