Starting phenix.real_space_refine on Tue Jun 17 05:08:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qeq_13937/06_2025/7qeq_13937.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qeq_13937/06_2025/7qeq_13937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qeq_13937/06_2025/7qeq_13937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qeq_13937/06_2025/7qeq_13937.map" model { file = "/net/cci-nas-00/data/ceres_data/7qeq_13937/06_2025/7qeq_13937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qeq_13937/06_2025/7qeq_13937.cif" } resolution = 1.9 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= 0.001 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: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 12792 2.51 5 N 2976 2.21 5 O 3377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19313 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "B" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "D" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "E" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "F" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "G" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "H" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "I" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "J" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "K" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "L" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Time building chain proxies: 14.43, per 1000 atoms: 0.75 Number of scatterers: 19313 At special positions: 0 Unit cell: (99.45, 109.65, 157.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 3377 8.00 N 2976 7.00 C 12792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 180 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.04 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 180 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 180 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 169 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 180 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 180 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 180 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 169 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 180 " distance=2.04 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 174 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 169 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 180 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 174 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 169 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 180 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 174 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 169 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 2.2 seconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 76.2% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 4.175A pdb=" N THR A 8 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 39 removed outlier: 4.323A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 103 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 217 Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 43 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 103 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 217 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 43 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 103 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL C 144 " --> pdb=" O ILE C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 217 Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 43 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 103 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL D 144 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 217 Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 18 through 39 removed outlier: 4.323A pdb=" N LEU E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 43 Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 103 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 217 Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 43 Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 103 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL F 144 " --> pdb=" O ILE F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 217 Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 43 Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 103 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL G 144 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 217 Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 43 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 103 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 217 Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 43 Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 103 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL I 144 " --> pdb=" O ILE I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 217 Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 43 Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 103 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL J 144 " --> pdb=" O ILE J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 217 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 43 Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 103 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL K 144 " --> pdb=" O ILE K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 217 Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 43 Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 103 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL L 144 " --> pdb=" O ILE L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 1404 hydrogen bonds defined for protein. 4104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5463 1.34 - 1.46: 5103 1.46 - 1.58: 8658 1.58 - 1.70: 0 1.70 - 1.81: 240 Bond restraints: 19464 Sorted by residual: bond pdb=" C1 LMT H 305 " pdb=" C2 LMT H 305 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C1 LMT L 303 " pdb=" C2 LMT L 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C1 LMT K 303 " pdb=" C2 LMT K 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.15e+00 bond pdb=" C1 LMT A 305 " pdb=" C2 LMT A 305 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" C1 LMT J 303 " pdb=" C2 LMT J 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.06e+00 ... (remaining 19459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 25413 1.58 - 3.16: 363 3.16 - 4.74: 144 4.74 - 6.31: 156 6.31 - 7.89: 144 Bond angle restraints: 26220 Sorted by residual: angle pdb=" C ASN K 176 " pdb=" CA ASN K 176 " pdb=" CB ASN K 176 " ideal model delta sigma weight residual 116.63 111.76 4.87 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN I 176 " pdb=" CA ASN I 176 " pdb=" CB ASN I 176 " ideal model delta sigma weight residual 116.63 111.76 4.87 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN H 176 " pdb=" CA ASN H 176 " pdb=" CB ASN H 176 " ideal model delta sigma weight residual 116.63 111.76 4.87 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN A 176 " pdb=" CA ASN A 176 " pdb=" CB ASN A 176 " ideal model delta sigma weight residual 116.63 111.77 4.86 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN E 176 " pdb=" CA ASN E 176 " pdb=" CB ASN E 176 " ideal model delta sigma weight residual 116.63 111.77 4.86 1.16e+00 7.43e-01 1.75e+01 ... (remaining 26215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 10470 16.16 - 32.31: 618 32.31 - 48.47: 211 48.47 - 64.63: 41 64.63 - 80.79: 12 Dihedral angle restraints: 11352 sinusoidal: 4680 harmonic: 6672 Sorted by residual: dihedral pdb=" CB GLU J 209 " pdb=" CG GLU J 209 " pdb=" CD GLU J 209 " pdb=" OE1 GLU J 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.79 80.79 1 3.00e+01 1.11e-03 8.96e+00 dihedral pdb=" CB GLU F 209 " pdb=" CG GLU F 209 " pdb=" CD GLU F 209 " pdb=" OE1 GLU F 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.79 80.79 1 3.00e+01 1.11e-03 8.96e+00 dihedral pdb=" CB GLU I 209 " pdb=" CG GLU I 209 " pdb=" CD GLU I 209 " pdb=" OE1 GLU I 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.78 80.78 1 3.00e+01 1.11e-03 8.96e+00 ... (remaining 11349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1776 0.026 - 0.052: 701 0.052 - 0.078: 339 0.078 - 0.104: 112 0.104 - 0.130: 24 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA THR K 86 " pdb=" N THR K 86 " pdb=" C THR K 86 " pdb=" CB THR K 86 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA THR I 86 " pdb=" N THR I 86 " pdb=" C THR I 86 " pdb=" CB THR I 86 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA THR C 86 " pdb=" N THR C 86 " pdb=" C THR C 86 " pdb=" CB THR C 86 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 2949 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP F 172 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.56e-01 pdb=" N PRO F 173 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO F 173 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 173 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP G 172 " -0.014 5.00e-02 4.00e+02 2.16e-02 7.49e-01 pdb=" N PRO G 173 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO G 173 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO G 173 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 172 " 0.014 5.00e-02 4.00e+02 2.16e-02 7.49e-01 pdb=" N PRO D 173 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO D 173 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 173 " 0.011 5.00e-02 4.00e+02 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 584 2.72 - 3.27: 19723 3.27 - 3.81: 31203 3.81 - 4.36: 38405 4.36 - 4.90: 65044 Nonbonded interactions: 154959 Sorted by model distance: nonbonded pdb=" O ILE H 71 " pdb=" OH TYR H 158 " model vdw 2.181 3.040 nonbonded pdb=" O ILE C 71 " pdb=" OH TYR C 158 " model vdw 2.181 3.040 nonbonded pdb=" O ILE I 71 " pdb=" OH TYR I 158 " model vdw 2.181 3.040 nonbonded pdb=" O ILE F 71 " pdb=" OH TYR F 158 " model vdw 2.181 3.040 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.181 3.040 ... (remaining 154954 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: 0.10 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'B' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'C' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'D' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'E' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'F' and (resid 4 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) selection = (chain 'G' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'H' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'I' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'J' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'K' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'L' and (resid 4 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) } 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: 5.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 45.160 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 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 : 0.005 0.050 19500 Z= 0.240 Angle : 0.868 7.892 26292 Z= 0.374 Chirality : 0.037 0.130 2952 Planarity : 0.002 0.022 3096 Dihedral : 12.392 80.787 6924 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.18 % Allowed : 6.51 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.60 (0.17), residues: 2220 helix: 2.03 (0.12), residues: 1500 sheet: 1.45 (0.39), residues: 204 loop : -2.18 (0.21), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 24 HIS 0.001 0.000 HIS A 94 PHE 0.013 0.001 PHE E 51 TYR 0.008 0.001 TYR I 65 ARG 0.002 0.000 ARG F 165 Details of bonding type rmsd hydrogen bonds : bond 0.24536 ( 1404) hydrogen bonds : angle 6.59046 ( 4104) SS BOND : bond 0.00283 ( 36) SS BOND : angle 1.16452 ( 72) covalent geometry : bond 0.00488 (19464) covalent geometry : angle 0.86733 (26220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 332 time to evaluate : 1.912 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 354 average time/residue: 1.0732 time to fit residues: 435.8787 Evaluate side-chains 290 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 102 optimal weight: 0.3980 chunk 126 optimal weight: 7.9990 chunk 196 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 57 GLN D 206 ASN E 57 GLN F 206 ASN G 57 GLN H 206 ASN J 57 GLN K 206 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.142998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.085158 restraints weight = 23667.928| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.69 r_work: 0.2836 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19500 Z= 0.161 Angle : 0.587 6.817 26292 Z= 0.328 Chirality : 0.043 0.166 2952 Planarity : 0.004 0.019 3096 Dihedral : 8.783 48.753 2808 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.56 % Allowed : 10.95 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.16 (0.17), residues: 2220 helix: 3.10 (0.12), residues: 1548 sheet: 2.87 (0.42), residues: 132 loop : -1.38 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 24 HIS 0.003 0.001 HIS F 16 PHE 0.014 0.002 PHE G 51 TYR 0.015 0.002 TYR B 65 ARG 0.002 0.000 ARG I 165 Details of bonding type rmsd hydrogen bonds : bond 0.07091 ( 1404) hydrogen bonds : angle 4.31563 ( 4104) SS BOND : bond 0.00299 ( 36) SS BOND : angle 1.15201 ( 72) covalent geometry : bond 0.00305 (19464) covalent geometry : angle 0.58426 (26220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 314 time to evaluate : 2.327 Fit side-chains outliers start: 52 outliers final: 21 residues processed: 341 average time/residue: 1.1804 time to fit residues: 459.4875 Evaluate side-chains 314 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 293 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 chunk 118 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN E 73 HIS I 73 HIS J 57 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.143171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.084692 restraints weight = 23715.018| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.70 r_work: 0.2841 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19500 Z= 0.145 Angle : 0.569 7.044 26292 Z= 0.308 Chirality : 0.043 0.203 2952 Planarity : 0.003 0.027 3096 Dihedral : 7.964 44.857 2808 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.71 % Allowed : 11.93 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.48 (0.17), residues: 2220 helix: 3.46 (0.12), residues: 1536 sheet: 2.84 (0.43), residues: 132 loop : -1.53 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 133 HIS 0.003 0.000 HIS E 73 PHE 0.014 0.001 PHE F 51 TYR 0.012 0.002 TYR K 65 ARG 0.002 0.000 ARG H 216 Details of bonding type rmsd hydrogen bonds : bond 0.06273 ( 1404) hydrogen bonds : angle 4.09222 ( 4104) SS BOND : bond 0.00302 ( 36) SS BOND : angle 1.06836 ( 72) covalent geometry : bond 0.00290 (19464) covalent geometry : angle 0.56655 (26220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 335 time to evaluate : 2.037 Fit side-chains REVERT: B 132 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7062 (mm) REVERT: D 132 LEU cc_start: 0.7734 (tt) cc_final: 0.7463 (mm) REVERT: E 132 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7142 (mm) REVERT: H 140 ILE cc_start: 0.8583 (pt) cc_final: 0.8218 (mp) REVERT: I 132 LEU cc_start: 0.7482 (tt) cc_final: 0.7036 (mm) REVERT: L 132 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7196 (mm) outliers start: 55 outliers final: 29 residues processed: 362 average time/residue: 1.1968 time to fit residues: 491.5889 Evaluate side-chains 347 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 315 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 213 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 196 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN J 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.142894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.084448 restraints weight = 23766.501| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.68 r_work: 0.2822 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19500 Z= 0.145 Angle : 0.572 7.805 26292 Z= 0.308 Chirality : 0.043 0.194 2952 Planarity : 0.003 0.018 3096 Dihedral : 7.410 44.869 2808 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.55 % Allowed : 14.20 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.72 (0.17), residues: 2220 helix: 3.72 (0.12), residues: 1536 sheet: 2.67 (0.43), residues: 132 loop : -1.65 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 133 HIS 0.002 0.000 HIS H 16 PHE 0.015 0.001 PHE G 51 TYR 0.014 0.002 TYR B 65 ARG 0.003 0.000 ARG J 216 Details of bonding type rmsd hydrogen bonds : bond 0.05855 ( 1404) hydrogen bonds : angle 3.99554 ( 4104) SS BOND : bond 0.00359 ( 36) SS BOND : angle 1.15296 ( 72) covalent geometry : bond 0.00308 (19464) covalent geometry : angle 0.56954 (26220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 331 time to evaluate : 1.989 Fit side-chains REVERT: B 132 LEU cc_start: 0.7434 (tt) cc_final: 0.7034 (mm) REVERT: D 132 LEU cc_start: 0.7706 (tt) cc_final: 0.7452 (mm) REVERT: E 132 LEU cc_start: 0.7508 (tt) cc_final: 0.7166 (mm) REVERT: I 132 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7051 (mm) REVERT: K 132 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7152 (mm) REVERT: L 132 LEU cc_start: 0.7548 (tt) cc_final: 0.7210 (mm) outliers start: 72 outliers final: 31 residues processed: 374 average time/residue: 1.0300 time to fit residues: 444.8218 Evaluate side-chains 353 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 320 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 140 optimal weight: 0.0050 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.143325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.085242 restraints weight = 23787.226| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.68 r_work: 0.2845 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19500 Z= 0.130 Angle : 0.546 7.559 26292 Z= 0.291 Chirality : 0.042 0.192 2952 Planarity : 0.003 0.019 3096 Dihedral : 6.913 44.526 2808 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.82 % Allowed : 15.93 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.95 (0.17), residues: 2220 helix: 3.88 (0.12), residues: 1548 sheet: 2.70 (0.43), residues: 132 loop : -1.63 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 133 HIS 0.002 0.000 HIS H 16 PHE 0.013 0.001 PHE C 51 TYR 0.011 0.002 TYR B 65 ARG 0.003 0.000 ARG F 216 Details of bonding type rmsd hydrogen bonds : bond 0.05354 ( 1404) hydrogen bonds : angle 3.87588 ( 4104) SS BOND : bond 0.00309 ( 36) SS BOND : angle 1.02157 ( 72) covalent geometry : bond 0.00267 (19464) covalent geometry : angle 0.54374 (26220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 338 time to evaluate : 2.137 Fit side-chains REVERT: A 140 ILE cc_start: 0.8536 (pt) cc_final: 0.8219 (mp) REVERT: B 132 LEU cc_start: 0.7402 (tt) cc_final: 0.7036 (mm) REVERT: D 132 LEU cc_start: 0.7661 (tt) cc_final: 0.7409 (mm) REVERT: E 132 LEU cc_start: 0.7484 (tt) cc_final: 0.7172 (mm) REVERT: G 132 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7135 (mm) REVERT: H 140 ILE cc_start: 0.8579 (pt) cc_final: 0.8307 (mp) REVERT: I 132 LEU cc_start: 0.7436 (tt) cc_final: 0.7028 (mm) REVERT: L 132 LEU cc_start: 0.7475 (tt) cc_final: 0.7168 (mm) outliers start: 37 outliers final: 17 residues processed: 358 average time/residue: 1.0883 time to fit residues: 449.3498 Evaluate side-chains 352 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 334 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 178 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.143031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.084583 restraints weight = 23849.629| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.68 r_work: 0.2829 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19500 Z= 0.136 Angle : 0.555 7.182 26292 Z= 0.296 Chirality : 0.042 0.193 2952 Planarity : 0.003 0.020 3096 Dihedral : 6.625 45.754 2808 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.97 % Allowed : 15.88 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.01 (0.17), residues: 2220 helix: 3.87 (0.12), residues: 1560 sheet: 2.58 (0.43), residues: 132 loop : -1.52 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 133 HIS 0.001 0.000 HIS B 73 PHE 0.014 0.001 PHE C 51 TYR 0.014 0.002 TYR E 65 ARG 0.002 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.05370 ( 1404) hydrogen bonds : angle 3.87399 ( 4104) SS BOND : bond 0.00349 ( 36) SS BOND : angle 1.09858 ( 72) covalent geometry : bond 0.00287 (19464) covalent geometry : angle 0.55305 (26220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 352 time to evaluate : 2.075 Fit side-chains REVERT: A 140 ILE cc_start: 0.8565 (pt) cc_final: 0.8261 (mp) REVERT: B 132 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7039 (mm) REVERT: D 132 LEU cc_start: 0.7656 (tt) cc_final: 0.7412 (mm) REVERT: E 132 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7169 (mm) REVERT: G 132 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7166 (mm) REVERT: H 140 ILE cc_start: 0.8594 (pt) cc_final: 0.8336 (mp) REVERT: I 132 LEU cc_start: 0.7410 (tt) cc_final: 0.7022 (mm) REVERT: I 140 ILE cc_start: 0.8448 (pt) cc_final: 0.8111 (mp) REVERT: K 132 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7184 (mm) REVERT: L 132 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7175 (mm) outliers start: 40 outliers final: 19 residues processed: 374 average time/residue: 1.0352 time to fit residues: 446.0022 Evaluate side-chains 358 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 334 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 189 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.143590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.085399 restraints weight = 23836.072| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.67 r_work: 0.2846 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19500 Z= 0.128 Angle : 0.552 7.871 26292 Z= 0.290 Chirality : 0.042 0.192 2952 Planarity : 0.003 0.020 3096 Dihedral : 6.356 45.636 2808 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.23 % Allowed : 16.91 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.09 (0.17), residues: 2220 helix: 4.04 (0.12), residues: 1548 sheet: 2.56 (0.43), residues: 132 loop : -1.70 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 134 HIS 0.001 0.000 HIS L 73 PHE 0.013 0.001 PHE F 51 TYR 0.012 0.002 TYR B 65 ARG 0.002 0.000 ARG J 216 Details of bonding type rmsd hydrogen bonds : bond 0.05109 ( 1404) hydrogen bonds : angle 3.81805 ( 4104) SS BOND : bond 0.00311 ( 36) SS BOND : angle 1.03246 ( 72) covalent geometry : bond 0.00268 (19464) covalent geometry : angle 0.55013 (26220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 348 time to evaluate : 2.255 Fit side-chains REVERT: A 140 ILE cc_start: 0.8555 (pt) cc_final: 0.8304 (mp) REVERT: B 132 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7086 (mm) REVERT: B 140 ILE cc_start: 0.8403 (pt) cc_final: 0.8199 (mp) REVERT: D 132 LEU cc_start: 0.7645 (tt) cc_final: 0.7408 (mm) REVERT: E 132 LEU cc_start: 0.7460 (tt) cc_final: 0.7170 (mm) REVERT: E 140 ILE cc_start: 0.8499 (pt) cc_final: 0.8214 (mp) REVERT: G 132 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7117 (mm) REVERT: H 140 ILE cc_start: 0.8564 (pt) cc_final: 0.8333 (mp) REVERT: I 132 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7004 (mm) REVERT: I 140 ILE cc_start: 0.8423 (pt) cc_final: 0.8092 (mp) REVERT: L 132 LEU cc_start: 0.7476 (tt) cc_final: 0.7178 (mm) outliers start: 25 outliers final: 13 residues processed: 362 average time/residue: 1.0492 time to fit residues: 437.5765 Evaluate side-chains 354 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 338 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 215 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 46 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 GLN L 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.141609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.082928 restraints weight = 23765.508| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.66 r_work: 0.2790 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19500 Z= 0.199 Angle : 0.629 8.501 26292 Z= 0.335 Chirality : 0.046 0.198 2952 Planarity : 0.003 0.027 3096 Dihedral : 7.008 54.975 2808 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.04 % Allowed : 17.85 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.93 (0.17), residues: 2220 helix: 3.89 (0.12), residues: 1548 sheet: 2.24 (0.41), residues: 132 loop : -1.58 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 134 HIS 0.002 0.000 HIS B 73 PHE 0.018 0.002 PHE G 51 TYR 0.021 0.002 TYR B 65 ARG 0.004 0.001 ARG L 165 Details of bonding type rmsd hydrogen bonds : bond 0.06047 ( 1404) hydrogen bonds : angle 4.03361 ( 4104) SS BOND : bond 0.00628 ( 36) SS BOND : angle 1.56206 ( 72) covalent geometry : bond 0.00461 (19464) covalent geometry : angle 0.62473 (26220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 339 time to evaluate : 1.967 Fit side-chains REVERT: B 132 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7120 (mm) REVERT: D 132 LEU cc_start: 0.7701 (tt) cc_final: 0.7433 (mm) REVERT: E 132 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7227 (mm) REVERT: G 132 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7125 (mm) REVERT: I 132 LEU cc_start: 0.7451 (tt) cc_final: 0.7046 (mm) REVERT: L 132 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7213 (mm) outliers start: 21 outliers final: 14 residues processed: 352 average time/residue: 1.0553 time to fit residues: 427.9409 Evaluate side-chains 353 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 335 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 204 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.142527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.084097 restraints weight = 23698.615| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.65 r_work: 0.2815 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19500 Z= 0.152 Angle : 0.592 9.569 26292 Z= 0.312 Chirality : 0.044 0.195 2952 Planarity : 0.003 0.020 3096 Dihedral : 6.915 58.812 2808 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.94 % Allowed : 18.00 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.99 (0.17), residues: 2220 helix: 3.97 (0.12), residues: 1548 sheet: 2.23 (0.42), residues: 132 loop : -1.68 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 134 HIS 0.002 0.000 HIS B 73 PHE 0.016 0.001 PHE F 51 TYR 0.015 0.002 TYR B 65 ARG 0.002 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.05555 ( 1404) hydrogen bonds : angle 3.92713 ( 4104) SS BOND : bond 0.00440 ( 36) SS BOND : angle 1.22301 ( 72) covalent geometry : bond 0.00340 (19464) covalent geometry : angle 0.58903 (26220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 342 time to evaluate : 2.244 Fit side-chains REVERT: B 132 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7098 (mm) REVERT: D 132 LEU cc_start: 0.7679 (tt) cc_final: 0.7414 (mm) REVERT: E 132 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7181 (mm) REVERT: G 132 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7098 (mm) REVERT: I 132 LEU cc_start: 0.7417 (tt) cc_final: 0.7029 (mm) REVERT: I 140 ILE cc_start: 0.8540 (pt) cc_final: 0.8204 (mp) REVERT: L 132 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7184 (mm) outliers start: 19 outliers final: 13 residues processed: 353 average time/residue: 1.0817 time to fit residues: 439.2644 Evaluate side-chains 356 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 339 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 188 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.143097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.084891 restraints weight = 23708.304| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.67 r_work: 0.2833 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19500 Z= 0.137 Angle : 0.582 10.147 26292 Z= 0.303 Chirality : 0.043 0.193 2952 Planarity : 0.003 0.020 3096 Dihedral : 6.669 59.970 2808 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.99 % Allowed : 18.15 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.04 (0.17), residues: 2220 helix: 4.03 (0.12), residues: 1548 sheet: 2.24 (0.42), residues: 132 loop : -1.73 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 134 HIS 0.001 0.000 HIS L 73 PHE 0.015 0.001 PHE J 51 TYR 0.013 0.002 TYR L 65 ARG 0.002 0.000 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.05257 ( 1404) hydrogen bonds : angle 3.86311 ( 4104) SS BOND : bond 0.00360 ( 36) SS BOND : angle 1.11708 ( 72) covalent geometry : bond 0.00298 (19464) covalent geometry : angle 0.58025 (26220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 352 time to evaluate : 1.956 Fit side-chains REVERT: A 140 ILE cc_start: 0.8671 (pt) cc_final: 0.8405 (mp) REVERT: B 132 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7080 (mm) REVERT: B 140 ILE cc_start: 0.8518 (pt) cc_final: 0.8216 (mp) REVERT: D 132 LEU cc_start: 0.7653 (tt) cc_final: 0.7407 (mm) REVERT: E 132 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7193 (mm) REVERT: E 140 ILE cc_start: 0.8498 (pt) cc_final: 0.8283 (mp) REVERT: G 132 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7093 (mm) REVERT: H 140 ILE cc_start: 0.8634 (pt) cc_final: 0.8380 (mp) REVERT: I 132 LEU cc_start: 0.7393 (tt) cc_final: 0.7034 (mm) REVERT: L 132 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7196 (mm) REVERT: L 140 ILE cc_start: 0.8501 (pt) cc_final: 0.8296 (mp) outliers start: 20 outliers final: 14 residues processed: 363 average time/residue: 1.0581 time to fit residues: 443.3147 Evaluate side-chains 357 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 339 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 65 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 GLN L 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.142826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.084568 restraints weight = 23842.956| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.65 r_work: 0.2824 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19500 Z= 0.143 Angle : 0.595 11.207 26292 Z= 0.310 Chirality : 0.043 0.194 2952 Planarity : 0.003 0.020 3096 Dihedral : 6.543 57.309 2808 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.94 % Allowed : 18.69 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.04 (0.17), residues: 2220 helix: 4.02 (0.12), residues: 1548 sheet: 2.25 (0.42), residues: 132 loop : -1.71 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 134 HIS 0.001 0.000 HIS L 73 PHE 0.015 0.001 PHE C 51 TYR 0.014 0.002 TYR I 65 ARG 0.002 0.000 ARG J 75 Details of bonding type rmsd hydrogen bonds : bond 0.05333 ( 1404) hydrogen bonds : angle 3.87483 ( 4104) SS BOND : bond 0.00392 ( 36) SS BOND : angle 1.15548 ( 72) covalent geometry : bond 0.00312 (19464) covalent geometry : angle 0.59233 (26220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25947.66 seconds wall clock time: 438 minutes 49.67 seconds (26329.67 seconds total)