Starting phenix.real_space_refine on Tue Jun 17 03:36:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qet_13940/06_2025/7qet_13940.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qet_13940/06_2025/7qet_13940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qet_13940/06_2025/7qet_13940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qet_13940/06_2025/7qet_13940.map" model { file = "/net/cci-nas-00/data/ceres_data/7qet_13940/06_2025/7qet_13940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qet_13940/06_2025/7qet_13940.cif" } resolution = 2.1 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 12720 2.51 5 N 2952 2.21 5 O 3365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19205 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "B" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "C" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "D" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "E" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "F" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "G" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "H" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "I" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "J" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "K" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "L" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} 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: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Time building chain proxies: 13.23, per 1000 atoms: 0.69 Number of scatterers: 19205 At special positions: 0 Unit cell: (99.45, 109.65, 155.55, 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 3365 8.00 N 2952 7.00 C 12720 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=2.03 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=2.04 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=2.03 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=2.04 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=2.04 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=2.04 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=2.04 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: 4.72 Conformation dependent library (CDL) restraints added in 2.3 seconds 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4296 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 75.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 4.147A pdb=" N THR A 8 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.743A 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 102 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 159 Processing helix chain 'A' and resid 184 through 216 removed outlier: 3.590A pdb=" N ARG A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 18 through 39 removed outlier: 3.688A pdb=" N ILE B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.744A 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 102 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 130 through 159 Processing helix chain 'B' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.742A 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 102 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 130 through 159 Processing helix chain 'C' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE D 23 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.743A 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 102 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 130 through 159 Processing helix chain 'D' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG D 216 " --> pdb=" O TYR D 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 4.743A 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 102 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 130 through 159 Processing helix chain 'E' and resid 184 through 216 removed outlier: 3.590A pdb=" N ARG E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE F 23 " --> pdb=" O SER F 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 4.743A 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 102 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 130 through 159 Processing helix chain 'F' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG F 216 " --> pdb=" O TYR F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 18 through 39 removed outlier: 3.688A pdb=" N ILE G 23 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 4.743A 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 102 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 130 through 159 Processing helix chain 'G' and resid 184 through 216 removed outlier: 3.590A pdb=" N ARG G 216 " --> pdb=" O TYR G 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 18 through 39 removed outlier: 3.688A pdb=" N ILE H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 4.743A 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 102 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 130 through 159 Processing helix chain 'H' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG H 216 " --> pdb=" O TYR H 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE I 23 " --> pdb=" O SER I 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 4.743A 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 102 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 130 through 159 Processing helix chain 'I' and resid 184 through 216 removed outlier: 3.590A pdb=" N ARG I 216 " --> pdb=" O TYR I 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE J 23 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) removed outlier: 4.743A 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 102 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 130 through 159 Processing helix chain 'J' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG J 216 " --> pdb=" O TYR J 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 18 through 39 removed outlier: 3.690A pdb=" N ILE K 23 " --> pdb=" O SER K 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) removed outlier: 4.742A 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 102 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 130 through 159 Processing helix chain 'K' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG K 216 " --> pdb=" O TYR K 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE L 23 " --> pdb=" O SER L 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 4.743A 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 102 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 130 through 159 Processing helix chain 'L' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG L 216 " --> pdb=" O TYR L 212 " (cutoff:3.500A) 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 1368 hydrogen bonds defined for protein. 3996 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: 5.74 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5424 1.34 - 1.46: 4495 1.46 - 1.58: 9197 1.58 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 19356 Sorted by residual: bond pdb=" C1 LMT H 303 " pdb=" C2 LMT H 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 LMT L 301 " pdb=" C2 LMT L 301 " 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 A 303 " pdb=" C2 LMT A 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C1 LMT I 303 " pdb=" C2 LMT I 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.08e+00 bond pdb=" C1 LMT E 303 " pdb=" C2 LMT E 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.06e+00 ... (remaining 19351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 25259 1.58 - 3.15: 414 3.15 - 4.73: 81 4.73 - 6.31: 202 6.31 - 7.89: 132 Bond angle restraints: 26088 Sorted by residual: angle pdb=" C6 LMT E 303 " pdb=" C7 LMT E 303 " pdb=" C8 LMT E 303 " ideal model delta sigma weight residual 117.26 109.37 7.89 3.00e+00 1.11e-01 6.91e+00 angle pdb=" C6 LMT H 303 " pdb=" C7 LMT H 303 " pdb=" C8 LMT H 303 " ideal model delta sigma weight residual 117.26 109.38 7.88 3.00e+00 1.11e-01 6.90e+00 angle pdb=" C6 LMT A 303 " pdb=" C7 LMT A 303 " pdb=" C8 LMT A 303 " ideal model delta sigma weight residual 117.26 109.40 7.86 3.00e+00 1.11e-01 6.86e+00 angle pdb=" C6 LMT I 303 " pdb=" C7 LMT I 303 " pdb=" C8 LMT I 303 " ideal model delta sigma weight residual 117.26 109.41 7.85 3.00e+00 1.11e-01 6.85e+00 angle pdb=" C6 LMT C 305 " pdb=" C7 LMT C 305 " pdb=" C8 LMT C 305 " ideal model delta sigma weight residual 117.26 109.41 7.85 3.00e+00 1.11e-01 6.85e+00 ... (remaining 26083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 10251 16.01 - 32.02: 717 32.02 - 48.03: 228 48.03 - 64.04: 48 64.04 - 80.05: 24 Dihedral angle restraints: 11268 sinusoidal: 4632 harmonic: 6636 Sorted by residual: 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 -80.05 80.05 1 3.00e+01 1.11e-03 8.82e+00 dihedral pdb=" CB GLU L 209 " pdb=" CG GLU L 209 " pdb=" CD GLU L 209 " pdb=" OE1 GLU L 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.04 80.04 1 3.00e+01 1.11e-03 8.82e+00 dihedral pdb=" CB GLU D 209 " pdb=" CG GLU D 209 " pdb=" CD GLU D 209 " pdb=" OE1 GLU D 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.03 80.03 1 3.00e+01 1.11e-03 8.82e+00 ... (remaining 11265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1450 0.025 - 0.049: 969 0.049 - 0.074: 328 0.074 - 0.098: 122 0.098 - 0.123: 71 Chirality restraints: 2940 Sorted by residual: chirality pdb=" CA PRO K 185 " pdb=" N PRO K 185 " pdb=" C PRO K 185 " pdb=" CB PRO K 185 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA PRO L 185 " pdb=" N PRO L 185 " pdb=" C PRO L 185 " pdb=" CB PRO L 185 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA PRO A 185 " pdb=" N PRO A 185 " pdb=" C PRO A 185 " pdb=" CB PRO A 185 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 2937 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 65 " 0.011 2.00e-02 2.50e+03 6.14e-03 7.54e-01 pdb=" CG TYR I 65 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR I 65 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR I 65 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR I 65 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR I 65 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR I 65 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR I 65 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 65 " 0.011 2.00e-02 2.50e+03 6.02e-03 7.25e-01 pdb=" CG TYR B 65 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR B 65 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 65 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 65 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 65 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 65 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 65 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 65 " -0.011 2.00e-02 2.50e+03 6.00e-03 7.20e-01 pdb=" CG TYR G 65 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR G 65 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR G 65 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR G 65 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 65 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR G 65 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR G 65 " -0.003 2.00e-02 2.50e+03 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 372 2.69 - 3.24: 18626 3.24 - 3.80: 30224 3.80 - 4.35: 40250 4.35 - 4.90: 65857 Nonbonded interactions: 155329 Sorted by model distance: nonbonded pdb=" O ILE H 71 " pdb=" OH TYR H 158 " model vdw 2.140 3.040 nonbonded pdb=" O ILE I 71 " pdb=" OH TYR I 158 " model vdw 2.140 3.040 nonbonded pdb=" O ILE J 71 " pdb=" OH TYR J 158 " model vdw 2.140 3.040 nonbonded pdb=" O ILE G 71 " pdb=" OH TYR G 158 " model vdw 2.140 3.040 nonbonded pdb=" O ILE D 71 " pdb=" OH TYR D 158 " model vdw 2.140 3.040 ... (remaining 155324 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: 0.010 Normalize map: mean=0, sd=1: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 44.810 Find NCS groups from input model: 1.220 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: 0.010 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 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 : 0.006 0.050 19392 Z= 0.268 Angle : 0.878 7.887 26160 Z= 0.367 Chirality : 0.039 0.123 2940 Planarity : 0.003 0.021 3084 Dihedral : 13.419 80.046 6864 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.38 % Allowed : 6.55 % Favored : 91.07 % 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: 1.49 (0.17), residues: 2208 helix: 1.53 (0.12), residues: 1524 sheet: 2.44 (0.43), residues: 132 loop : -0.86 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 24 HIS 0.002 0.001 HIS E 73 PHE 0.014 0.002 PHE K 51 TYR 0.011 0.002 TYR I 65 ARG 0.002 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.22548 ( 1368) hydrogen bonds : angle 6.23361 ( 3996) SS BOND : bond 0.00323 ( 36) SS BOND : angle 1.27880 ( 72) covalent geometry : bond 0.00576 (19356) covalent geometry : angle 0.87667 (26088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 302 time to evaluate : 2.001 Fit side-chains REVERT: B 94 HIS cc_start: 0.7281 (t-90) cc_final: 0.6977 (t-90) REVERT: C 94 HIS cc_start: 0.7221 (t-90) cc_final: 0.6972 (t-90) REVERT: D 32 ARG cc_start: 0.8939 (mtm180) cc_final: 0.8714 (mtm180) REVERT: F 94 HIS cc_start: 0.7203 (t-90) cc_final: 0.6912 (t-90) REVERT: I 94 HIS cc_start: 0.7248 (t-90) cc_final: 0.6996 (t-90) REVERT: J 94 HIS cc_start: 0.7177 (t-90) cc_final: 0.6902 (t-90) outliers start: 48 outliers final: 13 residues processed: 335 average time/residue: 1.3973 time to fit residues: 530.1670 Evaluate side-chains 273 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 260 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 38 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.6980 chunk 163 optimal weight: 0.3980 chunk 90 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 GLN G 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.137308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.082735 restraints weight = 25958.663| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.88 r_work: 0.2921 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19392 Z= 0.149 Angle : 0.561 5.699 26160 Z= 0.313 Chirality : 0.041 0.138 2940 Planarity : 0.004 0.020 3084 Dihedral : 9.328 58.113 2810 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.39 % Allowed : 11.56 % Favored : 87.05 % 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: 3.10 (0.17), residues: 2208 helix: 3.08 (0.12), residues: 1512 sheet: 2.73 (0.42), residues: 132 loop : -1.22 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 134 HIS 0.002 0.001 HIS L 94 PHE 0.017 0.002 PHE K 31 TYR 0.012 0.002 TYR J 65 ARG 0.003 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.06354 ( 1368) hydrogen bonds : angle 3.95571 ( 3996) SS BOND : bond 0.00208 ( 36) SS BOND : angle 1.03908 ( 72) covalent geometry : bond 0.00299 (19356) covalent geometry : angle 0.55910 (26088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 284 time to evaluate : 2.004 Fit side-chains REVERT: A 94 HIS cc_start: 0.7180 (t-90) cc_final: 0.6905 (t-90) REVERT: B 94 HIS cc_start: 0.7015 (t-90) cc_final: 0.6663 (t-90) REVERT: B 159 ASP cc_start: 0.8713 (t0) cc_final: 0.8366 (p0) REVERT: C 94 HIS cc_start: 0.6967 (t-90) cc_final: 0.6716 (t-90) REVERT: E 94 HIS cc_start: 0.7153 (t-90) cc_final: 0.6712 (t-90) REVERT: F 5 THR cc_start: 0.3223 (OUTLIER) cc_final: 0.3007 (p) REVERT: F 94 HIS cc_start: 0.7034 (t-90) cc_final: 0.6678 (t-90) REVERT: G 94 HIS cc_start: 0.6967 (t-90) cc_final: 0.6627 (t-90) REVERT: G 159 ASP cc_start: 0.8637 (t0) cc_final: 0.8177 (p0) REVERT: H 94 HIS cc_start: 0.7052 (t-90) cc_final: 0.6664 (t-90) REVERT: I 159 ASP cc_start: 0.8698 (t0) cc_final: 0.8374 (p0) REVERT: J 5 THR cc_start: 0.3222 (OUTLIER) cc_final: 0.3010 (p) REVERT: J 94 HIS cc_start: 0.6971 (t-90) cc_final: 0.6649 (t-90) REVERT: K 94 HIS cc_start: 0.7092 (t-90) cc_final: 0.6785 (t-90) REVERT: L 94 HIS cc_start: 0.7067 (t-90) cc_final: 0.6652 (t-90) outliers start: 28 outliers final: 8 residues processed: 298 average time/residue: 1.1609 time to fit residues: 395.6634 Evaluate side-chains 266 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 256 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 111 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 76 optimal weight: 0.0370 chunk 72 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.137955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.083098 restraints weight = 25987.217| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.88 r_work: 0.2927 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19392 Z= 0.133 Angle : 0.522 6.266 26160 Z= 0.290 Chirality : 0.041 0.163 2940 Planarity : 0.003 0.021 3084 Dihedral : 8.250 57.669 2800 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.67 % Allowed : 11.31 % Favored : 85.02 % 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: 3.35 (0.17), residues: 2208 helix: 3.29 (0.12), residues: 1524 sheet: 2.75 (0.43), residues: 132 loop : -1.28 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 134 HIS 0.002 0.000 HIS G 73 PHE 0.018 0.002 PHE A 31 TYR 0.011 0.002 TYR J 65 ARG 0.003 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.05515 ( 1368) hydrogen bonds : angle 3.70985 ( 3996) SS BOND : bond 0.00242 ( 36) SS BOND : angle 0.92240 ( 72) covalent geometry : bond 0.00286 (19356) covalent geometry : angle 0.52057 (26088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 263 time to evaluate : 2.274 Fit side-chains REVERT: A 94 HIS cc_start: 0.7063 (t-90) cc_final: 0.6852 (t-90) REVERT: B 94 HIS cc_start: 0.6968 (t-90) cc_final: 0.6765 (t-90) REVERT: B 159 ASP cc_start: 0.8698 (t0) cc_final: 0.8356 (p0) REVERT: C 94 HIS cc_start: 0.6921 (t-90) cc_final: 0.6663 (t-90) REVERT: D 94 HIS cc_start: 0.7067 (t-90) cc_final: 0.6812 (t-90) REVERT: E 94 HIS cc_start: 0.7042 (t-90) cc_final: 0.6637 (t-90) REVERT: F 94 HIS cc_start: 0.6931 (t-90) cc_final: 0.6485 (t-90) REVERT: G 94 HIS cc_start: 0.7060 (t-90) cc_final: 0.6766 (t-90) REVERT: G 159 ASP cc_start: 0.8671 (t0) cc_final: 0.8288 (p0) REVERT: H 94 HIS cc_start: 0.7039 (t-90) cc_final: 0.6712 (t-90) REVERT: I 159 ASP cc_start: 0.8694 (t0) cc_final: 0.8369 (p0) REVERT: J 94 HIS cc_start: 0.6917 (t-90) cc_final: 0.6653 (t-90) REVERT: K 94 HIS cc_start: 0.7031 (t-90) cc_final: 0.6782 (t-90) REVERT: L 94 HIS cc_start: 0.7042 (t-90) cc_final: 0.6679 (t-90) outliers start: 74 outliers final: 28 residues processed: 317 average time/residue: 1.1350 time to fit residues: 413.1612 Evaluate side-chains 285 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 81 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN E 57 GLN G 57 GLN I 57 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.136598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.081046 restraints weight = 26252.938| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.89 r_work: 0.2885 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19392 Z= 0.176 Angle : 0.577 7.584 26160 Z= 0.313 Chirality : 0.043 0.179 2940 Planarity : 0.003 0.024 3084 Dihedral : 8.250 56.023 2800 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.22 % Allowed : 13.94 % Favored : 82.84 % 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: 3.33 (0.17), residues: 2208 helix: 3.20 (0.12), residues: 1536 sheet: 2.57 (0.45), residues: 132 loop : -1.10 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 172 HIS 0.004 0.001 HIS F 73 PHE 0.020 0.002 PHE B 31 TYR 0.018 0.002 TYR B 65 ARG 0.006 0.001 ARG F 98 Details of bonding type rmsd hydrogen bonds : bond 0.05838 ( 1368) hydrogen bonds : angle 3.78164 ( 3996) SS BOND : bond 0.00377 ( 36) SS BOND : angle 1.19077 ( 72) covalent geometry : bond 0.00413 (19356) covalent geometry : angle 0.57403 (26088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 264 time to evaluate : 2.202 Fit side-chains REVERT: B 159 ASP cc_start: 0.8737 (t0) cc_final: 0.8370 (p0) REVERT: C 94 HIS cc_start: 0.6989 (t-90) cc_final: 0.6717 (t-90) REVERT: D 94 HIS cc_start: 0.7014 (t-90) cc_final: 0.6814 (t-90) REVERT: E 94 HIS cc_start: 0.6964 (t-90) cc_final: 0.6619 (t-90) REVERT: F 94 HIS cc_start: 0.6780 (t-90) cc_final: 0.6494 (t-90) REVERT: G 94 HIS cc_start: 0.7033 (t-90) cc_final: 0.6750 (t-90) REVERT: G 159 ASP cc_start: 0.8731 (t0) cc_final: 0.8262 (p0) REVERT: H 94 HIS cc_start: 0.7031 (t-90) cc_final: 0.6717 (t-90) REVERT: H 159 ASP cc_start: 0.8275 (p0) cc_final: 0.8031 (p0) REVERT: I 159 ASP cc_start: 0.8741 (t0) cc_final: 0.8385 (p0) REVERT: J 94 HIS cc_start: 0.6911 (t-90) cc_final: 0.6637 (t-90) REVERT: K 94 HIS cc_start: 0.7049 (t-90) cc_final: 0.6827 (t-90) REVERT: L 94 HIS cc_start: 0.7020 (t-90) cc_final: 0.6673 (t-90) outliers start: 65 outliers final: 34 residues processed: 309 average time/residue: 1.1044 time to fit residues: 392.4791 Evaluate side-chains 295 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 28 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 0.0670 chunk 58 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 180 optimal weight: 7.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.138159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.083163 restraints weight = 26319.846| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.88 r_work: 0.2926 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19392 Z= 0.129 Angle : 0.521 6.785 26160 Z= 0.283 Chirality : 0.041 0.175 2940 Planarity : 0.003 0.039 3084 Dihedral : 7.687 53.727 2800 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.73 % Allowed : 15.38 % Favored : 81.89 % 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: 3.53 (0.17), residues: 2208 helix: 3.39 (0.12), residues: 1536 sheet: 2.60 (0.45), residues: 132 loop : -1.17 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 133 HIS 0.002 0.000 HIS G 73 PHE 0.016 0.001 PHE B 31 TYR 0.011 0.001 TYR I 158 ARG 0.010 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.04965 ( 1368) hydrogen bonds : angle 3.60674 ( 3996) SS BOND : bond 0.00231 ( 36) SS BOND : angle 0.91053 ( 72) covalent geometry : bond 0.00284 (19356) covalent geometry : angle 0.51968 (26088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 2.181 Fit side-chains REVERT: B 159 ASP cc_start: 0.8698 (t0) cc_final: 0.8369 (p0) REVERT: C 94 HIS cc_start: 0.6965 (t-90) cc_final: 0.6712 (t-90) REVERT: E 94 HIS cc_start: 0.6991 (t-90) cc_final: 0.6668 (t-90) REVERT: F 89 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8619 (tt) REVERT: F 94 HIS cc_start: 0.6756 (t-90) cc_final: 0.6502 (t-90) REVERT: G 89 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8590 (tt) REVERT: G 94 HIS cc_start: 0.6990 (t-90) cc_final: 0.6716 (t-90) REVERT: G 159 ASP cc_start: 0.8716 (t0) cc_final: 0.8337 (p0) REVERT: H 94 HIS cc_start: 0.7009 (t-90) cc_final: 0.6725 (t-90) REVERT: I 159 ASP cc_start: 0.8700 (t0) cc_final: 0.8389 (p0) REVERT: J 89 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8634 (tt) REVERT: J 94 HIS cc_start: 0.6896 (t-90) cc_final: 0.6624 (t-90) REVERT: K 94 HIS cc_start: 0.7019 (t-90) cc_final: 0.6811 (t-90) REVERT: L 94 HIS cc_start: 0.7052 (t-90) cc_final: 0.6767 (t-90) outliers start: 55 outliers final: 37 residues processed: 299 average time/residue: 1.1488 time to fit residues: 393.4731 Evaluate side-chains 294 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 147 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 155 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.136386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.080919 restraints weight = 26437.716| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.87 r_work: 0.2880 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19392 Z= 0.186 Angle : 0.572 6.531 26160 Z= 0.311 Chirality : 0.043 0.180 2940 Planarity : 0.003 0.029 3084 Dihedral : 8.114 56.177 2800 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.27 % Allowed : 15.13 % Favored : 81.60 % 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: 3.42 (0.17), residues: 2208 helix: 3.29 (0.12), residues: 1548 sheet: 2.32 (0.45), residues: 132 loop : -1.18 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 172 HIS 0.004 0.001 HIS G 73 PHE 0.023 0.002 PHE B 31 TYR 0.017 0.002 TYR B 65 ARG 0.008 0.001 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.05719 ( 1368) hydrogen bonds : angle 3.72845 ( 3996) SS BOND : bond 0.00409 ( 36) SS BOND : angle 1.25638 ( 72) covalent geometry : bond 0.00446 (19356) covalent geometry : angle 0.56946 (26088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 264 time to evaluate : 2.107 Fit side-chains REVERT: A 159 ASP cc_start: 0.8297 (p0) cc_final: 0.8075 (p0) REVERT: B 159 ASP cc_start: 0.8738 (t0) cc_final: 0.8370 (p0) REVERT: B 215 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8321 (pp) REVERT: C 94 HIS cc_start: 0.6958 (t-90) cc_final: 0.6683 (t-90) REVERT: D 159 ASP cc_start: 0.8298 (p0) cc_final: 0.8068 (p0) REVERT: E 94 HIS cc_start: 0.6910 (t-90) cc_final: 0.6665 (t-90) REVERT: F 94 HIS cc_start: 0.6728 (t-90) cc_final: 0.6509 (t-90) REVERT: F 159 ASP cc_start: 0.8374 (p0) cc_final: 0.8146 (p0) REVERT: G 94 HIS cc_start: 0.6967 (t-90) cc_final: 0.6676 (t-90) REVERT: G 159 ASP cc_start: 0.8792 (t0) cc_final: 0.8345 (p0) REVERT: H 94 HIS cc_start: 0.7001 (t-90) cc_final: 0.6726 (t-90) REVERT: H 159 ASP cc_start: 0.8306 (p0) cc_final: 0.8085 (p0) REVERT: I 159 ASP cc_start: 0.8759 (t0) cc_final: 0.8391 (p0) REVERT: J 94 HIS cc_start: 0.6895 (t-90) cc_final: 0.6604 (t-90) REVERT: K 94 HIS cc_start: 0.7014 (t-90) cc_final: 0.6811 (t-90) REVERT: K 159 ASP cc_start: 0.8309 (p0) cc_final: 0.8088 (p0) REVERT: L 94 HIS cc_start: 0.7030 (t-90) cc_final: 0.6586 (t-90) REVERT: L 215 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8364 (pp) outliers start: 66 outliers final: 38 residues processed: 303 average time/residue: 1.1392 time to fit residues: 395.8738 Evaluate side-chains 301 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain L residue 215 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 117 optimal weight: 8.9990 chunk 72 optimal weight: 0.0070 chunk 182 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 166 optimal weight: 0.3980 chunk 118 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.4602 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.136376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.081003 restraints weight = 26104.506| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.87 r_work: 0.2882 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19392 Z= 0.182 Angle : 0.574 6.500 26160 Z= 0.314 Chirality : 0.043 0.180 2940 Planarity : 0.003 0.030 3084 Dihedral : 8.318 59.803 2800 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.62 % Allowed : 15.08 % Favored : 81.30 % 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: 3.37 (0.17), residues: 2208 helix: 3.26 (0.12), residues: 1548 sheet: 2.19 (0.45), residues: 132 loop : -1.17 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 172 HIS 0.003 0.001 HIS L 94 PHE 0.020 0.002 PHE B 31 TYR 0.015 0.002 TYR C 65 ARG 0.010 0.001 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.05640 ( 1368) hydrogen bonds : angle 3.69624 ( 3996) SS BOND : bond 0.00401 ( 36) SS BOND : angle 1.23167 ( 72) covalent geometry : bond 0.00436 (19356) covalent geometry : angle 0.57139 (26088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 268 time to evaluate : 2.012 Fit side-chains REVERT: A 159 ASP cc_start: 0.8274 (p0) cc_final: 0.8064 (p0) REVERT: B 215 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8404 (tt) REVERT: C 94 HIS cc_start: 0.6957 (t-90) cc_final: 0.6680 (t-90) REVERT: D 159 ASP cc_start: 0.8289 (p0) cc_final: 0.8067 (p0) REVERT: E 94 HIS cc_start: 0.7043 (t-90) cc_final: 0.6801 (t-90) REVERT: F 94 HIS cc_start: 0.6732 (t-90) cc_final: 0.6486 (t-90) REVERT: G 94 HIS cc_start: 0.7010 (t-90) cc_final: 0.6726 (t-90) REVERT: G 159 ASP cc_start: 0.8743 (t0) cc_final: 0.8329 (p0) REVERT: H 94 HIS cc_start: 0.6991 (t-90) cc_final: 0.6730 (t-90) REVERT: H 159 ASP cc_start: 0.8294 (p0) cc_final: 0.8081 (p0) REVERT: J 94 HIS cc_start: 0.6889 (t-90) cc_final: 0.6595 (t-90) REVERT: K 159 ASP cc_start: 0.8299 (p0) cc_final: 0.8082 (p0) REVERT: L 94 HIS cc_start: 0.6915 (t-90) cc_final: 0.6532 (t-90) outliers start: 73 outliers final: 44 residues processed: 315 average time/residue: 1.0835 time to fit residues: 391.9902 Evaluate side-chains 306 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 147 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 110 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 72 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 chunk 178 optimal weight: 0.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.138081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082982 restraints weight = 26406.724| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.88 r_work: 0.2924 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19392 Z= 0.131 Angle : 0.548 6.371 26160 Z= 0.299 Chirality : 0.041 0.172 2940 Planarity : 0.003 0.043 3084 Dihedral : 7.742 58.114 2800 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.53 % Allowed : 16.62 % Favored : 80.85 % 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: 3.60 (0.17), residues: 2208 helix: 3.47 (0.12), residues: 1548 sheet: 2.32 (0.44), residues: 132 loop : -1.22 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 133 HIS 0.002 0.000 HIS G 73 PHE 0.016 0.001 PHE B 31 TYR 0.010 0.001 TYR I 158 ARG 0.012 0.000 ARG L 98 Details of bonding type rmsd hydrogen bonds : bond 0.04821 ( 1368) hydrogen bonds : angle 3.50648 ( 3996) SS BOND : bond 0.00232 ( 36) SS BOND : angle 0.89224 ( 72) covalent geometry : bond 0.00284 (19356) covalent geometry : angle 0.54683 (26088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 266 time to evaluate : 1.928 Fit side-chains REVERT: B 159 ASP cc_start: 0.8676 (t0) cc_final: 0.8334 (p0) REVERT: C 94 HIS cc_start: 0.6957 (t-90) cc_final: 0.6699 (t-90) REVERT: E 94 HIS cc_start: 0.7036 (t-90) cc_final: 0.6816 (t-90) REVERT: F 94 HIS cc_start: 0.6732 (t-90) cc_final: 0.6522 (t-90) REVERT: G 94 HIS cc_start: 0.6953 (t-90) cc_final: 0.6703 (t-90) REVERT: G 159 ASP cc_start: 0.8712 (t0) cc_final: 0.8345 (p0) REVERT: H 94 HIS cc_start: 0.7030 (t-90) cc_final: 0.6794 (t-90) REVERT: I 159 ASP cc_start: 0.8708 (t0) cc_final: 0.8381 (p0) REVERT: J 94 HIS cc_start: 0.6912 (t-90) cc_final: 0.6571 (t-90) REVERT: L 94 HIS cc_start: 0.7070 (t-90) cc_final: 0.6833 (t-90) outliers start: 51 outliers final: 37 residues processed: 299 average time/residue: 1.1610 time to fit residues: 397.1355 Evaluate side-chains 291 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 147 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 154 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.137810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.082998 restraints weight = 26318.502| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.85 r_work: 0.2919 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19392 Z= 0.142 Angle : 0.564 6.444 26160 Z= 0.308 Chirality : 0.042 0.175 2940 Planarity : 0.003 0.042 3084 Dihedral : 7.505 59.433 2800 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.18 % Allowed : 16.72 % Favored : 81.10 % 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: 3.58 (0.17), residues: 2208 helix: 3.43 (0.12), residues: 1548 sheet: 2.28 (0.44), residues: 132 loop : -1.14 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 133 HIS 0.002 0.001 HIS D 73 PHE 0.023 0.002 PHE B 31 TYR 0.013 0.002 TYR B 158 ARG 0.012 0.001 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.05000 ( 1368) hydrogen bonds : angle 3.52315 ( 3996) SS BOND : bond 0.00263 ( 36) SS BOND : angle 0.96025 ( 72) covalent geometry : bond 0.00324 (19356) covalent geometry : angle 0.56243 (26088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 2.002 Fit side-chains REVERT: B 159 ASP cc_start: 0.8711 (t0) cc_final: 0.8357 (p0) REVERT: C 94 HIS cc_start: 0.6929 (t-90) cc_final: 0.6666 (t-90) REVERT: E 94 HIS cc_start: 0.7018 (t-90) cc_final: 0.6812 (t-90) REVERT: G 89 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8704 (tt) REVERT: G 94 HIS cc_start: 0.6984 (t-90) cc_final: 0.6727 (t-90) REVERT: G 159 ASP cc_start: 0.8736 (t0) cc_final: 0.8330 (p0) REVERT: H 94 HIS cc_start: 0.7034 (t-90) cc_final: 0.6801 (t-90) REVERT: I 159 ASP cc_start: 0.8704 (t0) cc_final: 0.8377 (p0) REVERT: J 94 HIS cc_start: 0.6889 (t-90) cc_final: 0.6537 (t-90) REVERT: L 94 HIS cc_start: 0.7029 (t-90) cc_final: 0.6808 (t-90) outliers start: 44 outliers final: 38 residues processed: 287 average time/residue: 1.2101 time to fit residues: 397.5008 Evaluate side-chains 295 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 147 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 170 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 180 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.136579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.081565 restraints weight = 26202.069| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.84 r_work: 0.2889 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 19392 Z= 0.195 Angle : 0.606 6.501 26160 Z= 0.331 Chirality : 0.044 0.182 2940 Planarity : 0.004 0.048 3084 Dihedral : 7.740 58.176 2800 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.33 % Allowed : 16.42 % Favored : 81.25 % 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: 3.38 (0.17), residues: 2208 helix: 3.23 (0.12), residues: 1548 sheet: 2.18 (0.44), residues: 132 loop : -1.03 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 172 HIS 0.003 0.001 HIS F 73 PHE 0.025 0.002 PHE B 31 TYR 0.017 0.002 TYR E 65 ARG 0.012 0.001 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.05650 ( 1368) hydrogen bonds : angle 3.65803 ( 3996) SS BOND : bond 0.00425 ( 36) SS BOND : angle 1.28495 ( 72) covalent geometry : bond 0.00472 (19356) covalent geometry : angle 0.60262 (26088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 1.999 Fit side-chains REVERT: A 159 ASP cc_start: 0.8290 (p0) cc_final: 0.8074 (p0) REVERT: C 94 HIS cc_start: 0.6944 (t-90) cc_final: 0.6660 (t-90) REVERT: D 159 ASP cc_start: 0.8293 (p0) cc_final: 0.8069 (p0) REVERT: E 94 HIS cc_start: 0.7008 (t-90) cc_final: 0.6790 (t-90) REVERT: F 7 GLN cc_start: 0.5334 (OUTLIER) cc_final: 0.4972 (pp30) REVERT: G 89 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8677 (tt) REVERT: G 94 HIS cc_start: 0.6950 (t-90) cc_final: 0.6692 (t-90) REVERT: G 159 ASP cc_start: 0.8750 (t0) cc_final: 0.8292 (p0) REVERT: H 94 HIS cc_start: 0.7036 (t-90) cc_final: 0.6794 (t-90) REVERT: H 159 ASP cc_start: 0.8301 (p0) cc_final: 0.8078 (p0) REVERT: J 94 HIS cc_start: 0.6852 (t-90) cc_final: 0.6531 (t-90) REVERT: K 159 ASP cc_start: 0.8290 (p0) cc_final: 0.8071 (p0) REVERT: L 94 HIS cc_start: 0.6960 (t-90) cc_final: 0.6722 (t-90) outliers start: 47 outliers final: 39 residues processed: 291 average time/residue: 1.1791 time to fit residues: 390.5570 Evaluate side-chains 303 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 262 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 7 GLN Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 147 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 137 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 160 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.137985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.083169 restraints weight = 26315.476| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.85 r_work: 0.2925 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19392 Z= 0.140 Angle : 0.557 6.412 26160 Z= 0.304 Chirality : 0.042 0.174 2940 Planarity : 0.003 0.049 3084 Dihedral : 7.253 58.212 2800 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.38 % Allowed : 16.27 % Favored : 81.35 % 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: 3.53 (0.17), residues: 2208 helix: 3.39 (0.12), residues: 1548 sheet: 2.22 (0.44), residues: 132 loop : -1.14 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 133 HIS 0.002 0.001 HIS D 73 PHE 0.022 0.002 PHE B 31 TYR 0.011 0.002 TYR B 158 ARG 0.013 0.001 ARG J 98 Details of bonding type rmsd hydrogen bonds : bond 0.04916 ( 1368) hydrogen bonds : angle 3.51209 ( 3996) SS BOND : bond 0.00251 ( 36) SS BOND : angle 0.95317 ( 72) covalent geometry : bond 0.00322 (19356) covalent geometry : angle 0.55593 (26088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20709.92 seconds wall clock time: 352 minutes 14.32 seconds (21134.32 seconds total)