Starting phenix.real_space_refine on Sat Sep 28 14:37:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/09_2024/7qeq_13937.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/09_2024/7qeq_13937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/09_2024/7qeq_13937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/09_2024/7qeq_13937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/09_2024/7qeq_13937.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/09_2024/7qeq_13937.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 12792 2.51 5 N 2976 2.21 5 O 3377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19313 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "B" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "D" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "E" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "F" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "G" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "H" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "I" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "J" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "K" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "L" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Time building chain proxies: 12.37, per 1000 atoms: 0.64 Number of scatterers: 19313 At special positions: 0 Unit cell: (99.45, 109.65, 157.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 3377 8.00 N 2976 7.00 C 12792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 180 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.04 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 180 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 180 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 169 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 180 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 180 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 180 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 169 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 180 " distance=2.04 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 174 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 169 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 180 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 174 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 169 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 180 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 174 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 169 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.38 Conformation dependent library (CDL) restraints added in 2.1 seconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 76.2% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 4.175A pdb=" N THR A 8 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 39 removed outlier: 4.323A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 103 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 217 Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 43 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 103 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 217 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 43 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 103 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL C 144 " --> pdb=" O ILE C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 217 Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 43 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 103 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL D 144 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 217 Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 18 through 39 removed outlier: 4.323A pdb=" N LEU E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 43 Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 103 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 217 Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 43 Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 103 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL F 144 " --> pdb=" O ILE F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 217 Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 43 Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 103 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL G 144 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 217 Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 43 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 103 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 217 Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 43 Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 103 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL I 144 " --> pdb=" O ILE I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 217 Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 43 Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 103 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL J 144 " --> pdb=" O ILE J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 217 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 43 Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 103 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL K 144 " --> pdb=" O ILE K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 217 Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 43 Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 103 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL L 144 " --> pdb=" O ILE L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 1404 hydrogen bonds defined for protein. 4104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.31 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5463 1.34 - 1.46: 5103 1.46 - 1.58: 8658 1.58 - 1.70: 0 1.70 - 1.81: 240 Bond restraints: 19464 Sorted by residual: bond pdb=" C1 LMT H 305 " pdb=" C2 LMT H 305 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C1 LMT L 303 " pdb=" C2 LMT L 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C1 LMT K 303 " pdb=" C2 LMT K 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.15e+00 bond pdb=" C1 LMT A 305 " pdb=" C2 LMT A 305 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" C1 LMT J 303 " pdb=" C2 LMT J 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.06e+00 ... (remaining 19459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 25413 1.58 - 3.16: 363 3.16 - 4.74: 144 4.74 - 6.31: 156 6.31 - 7.89: 144 Bond angle restraints: 26220 Sorted by residual: angle pdb=" C ASN K 176 " pdb=" CA ASN K 176 " pdb=" CB ASN K 176 " ideal model delta sigma weight residual 116.63 111.76 4.87 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN I 176 " pdb=" CA ASN I 176 " pdb=" CB ASN I 176 " ideal model delta sigma weight residual 116.63 111.76 4.87 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN H 176 " pdb=" CA ASN H 176 " pdb=" CB ASN H 176 " ideal model delta sigma weight residual 116.63 111.76 4.87 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN A 176 " pdb=" CA ASN A 176 " pdb=" CB ASN A 176 " ideal model delta sigma weight residual 116.63 111.77 4.86 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN E 176 " pdb=" CA ASN E 176 " pdb=" CB ASN E 176 " ideal model delta sigma weight residual 116.63 111.77 4.86 1.16e+00 7.43e-01 1.75e+01 ... (remaining 26215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 10470 16.16 - 32.31: 618 32.31 - 48.47: 211 48.47 - 64.63: 41 64.63 - 80.79: 12 Dihedral angle restraints: 11352 sinusoidal: 4680 harmonic: 6672 Sorted by residual: dihedral pdb=" CB GLU J 209 " pdb=" CG GLU J 209 " pdb=" CD GLU J 209 " pdb=" OE1 GLU J 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.79 80.79 1 3.00e+01 1.11e-03 8.96e+00 dihedral pdb=" CB GLU F 209 " pdb=" CG GLU F 209 " pdb=" CD GLU F 209 " pdb=" OE1 GLU F 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.79 80.79 1 3.00e+01 1.11e-03 8.96e+00 dihedral pdb=" CB GLU I 209 " pdb=" CG GLU I 209 " pdb=" CD GLU I 209 " pdb=" OE1 GLU I 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.78 80.78 1 3.00e+01 1.11e-03 8.96e+00 ... (remaining 11349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1776 0.026 - 0.052: 701 0.052 - 0.078: 339 0.078 - 0.104: 112 0.104 - 0.130: 24 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA THR K 86 " pdb=" N THR K 86 " pdb=" C THR K 86 " pdb=" CB THR K 86 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA THR I 86 " pdb=" N THR I 86 " pdb=" C THR I 86 " pdb=" CB THR I 86 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA THR C 86 " pdb=" N THR C 86 " pdb=" C THR C 86 " pdb=" CB THR C 86 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 2949 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP F 172 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.56e-01 pdb=" N PRO F 173 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO F 173 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 173 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP G 172 " -0.014 5.00e-02 4.00e+02 2.16e-02 7.49e-01 pdb=" N PRO G 173 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO G 173 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO G 173 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 172 " 0.014 5.00e-02 4.00e+02 2.16e-02 7.49e-01 pdb=" N PRO D 173 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO D 173 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 173 " 0.011 5.00e-02 4.00e+02 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 584 2.72 - 3.27: 19723 3.27 - 3.81: 31203 3.81 - 4.36: 38405 4.36 - 4.90: 65044 Nonbonded interactions: 154959 Sorted by model distance: nonbonded pdb=" O ILE H 71 " pdb=" OH TYR H 158 " model vdw 2.181 3.040 nonbonded pdb=" O ILE C 71 " pdb=" OH TYR C 158 " model vdw 2.181 3.040 nonbonded pdb=" O ILE I 71 " pdb=" OH TYR I 158 " model vdw 2.181 3.040 nonbonded pdb=" O ILE F 71 " pdb=" OH TYR F 158 " model vdw 2.181 3.040 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.181 3.040 ... (remaining 154954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'B' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'C' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'D' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'E' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'F' and (resid 4 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) selection = (chain 'G' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'H' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'I' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'J' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'K' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'L' and (resid 4 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.080 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: 0.720 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 41.550 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.090 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:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19464 Z= 0.321 Angle : 0.867 7.892 26220 Z= 0.374 Chirality : 0.037 0.130 2952 Planarity : 0.002 0.022 3096 Dihedral : 12.392 80.787 6924 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.18 % Allowed : 6.51 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.17), residues: 2220 helix: 2.03 (0.12), residues: 1500 sheet: 1.45 (0.39), residues: 204 loop : -2.18 (0.21), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 24 HIS 0.001 0.000 HIS A 94 PHE 0.013 0.001 PHE E 51 TYR 0.008 0.001 TYR I 65 ARG 0.002 0.000 ARG F 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 332 time to evaluate : 2.302 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 354 average time/residue: 0.9850 time to fit residues: 404.2893 Evaluate side-chains 290 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 102 optimal weight: 0.3980 chunk 126 optimal weight: 7.9990 chunk 196 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 57 GLN D 206 ASN E 57 GLN F 206 ASN G 57 GLN H 206 ASN J 57 GLN K 206 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19464 Z= 0.199 Angle : 0.584 6.817 26220 Z= 0.327 Chirality : 0.043 0.166 2952 Planarity : 0.004 0.019 3096 Dihedral : 8.783 48.753 2808 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.56 % Allowed : 10.95 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.17), residues: 2220 helix: 3.10 (0.12), residues: 1548 sheet: 2.87 (0.42), residues: 132 loop : -1.38 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 24 HIS 0.003 0.001 HIS F 16 PHE 0.014 0.002 PHE G 51 TYR 0.015 0.002 TYR B 65 ARG 0.002 0.000 ARG I 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 314 time to evaluate : 2.045 Fit side-chains outliers start: 52 outliers final: 21 residues processed: 341 average time/residue: 1.1592 time to fit residues: 450.5712 Evaluate side-chains 314 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 293 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 163 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 194 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 157 optimal weight: 0.2980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19464 Z= 0.169 Angle : 0.554 7.794 26220 Z= 0.297 Chirality : 0.042 0.201 2952 Planarity : 0.003 0.018 3096 Dihedral : 7.680 43.321 2808 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.11 % Allowed : 11.98 % Favored : 84.91 % 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: 3.55 (0.17), residues: 2220 helix: 3.46 (0.12), residues: 1548 sheet: 2.93 (0.44), residues: 132 loop : -1.47 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 133 HIS 0.002 0.000 HIS E 73 PHE 0.012 0.001 PHE F 51 TYR 0.010 0.002 TYR K 65 ARG 0.002 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 339 time to evaluate : 2.087 Fit side-chains REVERT: B 132 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7189 (mm) REVERT: E 132 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7298 (mm) REVERT: H 132 LEU cc_start: 0.7680 (tt) cc_final: 0.7462 (mm) REVERT: H 140 ILE cc_start: 0.8583 (pt) cc_final: 0.8327 (mp) REVERT: I 132 LEU cc_start: 0.7492 (tt) cc_final: 0.7178 (mm) REVERT: L 132 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7326 (mm) outliers start: 63 outliers final: 29 residues processed: 374 average time/residue: 1.1016 time to fit residues: 470.9641 Evaluate side-chains 345 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 313 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 213 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 197 optimal weight: 0.7980 chunk 208 optimal weight: 10.0000 chunk 103 optimal weight: 0.0870 chunk 186 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19464 Z= 0.175 Angle : 0.544 7.211 26220 Z= 0.291 Chirality : 0.042 0.192 2952 Planarity : 0.003 0.018 3096 Dihedral : 6.947 41.006 2808 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.25 % Allowed : 13.86 % Favored : 82.89 % 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: 3.84 (0.17), residues: 2220 helix: 3.82 (0.12), residues: 1536 sheet: 2.86 (0.43), residues: 132 loop : -1.69 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 133 HIS 0.002 0.000 HIS E 73 PHE 0.012 0.001 PHE G 51 TYR 0.012 0.002 TYR B 65 ARG 0.002 0.000 ARG J 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 332 time to evaluate : 2.287 Fit side-chains REVERT: B 132 LEU cc_start: 0.7448 (tt) cc_final: 0.7186 (mm) REVERT: D 217 TYR cc_start: 0.6178 (m-80) cc_final: 0.5970 (m-80) REVERT: G 132 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7244 (mm) REVERT: I 132 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7179 (mm) outliers start: 66 outliers final: 26 residues processed: 375 average time/residue: 1.0129 time to fit residues: 438.7218 Evaluate side-chains 352 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 324 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 0.0370 chunk 178 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS B 73 HIS C 73 HIS D 73 HIS E 94 HIS H 73 HIS H 94 HIS K 73 HIS L 94 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19464 Z= 0.239 Angle : 0.579 7.170 26220 Z= 0.313 Chirality : 0.044 0.197 2952 Planarity : 0.003 0.028 3096 Dihedral : 7.089 44.407 2808 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.12 % Allowed : 15.38 % Favored : 82.50 % 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: 3.86 (0.17), residues: 2220 helix: 3.87 (0.12), residues: 1536 sheet: 2.53 (0.42), residues: 132 loop : -1.69 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 133 HIS 0.003 0.000 HIS E 73 PHE 0.016 0.002 PHE G 51 TYR 0.018 0.002 TYR L 65 ARG 0.002 0.000 ARG B 165 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 335 time to evaluate : 2.018 Fit side-chains REVERT: B 132 LEU cc_start: 0.7464 (tt) cc_final: 0.7199 (mm) REVERT: I 132 LEU cc_start: 0.7511 (tt) cc_final: 0.7189 (mm) outliers start: 43 outliers final: 26 residues processed: 356 average time/residue: 1.0366 time to fit residues: 425.3147 Evaluate side-chains 358 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 332 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 208 optimal weight: 0.0020 chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19464 Z= 0.201 Angle : 0.552 7.163 26220 Z= 0.297 Chirality : 0.043 0.193 2952 Planarity : 0.003 0.018 3096 Dihedral : 6.868 46.420 2808 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.68 % Allowed : 16.22 % Favored : 82.10 % 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: 3.97 (0.17), residues: 2220 helix: 3.85 (0.12), residues: 1560 sheet: 2.45 (0.43), residues: 132 loop : -1.52 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 134 HIS 0.003 0.001 HIS E 73 PHE 0.015 0.001 PHE G 51 TYR 0.014 0.002 TYR E 65 ARG 0.002 0.000 ARG B 165 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 343 time to evaluate : 2.297 Fit side-chains REVERT: B 132 LEU cc_start: 0.7479 (tt) cc_final: 0.7225 (mm) REVERT: G 132 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7277 (mm) REVERT: I 132 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7181 (mm) REVERT: I 140 ILE cc_start: 0.8561 (pt) cc_final: 0.8280 (mp) REVERT: K 132 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7290 (mm) outliers start: 34 outliers final: 19 residues processed: 365 average time/residue: 1.0252 time to fit residues: 432.0230 Evaluate side-chains 355 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 333 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain K residue 215 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 175 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 130 optimal weight: 0.0370 chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19464 Z= 0.155 Angle : 0.532 9.010 26220 Z= 0.279 Chirality : 0.041 0.190 2952 Planarity : 0.003 0.019 3096 Dihedral : 6.280 43.430 2808 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.43 % Allowed : 16.57 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.18), residues: 2220 helix: 3.99 (0.12), residues: 1560 sheet: 2.56 (0.44), residues: 132 loop : -1.62 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 134 HIS 0.002 0.001 HIS E 73 PHE 0.011 0.001 PHE C 51 TYR 0.012 0.002 TYR C 158 ARG 0.001 0.000 ARG I 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 363 time to evaluate : 2.304 Fit side-chains REVERT: I 132 LEU cc_start: 0.7382 (tt) cc_final: 0.7140 (mm) REVERT: K 140 ILE cc_start: 0.8666 (pt) cc_final: 0.8411 (mp) outliers start: 29 outliers final: 14 residues processed: 382 average time/residue: 1.0352 time to fit residues: 456.0676 Evaluate side-chains 351 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 337 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19464 Z= 0.198 Angle : 0.570 8.768 26220 Z= 0.300 Chirality : 0.043 0.192 2952 Planarity : 0.003 0.019 3096 Dihedral : 6.241 44.571 2808 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.94 % Allowed : 17.90 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.17), residues: 2220 helix: 3.99 (0.12), residues: 1560 sheet: 2.45 (0.42), residues: 132 loop : -1.59 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 134 HIS 0.003 0.001 HIS I 73 PHE 0.014 0.001 PHE G 51 TYR 0.014 0.002 TYR B 65 ARG 0.002 0.000 ARG I 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 340 time to evaluate : 2.160 Fit side-chains REVERT: I 132 LEU cc_start: 0.7400 (tt) cc_final: 0.7147 (mm) outliers start: 19 outliers final: 17 residues processed: 351 average time/residue: 1.0521 time to fit residues: 425.4053 Evaluate side-chains 354 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 337 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 116 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19464 Z= 0.233 Angle : 0.596 9.205 26220 Z= 0.315 Chirality : 0.044 0.194 2952 Planarity : 0.003 0.021 3096 Dihedral : 6.511 49.900 2808 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.13 % Allowed : 18.15 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.08 (0.17), residues: 2220 helix: 4.04 (0.12), residues: 1548 sheet: 2.31 (0.42), residues: 132 loop : -1.67 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 134 HIS 0.003 0.001 HIS E 73 PHE 0.016 0.002 PHE G 51 TYR 0.017 0.002 TYR I 65 ARG 0.002 0.000 ARG L 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 342 time to evaluate : 2.219 Fit side-chains REVERT: G 132 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7253 (mm) REVERT: I 132 LEU cc_start: 0.7444 (tt) cc_final: 0.7176 (mm) outliers start: 23 outliers final: 17 residues processed: 356 average time/residue: 1.0554 time to fit residues: 432.5187 Evaluate side-chains 353 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 335 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 198 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19464 Z= 0.184 Angle : 0.572 9.981 26220 Z= 0.299 Chirality : 0.043 0.191 2952 Planarity : 0.003 0.019 3096 Dihedral : 6.228 50.767 2808 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.89 % Allowed : 18.54 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.19 (0.17), residues: 2220 helix: 4.15 (0.11), residues: 1548 sheet: 2.38 (0.42), residues: 132 loop : -1.72 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 134 HIS 0.002 0.000 HIS I 73 PHE 0.015 0.001 PHE I 29 TYR 0.012 0.002 TYR B 65 ARG 0.001 0.000 ARG I 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 339 time to evaluate : 2.205 Fit side-chains REVERT: G 132 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7187 (mm) REVERT: H 212 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.6719 (t80) REVERT: I 132 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7157 (mm) outliers start: 18 outliers final: 14 residues processed: 348 average time/residue: 1.0659 time to fit residues: 428.1686 Evaluate side-chains 356 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 339 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 176 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.143088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.084711 restraints weight = 23833.530| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.68 r_work: 0.2830 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19464 Z= 0.189 Angle : 0.580 11.019 26220 Z= 0.302 Chirality : 0.043 0.192 2952 Planarity : 0.003 0.019 3096 Dihedral : 6.039 52.866 2808 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.04 % Allowed : 18.59 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.22 (0.17), residues: 2220 helix: 4.17 (0.11), residues: 1548 sheet: 2.42 (0.42), residues: 132 loop : -1.72 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 134 HIS 0.003 0.001 HIS I 73 PHE 0.016 0.001 PHE L 29 TYR 0.014 0.002 TYR B 65 ARG 0.002 0.000 ARG K 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8324.06 seconds wall clock time: 145 minutes 45.40 seconds (8745.40 seconds total)